tests/testthat/test-adjust_rate.R
In januarharianto/respR: Import, Process, Analyse, and Calculate Rates from Respirometry Data
## library(testthat)
## rm(list=ls())
## testthat::test_file("tests/testthat/test-adjust_rate.R")
capture.output({ ## stops printing outputs on assigning
test_that("adjust_rate stops with wrong method", {
expect_error(adjust_rate(100, 10, method = "text"),
regexp = "adjust_rate: 'method' input not recognised")
})
# make objects for running tests ------------------------------------------
{
suppressWarnings(suppressMessages(insp_obj_single <- inspect(urchins.rd, time = 1, oxygen = 2, plot = F)))
suppressWarnings(suppressMessages(insp_obj_multiple <- inspect(urchins.rd, time = 1, oxygen = 2:5, plot = F)))
cr_obj_single <- calc_rate(insp_obj_single, from = 3, to = 40, by = "time", plot = F)
cr_obj_three <- calc_rate(insp_obj_single, from = c(3,13,23), to = c(12,22,32), by = "time", plot = F)
cr_obj_eight <- calc_rate(insp_obj_single, from = c(3,6,9,12,15,18,21,24), to = c(6,9,12,15,18,21,24,27), by = "time", plot = F)
ar_obj <- auto_rate(insp_obj_single, plot = F)
## auto_rate object with single rate
ar_obj_single <- ar_obj
ar_obj_single$summary <- ar_obj_single$summary[2,]
ar_obj_single$rate <- ar_obj_single$rate[2]
## bg objects
bg_single <- calc_rate.bg(urchins.rd, time = 1, oxygen = 18, plot = F)
bg_three <- calc_rate.bg(urchins.rd, time = 1, oxygen = 12:14, plot = F)
bg_four <- calc_rate.bg(urchins.rd, time = 1, oxygen = 12:15, plot = F)
bg_eight <- calc_rate.bg(urchins.rd, time = 1, oxygen = 12:19, plot = F)
## calc_rate objects
cr_single <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 18, plot = F), plot = F))
cr_three <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 12:14, plot = F), plot = F))
cr_four <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 12:15, plot = F), plot = F))
cr_eight <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 12:19, plot = F), plot = F))
# dfs with diff column numbers
bg_df2col <- urchins.rd[,c(1,18)]
bg_df3col <- urchins.rd[,c(1,18,19)]
bg_df7col <- urchins.rd[,c(1,18,19,18,19,18,19,18)]
# inspect of above
insp_bg_df2col <- suppressWarnings(suppressMessages(inspect(bg_df2col, time = 1, oxygen = 2, plot = F)))
insp_bg_df3col <- suppressWarnings(suppressMessages(inspect(bg_df3col, time = 1, oxygen = 2:3, plot = F)))
insp_bg_df7col <- suppressWarnings(suppressMessages(inspect(bg_df7col, time = 1, oxygen = 2:8, plot = F)))
# calc_rate.bg of above
crbg_df2col <- calc_rate.bg(bg_df2col, plot = F)
crbg_df3col <- calc_rate.bg(bg_df3col, plot = F)
crbg_df7col <- calc_rate.bg(bg_df7col, plot = F)
# objects for "linear" and "exponential" testing
# "pre" experiment background rate
# gives "low" bg rate of -0.0004567706
crbg_pre_2col <- urchins.rd[1:70, c(1,18)] %>%
calc_rate.bg(plot = FALSE)
crbg_pre_3col <- urchins.rd[1:70, c(1,18:19)] %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_pre_2col <- urchins.rd[1:70, c(1,18)]
bgdf_pre_3col <- urchins.rd[1:70, c(1,18:19)]
## as inspect
insp_pre_2col <- suppressWarnings(suppressMessages(inspect(urchins.rd[1:70, c(1,18)], plot = FALSE)))
insp_pre_3col <- suppressWarnings(suppressMessages(inspect(urchins.rd[1:70, c(1,18:19)], time = 1, oxygen = 2:3, plot = F)))
## as calc_rate - this for testing warning of rate timestamp outside time range of by/by2
cr_pre <- calc_rate(urchins.rd[1:70, c(1,18)], plot = FALSE)
# "post" experiment background rate
# gives "high" bg rate of -0.001268691
crbg_post_2col <- urchins.rd[230:271, c(1,19)] %>%
calc_rate.bg(plot = FALSE)
crbg_post_3col <- urchins.rd[230:271, c(1,18:19)] %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_post_2col <- urchins.rd[230:271, c(1,19)]
bgdf_post_3col <- urchins.rd[230:271, c(1,18:19)]
## as inspect
insp_post_2col <- suppressWarnings(suppressMessages(inspect(urchins.rd[230:271, c(1,19)], plot = FALSE)))
insp_post_3col <- suppressWarnings(suppressMessages(inspect(urchins.rd[230:271, c(1,18:19)], plot = FALSE)))
## versions of above with POSITIVE background rates
rev_pre <- urchins.rd[1:70, c(1,18:19)]
rev_pre[[2]] <- rev(rev_pre[[2]])
rev_pre[[3]] <- rev(rev_pre[[3]])
crbg_pre_2col_pos <- rev_pre[,1:2] %>%
calc_rate.bg(plot = FALSE)
crbg_pre_3col_pos <- rev_pre %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_pre_2col_pos <- rev_pre[,1:2]
bgdf_pre_3col_pos <- rev_pre
## as inspect
insp_pre_2col_pos <- suppressWarnings(suppressMessages(inspect(rev_pre[,1:2], plot = FALSE)))
insp_pre_3col_pos <- suppressWarnings(suppressMessages(inspect(rev_pre, time = 1, oxygen = 2:3, plot = F)))
## versions of above with POSITIVE background rates
rev_post <- urchins.rd[230:271, c(1,18:19)]
rev_post[[2]] <- rev(rev_post[[2]])
rev_post[[3]] <- rev(rev_post[[3]])
crbg_post_2col_pos <- rev_post[,1:2] %>%
calc_rate.bg(plot = FALSE)
crbg_post_3col_pos <- rev_post %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_post_2col_pos <- rev_post[,1:2]
bgdf_post_3col_pos <- rev_post
## as inspect
insp_post_2col_pos <- suppressWarnings(suppressMessages(inspect(rev_post[,1:2], plot = FALSE)))
insp_post_3col_pos <- suppressWarnings(suppressMessages(inspect(rev_post, time = 1, oxygen = 2:3, plot = F)))
## intermediately timed data of a specimen
# gives specimen rate of -0.0280796
## as df
spec_df <- urchins.rd[71:199, c(1,2)]
## as inspect
spec_insp <- suppressWarnings(suppressMessages(inspect(urchins.rd[71:199, c(1,2)], plot = FALSE)))
## as calc_rate object
spec_cr <- urchins.rd[71:199, c(1,2)] %>%
calc_rate(plot = FALSE)
## as auto_rate object - gives three rates
spec_ar <- urchins.rd[71:199, c(1,2)] %>%
auto_rate(plot = FALSE)
## as auto_rate object - with single rate
spec_ar_single <- spec_ar
spec_ar_single$summary <- spec_ar_single$summary[2,]
spec_ar_single$rate <- spec_ar_single$rate[2]
## objs with rates of different sign
cr_obj_mixed_sign <- calc_rate(intermittent.rd, from = c(30, 1000, 1900, 2000),
to = c(130, 1100, 2000, 2100), by = "time", plot = FALSE)
cr_obj_pos <- calc_rate(intermittent.rd, from = c(1900, 2000, 3550, 3600),
to = c(2000, 2100, 3650, 3700), by = "time", plot = FALSE)
ar_obj_pos <- auto_rate(
data.frame(urchins.rd[[1]], rev(urchins.rd[[2]])), plot = FALSE)
ar_obj_mixed_sign <- auto_rate(intermittent.rd, plot = FALSE)
## auto_rate objects of different methods with lots of rates
ar_obj_highest <- auto_rate(urchins.rd[,1:2], method = "highest", plot = F)
ar_obj_lowest <- auto_rate(urchins.rd[,1:2], method = "lowest", plot = F)
ar_obj_interval <- auto_rate(urchins.rd[,1:2], method = "interval", width = 0.05, plot = F)
} # end make objects
# Tests -------------------------------------------------------------------
# method = "value" -------------------------------------------------------
test_that("adjust_rate: method = 'value' - correct message", {
# if NULL
expect_message(adjust_rate(x = -0.1, by = -0.005, method = "value"),
"adjust_rate: Rate adjustments applied using \"value\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'value' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(NULL, by = -0.005, method = "value"),
"adjust_rate: for method = 'value' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate("text", by = -0.005, method = "value"),
"adjust_rate: for method = 'value' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(bg_single, by = -0.005, method = "value"),
"adjust_rate: for method = 'value' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'value' - stops if 'by' is not a single numeric or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, by = c(1,2), method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
expect_error(adjust_rate(ar_obj, by = "text", method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
expect_error(adjust_rate(ar_obj, by = ar_obj, method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
expect_error(adjust_rate(ar_obj, by = crbg_df3col, method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
# Causes obscure R CMD CHECK error
#expect_error(adjust_rate(ar_obj, by = bg_df2col, method = "value"),
# "adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
})
test_that("adjust_rate: method = 'value' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, by = -0.005, by2 = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_x = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by2 = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'value' - outputs correct results with numeric 'x', numeric 'by' inputs.", {
## single values for both
rate = -0.01
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by)
## multiple values for rate
rate = c(-0.01, -0.02, -0.03)
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by)
## should always be equal to 'mean' method
rate = c(-0.01, -0.02, -0.03)
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
adjust_rate(rate, by = by, method = "mean")$rate.adjusted)
})
test_that("adjust_rate: method = 'value' - outputs correct results with calc_rate 'x', numeric 'by' inputs.", {
## calc_rate object with single rate, adjusted by single by
rate = cr_obj_single
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
## calc_rate object with multiple rates, adjusted by single by
rate = cr_obj_three
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
})
test_that("adjust_rate: method = 'value' - outputs correct results with auto_rate 'x', numeric 'by' inputs.", {
## auto_rate object adjusted by single by
rate = ar_obj
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
rate = ar_obj_single
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
rate = ar_obj_highest
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
rate = ar_obj_interval
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
})
test_that("adjust_rate: method = 'value' - outputs correct results with numeric 'x', calc_rate.bg 'by' inputs.", {
## single x, calc_rate.bg with single bg rate
rate = -0.01
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by$rate.bg)
## multiple x, calc_rate.bg with single bg rate
rate = c(-0.01, -0.02, -0.03)
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by$rate.bg)
})
test_that("adjust_rate: method = 'value' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_single
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
## multiple calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_three
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
})
test_that("adjust_rate: method = 'value' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
rate = ar_obj
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
rate = ar_obj_single
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
rate = ar_obj_highest
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
rate = ar_obj_interval
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
})
## added ability to use calc_rate objects as `by` in March 2022
## This is the only test that it works. Not gonna do it for every x input
test_that("adjust_rate: method = 'value' - outputs correct results with auto_rate 'x', calc_rate 'by' inputs.", {
rate = ar_obj
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
rate = ar_obj_single
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
rate = ar_obj_highest
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
rate = ar_obj_interval
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
})
# method = "mean" ---------------------------------------------------------
test_that("adjust_rate: method = 'mean' - correct message", {
# if NULL
expect_message(adjust_rate(cr_obj_three, by = -0.005),
"adjust_rate: Rate adjustments applied using \"mean\" method.",
fixed = TRUE)
# if method = "mean" specified
expect_message(adjust_rate(cr_obj_single, method = "mean", by = -0.005),
"adjust_rate: Rate adjustments applied using \"mean\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'mean' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(NULL, by = -0.005),
"adjust_rate: for method = 'mean' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate("text", by = -0.005),
"adjust_rate: for method = 'mean' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(bg_single, by = -0.005),
"adjust_rate: for method = 'mean' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'mean' - stops if 'by' is not numeric or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, by = "text"),
"adjust_rate: for method = 'mean' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
expect_error(adjust_rate(ar_obj, by = ar_obj),
"adjust_rate: for method = 'mean' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
})
test_that("adjust_rate: method = 'mean' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, by = -0.005, by2 = 0.003),
"adjust_rate: for method = 'mean' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_x = 0.003),
"adjust_rate: for method = 'mean' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by = 0.003),
"adjust_rate: for method = 'mean' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by2 = 0.003),
"adjust_rate: for method = 'mean' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'mean' - outputs correct results with numeric 'x', numeric 'by' inputs.", {
## single values for both
rate = -0.01
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for rate
rate = c(-0.01, -0.02, -0.03)
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for by
rate = -0.01
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for both - equal lengths
rate = c(-0.01, -0.02, -0.03)
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for both - different lengths
rate = c(-0.01, -0.02, -0.03, -0.04, -0.05)
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
rate = c(-0.01, -0.02, -0.03)
by = c(-0.001, -0.002, -0.003, -0.004, -0.005)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with calc_rate 'x', numeric 'by' inputs.", {
## calc_rate object with single rate, adjusted by single by
rate = cr_obj_single
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with multiple rates, adjusted by single by
rate = cr_obj_three
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with single rate, adjusted by multiple by
rate = cr_obj_single
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with multiple rates, adjusted by multiple by - equal lengths
rate = cr_obj_three
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with multiple rates, adjusted by multiple by - different lengths
rate = cr_obj_three
by = c(-0.001, -0.002)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = cr_obj_three
by = c(-0.001, -0.002, -0.003, -0.004, -0.005)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with auto_rate 'x', numeric 'by' inputs.", {
## auto_rate object adjusted by single by
rate = ar_obj
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## auto_rate object adjusted by multiple by
rate = ar_obj
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = ar_obj
by = c(-0.001, -0.002, -0.003, -0.004, -0.005)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## auto_rate object with multiple rates, adjusted by multiple by - equal lengths
rate = ar_obj
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## auto_rate object with multiple rates, adjusted by multiple by - equal lengths
rate = ar_obj_highest
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = ar_obj_interval
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = ar_obj_single
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with numeric 'x', calc_rate.bg 'by' inputs.", {
## single x, calc_rate.bg with single bg rate
rate = -0.01
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
## multiple x, calc_rate.bg with single bg rate
rate = c(-0.01, -0.02, -0.03)
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
## single x, calc_rate.bg with multiple bg rate
rate = -0.01
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
## multiple x, calc_rate.bg with multiple bg rate
rate = c(-0.01, -0.02, -0.03)
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_single
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## multiple calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_three
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## single calc_rate x, calc_rate.bg with multiple bg rate
rate = cr_obj_single
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## multiple calc_rate x, calc_rate.bg with multiple bg rate
rate = cr_obj_three
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
## single auto_rate x, calc_rate.bg with single bg rate
rate = ar_obj
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## single auto_rate x, calc_rate.bg with multiple bg rate
rate = ar_obj
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
rate = ar_obj_highest
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
rate = ar_obj_interval
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
rate = ar_obj_single
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with auto_rate 'x', calc_rate 'by' inputs.", {
## single auto_rate x, calc_rate.bg with single bg rate
rate = ar_obj
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
## single auto_rate x, calc_rate with multiple bg rate
rate = ar_obj
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
rate = ar_obj_highest
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
rate = ar_obj_interval
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
rate = ar_obj_single
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
})
# method = "paired" -------------------------------------------------------
test_that("adjust_rate: method = 'paired' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(cr_obj_single, method = "paired", by = -0.005),
"adjust_rate: Rate adjustments applied using \"paired\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'paired' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate("text", method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(bg_single, method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'paired' - stops if 'by' is not numeric or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, method = "paired", by = "text"),
"adjust_rate: for method = 'paired' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
expect_error(adjust_rate(ar_obj, method = "paired", by = ar_obj),
"adjust_rate: for method = 'paired' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
})
test_that("adjust_rate: method = 'paired' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, by2 = 0.003),
"adjust_rate: for method = 'paired' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, time_x = 0.003),
"adjust_rate: for method = 'paired' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, time_by = 0.003),
"adjust_rate: for method = 'paired' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, time_by2 = 0.003),
"adjust_rate: for method = 'paired' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'paired' - stops if 'x' and 'by' are not same length", {
expect_error(adjust_rate(-0.05, method = "paired", by = c(-0.004, -0.005)),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(cr_obj_single, method = "paired", by = c(-0.004, -0.005)),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(ar_obj, method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(ar_obj, method = "paired", by = bg_single),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(ar_obj, method = "paired", by = bg_three),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
})
test_that("adjust_rate: method = 'paired' - outputs correct results with numeric 'x', numeric 'by' inputs.", {
## single values
rate = -0.01
by = -0.001
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate - (by))
## multiple values
rate = c(-0.01, -0.02, -0.03)
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate - (by))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with calc_rate 'x', numeric 'by' inputs.", {
## single values
rate = cr_obj_single
by = -0.001
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by))
## multiple values
rate = cr_obj_three
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with auto_rate 'x', numeric 'by' inputs.", {
rate = ar_obj
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single values
rate = cr_obj_single
by = bg_single
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
## multiple values
rate = cr_obj_three
by = bg_three
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
rate = cr_obj_eight
by = bg_eight
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
rate = ar_obj
by = bg_four
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with calc_rate 'x', calc_rate 'by' inputs.", {
# all of these adjustments should equal zero
## single values
rate = cr_obj_single
by = cr_obj_single
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate))
## multiple values
rate = cr_obj_three
by = cr_obj_three
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate))
rate = cr_obj_eight
by = cr_obj_eight
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate))
})
# method = "concurrent" ---------------------------------------------------
test_that("adjust_rate: method = 'concurrent' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(cr_obj_single, method = "concurrent", by = bg_df2col),
"adjust_rate: Rate adjustments applied using \"concurrent\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'concurrent' - stops if 'x' is not calc_rate or auto_rate", {
expect_error(adjust_rate("text", method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(bg_df2col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(bg_df2col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(bg_df7col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(insp_bg_df2col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(insp_bg_df7col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
})
test_that("adjust_rate: method = 'concurrent' - stops if 'by' is not data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, method = "concurrent", by = "text"),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
expect_error(adjust_rate(ar_obj, method = "concurrent", by = -0.0005),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
expect_error(adjust_rate(ar_obj, method = "concurrent", by = c(-0.0005,-0.0004,-0.0003)),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
# expect_error(adjust_rate(ar_obj, method = "concurrent", by = cr_obj_single),
# "adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
expect_error(adjust_rate(ar_obj, method = "concurrent", by = ar_obj),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
})
test_that("adjust_rate: method = 'concurrent' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, by2 = 0.003),
"adjust_rate: for method = 'concurrent' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, time_x = 0.003),
"adjust_rate: for method = 'concurrent' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, time_by = 0.003),
"adjust_rate: for method = 'concurrent' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, time_by2 = 0.003),
"adjust_rate: for method = 'concurrent' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'concurrent' - warns if 'x' and 'by' are differ in length by more than 5%", {
expect_warning(adjust_rate(cr_obj_single, method = "concurrent", by = urchins.rd[1:250,]),
"adjust_rate: 'x' and 'by' inputs differ in length by more than 5%.")
expect_warning(adjust_rate(cr_obj_single, method = "concurrent", by = sardine.rd),
"adjust_rate: 'x' and 'by' inputs differ in length by more than 5%.")
})
test_that("adjust_rate: method = 'concurrent' - warns if 'by' is missing some time values used for rates in 'x'.", {
expect_warning(adjust_rate(cr_obj_single, method = "concurrent", by = urchins.rd[1:240,]),
"adjust_rate: Some time values used in 'x' rate calculations not present in 'by' background data.")
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', data.frame 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, seven concurrent blanks
rate <- cr_obj_single
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, seven concurrent blanks
rate <- cr_obj_three
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, seven concurrent blanks
rate <- cr_obj_eight
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', inspect 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- insp_bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- insp_bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- insp_bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, seven concurrent blanks
rate <- cr_obj_single
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, seven concurrent blanks
rate <- cr_obj_three
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, seven concurrent blanks
rate <- cr_obj_eight
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- crbg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- crbg_df2col
o_rate <- rate$rate
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- crbg_df2col
o_rate <- rate$rate
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, seven concurrent blanks
rate <- cr_obj_single
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, seven concurrent blanks
rate <- cr_obj_three
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, seven concurrent blanks
rate <- cr_obj_eight
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with auto_rate 'x', data.frame 'by' inputs.", {
## auto_rate obj, single concurrent blank
rate <- ar_obj
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, single concurrent blank
rate <- ar_obj_single
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with MANY rates, single concurrent blank
rate <- ar_obj_highest
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, two concurrent blanks
rate <- ar_obj
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, two concurrent blanks
rate <- ar_obj_single
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, seven concurrent blanks
rate <- ar_obj
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, seven concurrent blanks
rate <- ar_obj_single
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with auto_rate 'x', inspect 'by' inputs.", {
## auto_rate obj, single concurrent blank
rate <- ar_obj
by <- insp_bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, single concurrent blank
rate <- ar_obj_single
by <- insp_bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, two concurrent blanks
rate <- ar_obj
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## ## auto_rate obj with single rate, two concurrent blanks
rate <- ar_obj_single
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, seven concurrent blanks
rate <- ar_obj
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, seven concurrent blanks
rate <- ar_obj_single
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
## auto_rate obj, single concurrent blank
rate <- ar_obj
by <- crbg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, single concurrent blank
rate <- ar_obj_single
by <- crbg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, two concurrent blanks
rate <- ar_obj
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## ## auto_rate obj with single rate, two concurrent blanks
rate <- ar_obj_single
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, seven concurrent blanks
rate <- ar_obj
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, seven concurrent blanks
rate <- ar_obj_single
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', calc_rate 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- calc_rate(insp_bg_df2col, plot = F)
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(insp_bg_df2col, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- calc_rate(insp_bg_df2col, plot = F)
o_rate <- rate$rate
adj <- calc_rate(insp_bg_df2col, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- calc_rate(insp_bg_df2col)
o_rate <- rate$rate
adj <- calc_rate(insp_bg_df2col, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- suppressWarnings(calc_rate(insp_bg_df3col, plot = F))
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(insp_bg_df3col$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(insp_bg_df3col$dataframe[,c(1,2)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- suppressWarnings(calc_rate(insp_bg_df3col, plot = F))
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(insp_bg_df3col$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(insp_bg_df3col$dataframe[,c(1,2)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- suppressWarnings(calc_rate(insp_bg_df3col, plot = F))
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,2)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
# method = "linear" -------------------------------------------------------
test_that("adjust_rate: method = 'linear' - accepts calc_rate objects as 'by'", {
expect_error(suppressWarnings(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = cr_obj_single, time_by = NULL,
by2 = -0.003, time_by2 = 40)),
NA)
})
test_that("adjust_rate: method = 'linear' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: Rate adjustments applied using \"linear\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'linear' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(x = NULL, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = "text", time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = crbg_df2col, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = urchins.rd, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'linear' - stops if 'x' is numeric, and 'time_x' not also numeric, not entered or is unequal length", {
expect_error(adjust_rate(x = -0.03, time_x = NULL, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = c(20,21), method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = "text", method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = bg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = crbg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
})
test_that("adjust_rate: method = 'linear' - stops if 'x' is calc_rate or auto_rate, and 'time_x' is not NULL", {
expect_error(adjust_rate(x = cr_obj_single, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = cr_obj_single, time_x = bg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = bg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = NULL, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = c(-0.001,-0.002), time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = "text", time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = ar_obj, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by' is a single numeric value, and 'time_by' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = NULL,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
})
test_that("adjust_rate: method = 'linear' - stops if 'by' is dataframe, calc_rate.bg, or inspect, and 'time_by' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = insp_bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by2' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = NULL, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = c(-0.001,-0.002), time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = "text", time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = ar_obj, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by2' is a single numeric value, and 'time_by2' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = NULL,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
})
test_that("adjust_rate: method = 'linear' - stops if 'by2' is dataframe, calc_rate.bg, or inspect, and 'time_by2' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = insp_bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
})
test_that("adjust_rate: method = 'linear' - stops if 'time_by' and 'time_by2' are wrong way round (either entered or extracted from objects)", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = 40,
by2 = -0.003, time_by2 = 0),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_post_2col, time_by = NULL,
by2 = crbg_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_post_2col, time_by = NULL,
by2 = insp_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bgdf_post_2col, time_by = NULL,
by2 = bgdf_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
})
test_that("adjust_rate: method = 'linear' - warns if any timestamps of 'x' rates are outside (i.e. before/after) the time_by' and 'time_by2' time range", {
# one rate outside
expect_warning(adjust_rate(x = -0.03, time_x = 10, method = "linear", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, both outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,15), method = "linear", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, one outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,25), method = "linear", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# using input objects
expect_warning(adjust_rate(x = cr_pre, time_x = NULL, method = "linear", by = spec_insp, time_by = NULL,
by2 = insp_post_2col, time_by2 = NULL),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
})
test_that("adjust_rate: method = 'linear' - warns if 'by' and 'by2' rate values have opposite sign", {
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = 0.003, time_by2 = 40),
"adjust_rate: background rates in 'by' and 'by2' differ in sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: background rates in 'by' and 'by2' differ in sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0.002, time_by = 0,
by2 = crbg_post_2col, time_by2 = NULL),
"adjust_rate: background rates in 'by' and 'by2' differ in sign \\(i.e. one is \\+ve, one is \\-ve\\).")
## test the warning ISN'T SHOWN when either (or both) are zero
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0, time_by = 0,
by2 = -0.003, time_by2 = 40),
NA)
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.003, time_by = 0,
by2 = 0, time_by2 = 40),
NA)
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0, time_by = 0,
by2 = 0, time_by2 = 40),
NA)
})
## These are tests of exact values we KNOW are correct - see various tests file for originals
test_that("adjust_rate: method = 'linear' - outputs KNOWN correct results.", {
## all negative
method <- "linear"
x <- -100
time_x <- 50
by <- 0
time_by <- 0
by2 <- -1
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
-99.5)
## all positive
method <- "linear"
x <- 100
time_x <- 50
by <- 0
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
99.5)
method <- "linear"
x <- 100
time_x <- 20
by <- 0
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
99.8)
method <- "linear"
x <- 100
time_x <- 50
by <- -1
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(suppressWarnings(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2))$rate.adjusted,
100)
method <- "linear"
x <- -100
time_x <- 50
by <- -1
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(suppressWarnings(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2))$rate.adjusted,
-100)
## numeric single inputs
expect_error(adjust_rate(x = -100, by = 0, by2 = -50, time_x = 50,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -100, by = 0, by2 = -50, time_x = 50,
time_by = 0, time_by2 = 100, method = "linear")$rate.adjusted,
-75)
## with calc_rate.bg for by, by2 and both
bg_obj1 <- suppressMessages(calc_rate.bg(urchins.rd[1:10,], 1, 18, plot = F))
bg_obj2 <- suppressMessages(calc_rate.bg(urchins.rd[250:271,], 1, 18, plot = F))
## by
expect_error(adjust_rate(x = -0.033, by = bg_obj1, by2 = -0.007030772, time_x = 15,
time_by = NULL, time_by2 = 43.25, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -0.033, by = bg_obj1, by2 = -0.007030772, time_x = 15,
time_by = NULL, time_by2 = 43.25, method = "linear")$adjustment,
-0.005878997)
## by2
expect_error(adjust_rate(x = -0.033, by = -0.005298013, by2 = bg_obj2, time_x = 15,
time_by = 0.75, time_by2 = NULL, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -0.033, by = -0.005298013, by2 = bg_obj2, time_x = 15,
time_by = 0.75, time_by2 = NULL, method = "linear")$adjustment,
-0.005878997)
## both
expect_error(adjust_rate(x = -0.033, by = bg_obj1, by2 = bg_obj2, time_x = 15,
time_by = NULL, time_by2 = NULL, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -0.033, by = bg_obj1, by2 = bg_obj2, time_x = 15,
time_by = NULL, time_by2 = NULL, method = "linear")$adjustment,
-0.005878997)
## numeric vector inputs
expect_error(adjust_rate(x = -c(100,110,120), by = 0, by2 = -50, time_x = c(50,60,70),
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -c(100,110,120), by = 0, by2 = -50, time_x = c(50,60,70),
time_by = 0, time_by2 = 100, method = "linear")$rate.adjusted,
c(-75, -80, -85))
## calc_rate input - one rate
cr_obj <- suppressWarnings(calc_rate(urchins.rd, plot = F)) ## whole dataset
## accepts calc_rate object
expect_error(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
## should apply exactly half of the by2 correction if over same time period
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$adjustment,
-0.01/2)
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$rate.adjusted,
-0.02282768)
## calc_rate input - multiples rates
cr_obj <- suppressWarnings(calc_rate(urchins.rd, from = c(0,10,20,30), to = c(10,20,30,40), plot = F))
## accepts calc_rate object
expect_error(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
## should apply a ninth to seven ninths of the by2 correction if over same time period
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$adjustment,
c(-0.01*1/9, -0.01*3/9, -0.01*5/9, -0.01*7/9))
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$rate.adjusted,
c(-0.03178548, -0.02555831, -0.02166402, -0.01793542))
## auto_rate input
ar_obj <- suppressWarnings(auto_rate(urchins.rd, plot = F))
## accepts auto_rate object
expect_error(adjust_rate(x = ar_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
## values
expect_equal(adjust_rate(x = ar_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$adjustment,
c(-0.003477778, -0.007422222, -0.001066667, -0.001222222))
expect_equal(adjust_rate(x = ar_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$rate.adjusted,
c(-0.02578789, -0.01791415, -0.03132537, -0.03072295))
})
# method = "exponential" --------------------------------------------------
test_that("adjust_rate: method = 'exponential' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: Rate adjustments applied using \"exponential\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'exponential' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(x = NULL, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = "text", time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = crbg_df2col, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = urchins.rd, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'x' is numeric, and 'time_x' not also numeric, not entered or is unequal length", {
expect_error(adjust_rate(x = -0.03, time_x = NULL, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = c(20,21), method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = "text", method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = bg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = crbg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'x' is calc_rate or auto_rate, and 'time_x' is not NULL", {
expect_error(adjust_rate(x = cr_obj_single, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = cr_obj_single, time_x = bg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = bg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = NULL, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = c(-0.001,-0.002), time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = "text", time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = ar_obj, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' is a single numeric value, and 'time_by' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = NULL,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' is dataframe, calc_rate.bg, or inspect, and 'time_by' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = insp_bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by2' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = NULL, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = c(-0.001,-0.002), time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = "text", time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = ar_obj, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by2' is a single numeric value, and 'time_by2' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = NULL,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by2' is dataframe, calc_rate.bg, or inspect, and 'time_by2' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = insp_bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'time_by' and 'time_by2' are wrong way round (either entered or extracted from objects)", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = 40,
by2 = -0.003, time_by2 = 0),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_post_2col, time_by = NULL,
by2 = crbg_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_post_2col, time_by = NULL,
by2 = insp_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bgdf_post_2col, time_by = NULL,
by2 = bgdf_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
})
test_that("adjust_rate: method = 'exponential' - warns if any timestamps of 'x' rates are outside (i.e. before/after) the time_by' and 'time_by2' time range", {
# one rate outside
expect_warning(adjust_rate(x = -0.03, time_x = 10, method = "exponential", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, both outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,15), method = "exponential", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, one outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,25), method = "exponential", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# using input objects
expect_warning(adjust_rate(x = cr_pre, time_x = NULL, method = "exponential", by = spec_insp, time_by = NULL,
by2 = insp_post_2col, time_by2 = NULL),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' and 'by2' rate values have opposite sign", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential",
by = -0.002, time_by = 0,
by2 = 0.003, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when 'by' and 'by2' background rates are not the same sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when 'by' and 'by2' background rates are not the same sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0.002, time_by = 0,
by2 = crbg_post_2col, time_by2 = NULL),
"adjust_rate: method = \"exponential\" cannot be used when 'by' and 'by2' background rates are not the same sign \\(i.e. one is \\+ve, one is \\-ve\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' or 'by2' rate values are zero", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0, time_by = 0,
by2 = 0.003, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when a 'by' or 'by2' background rate is zero.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0.002, time_by = 0,
by2 = 0, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when a 'by' or 'by2' background rate is zero.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0, time_by = 0,
by2 = 0, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when a 'by' or 'by2' background rate is zero.")
})
test_that("adjust_rate: method = 'exponential' - outputs KNOWN correct results.", {
## These values checked in Excel ¯\_(ツ)_/¯
## all negative
method <- "exponential"
x <- -100
time_x <- 50
by <- -1
time_by <- 0
by2 <- -2
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
-98.58579,
tolerance = 0.00001)
## all positive
method <- "exponential"
x <- 89.67
time_x <- 21.3
by <- 7.1
time_by <- 3
by2 <- 17.8
time_by2 <- 67
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
80.43592,
tolerance = 0.00001)
})
# S3 tests ----------------------------------------------------------------
test_that("adjust_rate can be printed - if adjustment done to calc_rate or auto_rate object", {
cr <- suppressWarnings(adjust_rate(calc_rate(sardine.rd, plot = F), 0.001))
ar <- suppressWarnings(adjust_rate(auto_rate(sardine.rd, plot = F), 0.001))
expect_output(print(cr))
expect_output(print(ar))
})
test_that("adjust_rate can be printed - if adjustment done to numeric value", {
nr <- adjust_rate(0.1, 0.001)
expect_output(print(nr))
})
test_that("adjust_rate S3 generics work", {
cr <- suppressWarnings(adjust_rate(calc_rate(sardine.rd, plot = F), 0.001))
ar <- suppressWarnings(adjust_rate(auto_rate(sardine.rd, plot = F), 0.001))
nr <- suppressWarnings(adjust_rate(0.1, 0.001))
expect_output(summary(cr))
expect_output(summary(ar))
expect_output(summary(nr))
expect_is(summary(cr, export = TRUE),
"data.table")
expect_output(print(cr))
expect_output(print(ar))
expect_output(print(nr))
expect_output(suppressWarnings(mean(cr)))
expect_output(suppressWarnings(mean(ar)))
expect_output(suppressWarnings(mean(nr)))
expect_is(suppressWarnings(mean(cr, export = TRUE)),
"numeric")
# errors
expect_error(print(cr, pos = 2:3),
"print.adjust_rate: 'pos' must be a single value. To examine multiple results use summary().")
expect_error(print(cr, pos = 2),
"print.adjust_rate: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_output(summary(cr, pos = 1),
"Summary of rate results from entered 'pos' rank\\(s):")
expect_output(summary(cr, pos = 1),
"Adjustment was applied using 'mean' method.")
expect_error(summary(cr, pos = 2),
"summary.adjust_rate: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_error(mean(cr, pos = 2),
"mean.adjust_rate: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_output(mean(cr, pos = 1),
"Mean of adjusted rate results from entered 'pos' ranks:")
expect_message(mean(cr, pos = 1),
"Only 1 rate found. Returning mean rate anyway...")
})
test_that("adjust_rate applies mean method by default", {
## should adjust all by 4
ar <- adjust_rate(x = c(10,20,30,40,50), by = c(2,3,4,5,6))
expect_equal(ar$rate.adjusted,
c(6,16,26,36,46))
})
test_that("adjust_rate - stops with plot()", {
ar <- adjust_rate(x = c(10,20,30,40,50), by = c(2,3,4,5,6))
expect_message(plot(ar),
regexp = "adjust_rate: plot\\(\\) is not available for 'adjust_rate' objects.")
})
# })
}) ## end capture.output
januarharianto/respR documentation built on April 20, 2024, 4:34 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## library(testthat)
## rm(list=ls())
## testthat::test_file("tests/testthat/test-adjust_rate.R")
capture.output({ ## stops printing outputs on assigning
test_that("adjust_rate stops with wrong method", {
expect_error(adjust_rate(100, 10, method = "text"),
regexp = "adjust_rate: 'method' input not recognised")
})
# make objects for running tests ------------------------------------------
{
suppressWarnings(suppressMessages(insp_obj_single <- inspect(urchins.rd, time = 1, oxygen = 2, plot = F)))
suppressWarnings(suppressMessages(insp_obj_multiple <- inspect(urchins.rd, time = 1, oxygen = 2:5, plot = F)))
cr_obj_single <- calc_rate(insp_obj_single, from = 3, to = 40, by = "time", plot = F)
cr_obj_three <- calc_rate(insp_obj_single, from = c(3,13,23), to = c(12,22,32), by = "time", plot = F)
cr_obj_eight <- calc_rate(insp_obj_single, from = c(3,6,9,12,15,18,21,24), to = c(6,9,12,15,18,21,24,27), by = "time", plot = F)
ar_obj <- auto_rate(insp_obj_single, plot = F)
## auto_rate object with single rate
ar_obj_single <- ar_obj
ar_obj_single$summary <- ar_obj_single$summary[2,]
ar_obj_single$rate <- ar_obj_single$rate[2]
## bg objects
bg_single <- calc_rate.bg(urchins.rd, time = 1, oxygen = 18, plot = F)
bg_three <- calc_rate.bg(urchins.rd, time = 1, oxygen = 12:14, plot = F)
bg_four <- calc_rate.bg(urchins.rd, time = 1, oxygen = 12:15, plot = F)
bg_eight <- calc_rate.bg(urchins.rd, time = 1, oxygen = 12:19, plot = F)
## calc_rate objects
cr_single <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 18, plot = F), plot = F))
cr_three <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 12:14, plot = F), plot = F))
cr_four <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 12:15, plot = F), plot = F))
cr_eight <- suppressWarnings(calc_rate(inspect(urchins.rd, time = 1, oxygen = 12:19, plot = F), plot = F))
# dfs with diff column numbers
bg_df2col <- urchins.rd[,c(1,18)]
bg_df3col <- urchins.rd[,c(1,18,19)]
bg_df7col <- urchins.rd[,c(1,18,19,18,19,18,19,18)]
# inspect of above
insp_bg_df2col <- suppressWarnings(suppressMessages(inspect(bg_df2col, time = 1, oxygen = 2, plot = F)))
insp_bg_df3col <- suppressWarnings(suppressMessages(inspect(bg_df3col, time = 1, oxygen = 2:3, plot = F)))
insp_bg_df7col <- suppressWarnings(suppressMessages(inspect(bg_df7col, time = 1, oxygen = 2:8, plot = F)))
# calc_rate.bg of above
crbg_df2col <- calc_rate.bg(bg_df2col, plot = F)
crbg_df3col <- calc_rate.bg(bg_df3col, plot = F)
crbg_df7col <- calc_rate.bg(bg_df7col, plot = F)
# objects for "linear" and "exponential" testing
# "pre" experiment background rate
# gives "low" bg rate of -0.0004567706
crbg_pre_2col <- urchins.rd[1:70, c(1,18)] %>%
calc_rate.bg(plot = FALSE)
crbg_pre_3col <- urchins.rd[1:70, c(1,18:19)] %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_pre_2col <- urchins.rd[1:70, c(1,18)]
bgdf_pre_3col <- urchins.rd[1:70, c(1,18:19)]
## as inspect
insp_pre_2col <- suppressWarnings(suppressMessages(inspect(urchins.rd[1:70, c(1,18)], plot = FALSE)))
insp_pre_3col <- suppressWarnings(suppressMessages(inspect(urchins.rd[1:70, c(1,18:19)], time = 1, oxygen = 2:3, plot = F)))
## as calc_rate - this for testing warning of rate timestamp outside time range of by/by2
cr_pre <- calc_rate(urchins.rd[1:70, c(1,18)], plot = FALSE)
# "post" experiment background rate
# gives "high" bg rate of -0.001268691
crbg_post_2col <- urchins.rd[230:271, c(1,19)] %>%
calc_rate.bg(plot = FALSE)
crbg_post_3col <- urchins.rd[230:271, c(1,18:19)] %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_post_2col <- urchins.rd[230:271, c(1,19)]
bgdf_post_3col <- urchins.rd[230:271, c(1,18:19)]
## as inspect
insp_post_2col <- suppressWarnings(suppressMessages(inspect(urchins.rd[230:271, c(1,19)], plot = FALSE)))
insp_post_3col <- suppressWarnings(suppressMessages(inspect(urchins.rd[230:271, c(1,18:19)], plot = FALSE)))
## versions of above with POSITIVE background rates
rev_pre <- urchins.rd[1:70, c(1,18:19)]
rev_pre[[2]] <- rev(rev_pre[[2]])
rev_pre[[3]] <- rev(rev_pre[[3]])
crbg_pre_2col_pos <- rev_pre[,1:2] %>%
calc_rate.bg(plot = FALSE)
crbg_pre_3col_pos <- rev_pre %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_pre_2col_pos <- rev_pre[,1:2]
bgdf_pre_3col_pos <- rev_pre
## as inspect
insp_pre_2col_pos <- suppressWarnings(suppressMessages(inspect(rev_pre[,1:2], plot = FALSE)))
insp_pre_3col_pos <- suppressWarnings(suppressMessages(inspect(rev_pre, time = 1, oxygen = 2:3, plot = F)))
## versions of above with POSITIVE background rates
rev_post <- urchins.rd[230:271, c(1,18:19)]
rev_post[[2]] <- rev(rev_post[[2]])
rev_post[[3]] <- rev(rev_post[[3]])
crbg_post_2col_pos <- rev_post[,1:2] %>%
calc_rate.bg(plot = FALSE)
crbg_post_3col_pos <- rev_post %>%
calc_rate.bg(plot = FALSE)
## as df
bgdf_post_2col_pos <- rev_post[,1:2]
bgdf_post_3col_pos <- rev_post
## as inspect
insp_post_2col_pos <- suppressWarnings(suppressMessages(inspect(rev_post[,1:2], plot = FALSE)))
insp_post_3col_pos <- suppressWarnings(suppressMessages(inspect(rev_post, time = 1, oxygen = 2:3, plot = F)))
## intermediately timed data of a specimen
# gives specimen rate of -0.0280796
## as df
spec_df <- urchins.rd[71:199, c(1,2)]
## as inspect
spec_insp <- suppressWarnings(suppressMessages(inspect(urchins.rd[71:199, c(1,2)], plot = FALSE)))
## as calc_rate object
spec_cr <- urchins.rd[71:199, c(1,2)] %>%
calc_rate(plot = FALSE)
## as auto_rate object - gives three rates
spec_ar <- urchins.rd[71:199, c(1,2)] %>%
auto_rate(plot = FALSE)
## as auto_rate object - with single rate
spec_ar_single <- spec_ar
spec_ar_single$summary <- spec_ar_single$summary[2,]
spec_ar_single$rate <- spec_ar_single$rate[2]
## objs with rates of different sign
cr_obj_mixed_sign <- calc_rate(intermittent.rd, from = c(30, 1000, 1900, 2000),
to = c(130, 1100, 2000, 2100), by = "time", plot = FALSE)
cr_obj_pos <- calc_rate(intermittent.rd, from = c(1900, 2000, 3550, 3600),
to = c(2000, 2100, 3650, 3700), by = "time", plot = FALSE)
ar_obj_pos <- auto_rate(
data.frame(urchins.rd[[1]], rev(urchins.rd[[2]])), plot = FALSE)
ar_obj_mixed_sign <- auto_rate(intermittent.rd, plot = FALSE)
## auto_rate objects of different methods with lots of rates
ar_obj_highest <- auto_rate(urchins.rd[,1:2], method = "highest", plot = F)
ar_obj_lowest <- auto_rate(urchins.rd[,1:2], method = "lowest", plot = F)
ar_obj_interval <- auto_rate(urchins.rd[,1:2], method = "interval", width = 0.05, plot = F)
} # end make objects
# Tests -------------------------------------------------------------------
# method = "value" -------------------------------------------------------
test_that("adjust_rate: method = 'value' - correct message", {
# if NULL
expect_message(adjust_rate(x = -0.1, by = -0.005, method = "value"),
"adjust_rate: Rate adjustments applied using \"value\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'value' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(NULL, by = -0.005, method = "value"),
"adjust_rate: for method = 'value' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate("text", by = -0.005, method = "value"),
"adjust_rate: for method = 'value' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(bg_single, by = -0.005, method = "value"),
"adjust_rate: for method = 'value' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'value' - stops if 'by' is not a single numeric or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, by = c(1,2), method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
expect_error(adjust_rate(ar_obj, by = "text", method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
expect_error(adjust_rate(ar_obj, by = ar_obj, method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
expect_error(adjust_rate(ar_obj, by = crbg_df3col, method = "value"),
"adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
# Causes obscure R CMD CHECK error
#expect_error(adjust_rate(ar_obj, by = bg_df2col, method = "value"),
# "adjust_rate: for method = 'value' the 'by' input must be a single numeric value, 'calc_rate.bg' object with one value in '\\$rate.bg', or `calc_rate` object with one value in '\\$rate'")
})
test_that("adjust_rate: method = 'value' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, by = -0.005, by2 = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_x = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by2 = 0.003, method = "value"),
"adjust_rate: for method = 'value' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'value' - outputs correct results with numeric 'x', numeric 'by' inputs.", {
## single values for both
rate = -0.01
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by)
## multiple values for rate
rate = c(-0.01, -0.02, -0.03)
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by)
## should always be equal to 'mean' method
rate = c(-0.01, -0.02, -0.03)
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
adjust_rate(rate, by = by, method = "mean")$rate.adjusted)
})
test_that("adjust_rate: method = 'value' - outputs correct results with calc_rate 'x', numeric 'by' inputs.", {
## calc_rate object with single rate, adjusted by single by
rate = cr_obj_single
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
## calc_rate object with multiple rates, adjusted by single by
rate = cr_obj_three
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
})
test_that("adjust_rate: method = 'value' - outputs correct results with auto_rate 'x', numeric 'by' inputs.", {
## auto_rate object adjusted by single by
rate = ar_obj
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
rate = ar_obj_single
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
rate = ar_obj_highest
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
rate = ar_obj_interval
by = -0.001
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by)
})
test_that("adjust_rate: method = 'value' - outputs correct results with numeric 'x', calc_rate.bg 'by' inputs.", {
## single x, calc_rate.bg with single bg rate
rate = -0.01
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by$rate.bg)
## multiple x, calc_rate.bg with single bg rate
rate = c(-0.01, -0.02, -0.03)
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate - by$rate.bg)
})
test_that("adjust_rate: method = 'value' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_single
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
## multiple calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_three
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
})
test_that("adjust_rate: method = 'value' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
rate = ar_obj
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
rate = ar_obj_single
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
rate = ar_obj_highest
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
rate = ar_obj_interval
by = bg_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate.bg)
})
## added ability to use calc_rate objects as `by` in March 2022
## This is the only test that it works. Not gonna do it for every x input
test_that("adjust_rate: method = 'value' - outputs correct results with auto_rate 'x', calc_rate 'by' inputs.", {
rate = ar_obj
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
rate = ar_obj_single
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
rate = ar_obj_highest
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
rate = ar_obj_interval
by = cr_obj_single
expect_equal(adjust_rate(rate, by = by, method = "value")$rate.adjusted,
rate$rate - by$rate)
})
# method = "mean" ---------------------------------------------------------
test_that("adjust_rate: method = 'mean' - correct message", {
# if NULL
expect_message(adjust_rate(cr_obj_three, by = -0.005),
"adjust_rate: Rate adjustments applied using \"mean\" method.",
fixed = TRUE)
# if method = "mean" specified
expect_message(adjust_rate(cr_obj_single, method = "mean", by = -0.005),
"adjust_rate: Rate adjustments applied using \"mean\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'mean' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(NULL, by = -0.005),
"adjust_rate: for method = 'mean' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate("text", by = -0.005),
"adjust_rate: for method = 'mean' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(bg_single, by = -0.005),
"adjust_rate: for method = 'mean' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'mean' - stops if 'by' is not numeric or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, by = "text"),
"adjust_rate: for method = 'mean' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
expect_error(adjust_rate(ar_obj, by = ar_obj),
"adjust_rate: for method = 'mean' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
})
test_that("adjust_rate: method = 'mean' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, by = -0.005, by2 = 0.003),
"adjust_rate: for method = 'mean' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_x = 0.003),
"adjust_rate: for method = 'mean' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by = 0.003),
"adjust_rate: for method = 'mean' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, by = -0.005, time_by2 = 0.003),
"adjust_rate: for method = 'mean' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'mean' - outputs correct results with numeric 'x', numeric 'by' inputs.", {
## single values for both
rate = -0.01
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for rate
rate = c(-0.01, -0.02, -0.03)
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for by
rate = -0.01
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for both - equal lengths
rate = c(-0.01, -0.02, -0.03)
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
## multiple values for both - different lengths
rate = c(-0.01, -0.02, -0.03, -0.04, -0.05)
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
rate = c(-0.01, -0.02, -0.03)
by = c(-0.001, -0.002, -0.003, -0.004, -0.005)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with calc_rate 'x', numeric 'by' inputs.", {
## calc_rate object with single rate, adjusted by single by
rate = cr_obj_single
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with multiple rates, adjusted by single by
rate = cr_obj_three
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with single rate, adjusted by multiple by
rate = cr_obj_single
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with multiple rates, adjusted by multiple by - equal lengths
rate = cr_obj_three
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## calc_rate object with multiple rates, adjusted by multiple by - different lengths
rate = cr_obj_three
by = c(-0.001, -0.002)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = cr_obj_three
by = c(-0.001, -0.002, -0.003, -0.004, -0.005)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with auto_rate 'x', numeric 'by' inputs.", {
## auto_rate object adjusted by single by
rate = ar_obj
by = -0.001
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## auto_rate object adjusted by multiple by
rate = ar_obj
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = ar_obj
by = c(-0.001, -0.002, -0.003, -0.004, -0.005)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## auto_rate object with multiple rates, adjusted by multiple by - equal lengths
rate = ar_obj
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
## auto_rate object with multiple rates, adjusted by multiple by - equal lengths
rate = ar_obj_highest
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = ar_obj_interval
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
rate = ar_obj_single
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with numeric 'x', calc_rate.bg 'by' inputs.", {
## single x, calc_rate.bg with single bg rate
rate = -0.01
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
## multiple x, calc_rate.bg with single bg rate
rate = c(-0.01, -0.02, -0.03)
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
## single x, calc_rate.bg with multiple bg rate
rate = -0.01
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
## multiple x, calc_rate.bg with multiple bg rate
rate = c(-0.01, -0.02, -0.03)
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate - mean(by$rate.bg))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_single
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## multiple calc_rate x, calc_rate.bg with single bg rate
rate = cr_obj_three
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## single calc_rate x, calc_rate.bg with multiple bg rate
rate = cr_obj_single
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## multiple calc_rate x, calc_rate.bg with multiple bg rate
rate = cr_obj_three
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
## single auto_rate x, calc_rate.bg with single bg rate
rate = ar_obj
by = bg_single
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
## single auto_rate x, calc_rate.bg with multiple bg rate
rate = ar_obj
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
rate = ar_obj_highest
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
rate = ar_obj_interval
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
rate = ar_obj_single
by = bg_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate.bg))
})
test_that("adjust_rate: method = 'mean' - outputs correct results with auto_rate 'x', calc_rate 'by' inputs.", {
## single auto_rate x, calc_rate.bg with single bg rate
rate = ar_obj
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
## single auto_rate x, calc_rate with multiple bg rate
rate = ar_obj
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
rate = ar_obj_highest
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
rate = ar_obj_interval
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
rate = ar_obj_single
by = cr_obj_three
expect_equal(adjust_rate(rate, by = by)$rate.adjusted,
rate$rate - mean(by$rate))
})
# method = "paired" -------------------------------------------------------
test_that("adjust_rate: method = 'paired' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(cr_obj_single, method = "paired", by = -0.005),
"adjust_rate: Rate adjustments applied using \"paired\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'paired' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate("text", method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(bg_single, method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' input must be numeric or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'paired' - stops if 'by' is not numeric or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, method = "paired", by = "text"),
"adjust_rate: for method = 'paired' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
expect_error(adjust_rate(ar_obj, method = "paired", by = ar_obj),
"adjust_rate: for method = 'paired' the 'by' input must be numeric, object of class 'calc_rate.bg', or object of class 'calc_rate'.")
})
test_that("adjust_rate: method = 'paired' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, by2 = 0.003),
"adjust_rate: for method = 'paired' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, time_x = 0.003),
"adjust_rate: for method = 'paired' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, time_by = 0.003),
"adjust_rate: for method = 'paired' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005, time_by2 = 0.003),
"adjust_rate: for method = 'paired' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'paired' - stops if 'x' and 'by' are not same length", {
expect_error(adjust_rate(-0.05, method = "paired", by = c(-0.004, -0.005)),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(cr_obj_single, method = "paired", by = c(-0.004, -0.005)),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(cr_obj_three, method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(ar_obj, method = "paired", by = -0.005),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(ar_obj, method = "paired", by = bg_single),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
expect_error(adjust_rate(ar_obj, method = "paired", by = bg_three),
"adjust_rate: for method = 'paired' the 'x' and 'by' inputs should have the same number of rates.")
})
test_that("adjust_rate: method = 'paired' - outputs correct results with numeric 'x', numeric 'by' inputs.", {
## single values
rate = -0.01
by = -0.001
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate - (by))
## multiple values
rate = c(-0.01, -0.02, -0.03)
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate - (by))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with calc_rate 'x', numeric 'by' inputs.", {
## single values
rate = cr_obj_single
by = -0.001
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by))
## multiple values
rate = cr_obj_three
by = c(-0.001, -0.002, -0.003)
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with auto_rate 'x', numeric 'by' inputs.", {
rate = ar_obj
by = c(-0.001, -0.002, -0.003, -0.004)
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single values
rate = cr_obj_single
by = bg_single
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
## multiple values
rate = cr_obj_three
by = bg_three
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
rate = cr_obj_eight
by = bg_eight
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
rate = ar_obj
by = bg_four
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate.bg))
})
test_that("adjust_rate: method = 'paired' - outputs correct results with calc_rate 'x', calc_rate 'by' inputs.", {
# all of these adjustments should equal zero
## single values
rate = cr_obj_single
by = cr_obj_single
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate))
## multiple values
rate = cr_obj_three
by = cr_obj_three
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate))
rate = cr_obj_eight
by = cr_obj_eight
expect_equal(adjust_rate(rate, method = "paired", by = by)$rate.adjusted,
rate$rate - (by$rate))
})
# method = "concurrent" ---------------------------------------------------
test_that("adjust_rate: method = 'concurrent' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(cr_obj_single, method = "concurrent", by = bg_df2col),
"adjust_rate: Rate adjustments applied using \"concurrent\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'concurrent' - stops if 'x' is not calc_rate or auto_rate", {
expect_error(adjust_rate("text", method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(bg_df2col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(bg_df2col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(bg_df7col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(insp_bg_df2col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
expect_error(adjust_rate(insp_bg_df7col, method = "concurrent", by = bg_df2col),
"adjust_rate: For method = \"concurrent\" the 'x' input must be a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' object.")
})
test_that("adjust_rate: method = 'concurrent' - stops if 'by' is not data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(ar_obj, method = "concurrent", by = "text"),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
expect_error(adjust_rate(ar_obj, method = "concurrent", by = -0.0005),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
expect_error(adjust_rate(ar_obj, method = "concurrent", by = c(-0.0005,-0.0004,-0.0003)),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
# expect_error(adjust_rate(ar_obj, method = "concurrent", by = cr_obj_single),
# "adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
expect_error(adjust_rate(ar_obj, method = "concurrent", by = ar_obj),
"adjust_rate: For method = \"concurrent\" the 'by' input must be a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object.")
})
test_that("adjust_rate: method = 'concurrent' - stops if 'by2', 'time_x', 'time_by', or 'time_by2' have inputs.", {
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, by2 = 0.003),
"adjust_rate: for method = 'concurrent' the 'by2' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, time_x = 0.003),
"adjust_rate: for method = 'concurrent' the 'time_x' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, time_by = 0.003),
"adjust_rate: for method = 'concurrent' the 'time_by' input should be NULL.")
expect_error(adjust_rate(cr_obj_three, method = "concurrent", by = bg_df2col, time_by2 = 0.003),
"adjust_rate: for method = 'concurrent' the 'time_by2' input should be NULL.")
})
test_that("adjust_rate: method = 'concurrent' - warns if 'x' and 'by' are differ in length by more than 5%", {
expect_warning(adjust_rate(cr_obj_single, method = "concurrent", by = urchins.rd[1:250,]),
"adjust_rate: 'x' and 'by' inputs differ in length by more than 5%.")
expect_warning(adjust_rate(cr_obj_single, method = "concurrent", by = sardine.rd),
"adjust_rate: 'x' and 'by' inputs differ in length by more than 5%.")
})
test_that("adjust_rate: method = 'concurrent' - warns if 'by' is missing some time values used for rates in 'x'.", {
expect_warning(adjust_rate(cr_obj_single, method = "concurrent", by = urchins.rd[1:240,]),
"adjust_rate: Some time values used in 'x' rate calculations not present in 'by' background data.")
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', data.frame 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, seven concurrent blanks
rate <- cr_obj_single
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, seven concurrent blanks
rate <- cr_obj_three
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, seven concurrent blanks
rate <- cr_obj_eight
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', inspect 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- insp_bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- insp_bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- insp_bg_df2col
o_rate <- rate$rate
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, seven concurrent blanks
rate <- cr_obj_single
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, seven concurrent blanks
rate <- cr_obj_three
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, seven concurrent blanks
rate <- cr_obj_eight
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', calc_rate.bg 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- crbg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- crbg_df2col
o_rate <- rate$rate
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- crbg_df2col
o_rate <- rate$rate
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, seven concurrent blanks
rate <- cr_obj_single
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, seven concurrent blanks
rate <- cr_obj_three
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, seven concurrent blanks
rate <- cr_obj_eight
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with auto_rate 'x', data.frame 'by' inputs.", {
## auto_rate obj, single concurrent blank
rate <- ar_obj
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, single concurrent blank
rate <- ar_obj_single
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with MANY rates, single concurrent blank
rate <- ar_obj_highest
by <- bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, two concurrent blanks
rate <- ar_obj
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, two concurrent blanks
rate <- ar_obj_single
by <- bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, seven concurrent blanks
rate <- ar_obj
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, seven concurrent blanks
rate <- ar_obj_single
by <- bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with auto_rate 'x', inspect 'by' inputs.", {
## auto_rate obj, single concurrent blank
rate <- ar_obj
by <- insp_bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, single concurrent blank
rate <- ar_obj_single
by <- insp_bg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, two concurrent blanks
rate <- ar_obj
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## ## auto_rate obj with single rate, two concurrent blanks
rate <- ar_obj_single
by <- insp_bg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, seven concurrent blanks
rate <- ar_obj
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, seven concurrent blanks
rate <- ar_obj_single
by <- insp_bg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with auto_rate 'x', calc_rate.bg 'by' inputs.", {
## auto_rate obj, single concurrent blank
rate <- ar_obj
by <- crbg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, single concurrent blank
rate <- ar_obj_single
by <- crbg_df2col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(by$dataframe, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, two concurrent blanks
rate <- ar_obj
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## ## auto_rate obj with single rate, two concurrent blanks
rate <- ar_obj_single
by <- crbg_df3col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj, seven concurrent blanks
rate <- ar_obj
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## auto_rate obj with single rate, seven concurrent blanks
rate <- ar_obj_single
by <- crbg_df7col
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,3)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj3 <- calc_rate(by$dataframe[,c(1,4)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj4 <- calc_rate(by$dataframe[,c(1,5)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj5 <- calc_rate(by$dataframe[,c(1,6)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj6 <- calc_rate(by$dataframe[,c(1,7)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj7 <- calc_rate(by$dataframe[,c(1,8)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2+adj3+adj4+adj5+adj6+adj7)/7
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
test_that("adjust_rate: method = 'concurrent' - outputs correct results with calc_rate 'x', calc_rate 'by' inputs.", {
## single rate value, single concurrent blank
rate <- cr_obj_single
by <- calc_rate(insp_bg_df2col, plot = F)
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj <- calc_rate(insp_bg_df2col, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, single concurrent blank
rate <- cr_obj_three
by <- calc_rate(insp_bg_df2col, plot = F)
o_rate <- rate$rate
adj <- calc_rate(insp_bg_df2col, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, single concurrent blank
rate <- cr_obj_eight
by <- calc_rate(insp_bg_df2col)
o_rate <- rate$rate
adj <- calc_rate(insp_bg_df2col, from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## single rate value, two concurrent blanks
rate <- cr_obj_single
by <- suppressWarnings(calc_rate(insp_bg_df3col, plot = F))
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(insp_bg_df3col$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(insp_bg_df3col$dataframe[,c(1,2)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## three rate values, two concurrent blanks
rate <- cr_obj_three
by <- suppressWarnings(calc_rate(insp_bg_df3col, plot = F))
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(insp_bg_df3col$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(insp_bg_df3col$dataframe[,c(1,2)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
## eight rate values, two concurrent blanks
rate <- cr_obj_eight
by <- suppressWarnings(calc_rate(insp_bg_df3col, plot = F))
# rate should be this
o_rate <- rate$rate
# adjustment should be this
adj1 <- calc_rate(by$dataframe[,1:2], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj2 <- calc_rate(by$dataframe[,c(1,2)], from = rate$summary$time, to = rate$summary$endtime, by = "time", plot = F)$rate
adj <- (adj1+adj2)/2
expect_equal(adjust_rate(rate, method = "concurrent", by = by)$rate.adjusted,
o_rate - (adj))
})
# method = "linear" -------------------------------------------------------
test_that("adjust_rate: method = 'linear' - accepts calc_rate objects as 'by'", {
expect_error(suppressWarnings(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = cr_obj_single, time_by = NULL,
by2 = -0.003, time_by2 = 40)),
NA)
})
test_that("adjust_rate: method = 'linear' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: Rate adjustments applied using \"linear\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'linear' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(x = NULL, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = "text", time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = crbg_df2col, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = urchins.rd, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'linear' - stops if 'x' is numeric, and 'time_x' not also numeric, not entered or is unequal length", {
expect_error(adjust_rate(x = -0.03, time_x = NULL, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = c(20,21), method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = "text", method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = bg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = crbg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
})
test_that("adjust_rate: method = 'linear' - stops if 'x' is calc_rate or auto_rate, and 'time_x' is not NULL", {
expect_error(adjust_rate(x = cr_obj_single, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = cr_obj_single, time_x = bg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = bg_df2col, method = "linear", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = NULL, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = c(-0.001,-0.002), time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = "text", time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = ar_obj, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by' is a single numeric value, and 'time_by' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = NULL,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
})
test_that("adjust_rate: method = 'linear' - stops if 'by' is dataframe, calc_rate.bg, or inspect, and 'time_by' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_bg_df2col, time_by = insp_bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by2' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = NULL, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = c(-0.001,-0.002), time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = "text", time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = ar_obj, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'linear' - stops if 'by2' is a single numeric value, and 'time_by2' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = NULL,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = -0.002, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
})
test_that("adjust_rate: method = 'linear' - stops if 'by2' is dataframe, calc_rate.bg, or inspect, and 'time_by2' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = bg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = crbg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by2 = insp_bg_df2col, time_by2 = insp_bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"linear\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
})
test_that("adjust_rate: method = 'linear' - stops if 'time_by' and 'time_by2' are wrong way round (either entered or extracted from objects)", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = 40,
by2 = -0.003, time_by2 = 0),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = crbg_post_2col, time_by = NULL,
by2 = crbg_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = insp_post_2col, time_by = NULL,
by2 = insp_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = bgdf_post_2col, time_by = NULL,
by2 = bgdf_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
})
test_that("adjust_rate: method = 'linear' - warns if any timestamps of 'x' rates are outside (i.e. before/after) the time_by' and 'time_by2' time range", {
# one rate outside
expect_warning(adjust_rate(x = -0.03, time_x = 10, method = "linear", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, both outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,15), method = "linear", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, one outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,25), method = "linear", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# using input objects
expect_warning(adjust_rate(x = cr_pre, time_x = NULL, method = "linear", by = spec_insp, time_by = NULL,
by2 = insp_post_2col, time_by2 = NULL),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
})
test_that("adjust_rate: method = 'linear' - warns if 'by' and 'by2' rate values have opposite sign", {
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.002, time_by = 0,
by2 = 0.003, time_by2 = 40),
"adjust_rate: background rates in 'by' and 'by2' differ in sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: background rates in 'by' and 'by2' differ in sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0.002, time_by = 0,
by2 = crbg_post_2col, time_by2 = NULL),
"adjust_rate: background rates in 'by' and 'by2' differ in sign \\(i.e. one is \\+ve, one is \\-ve\\).")
## test the warning ISN'T SHOWN when either (or both) are zero
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0, time_by = 0,
by2 = -0.003, time_by2 = 40),
NA)
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = -0.003, time_by = 0,
by2 = 0, time_by2 = 40),
NA)
expect_warning(adjust_rate(x = -0.03, time_x = 20, method = "linear", by = 0, time_by = 0,
by2 = 0, time_by2 = 40),
NA)
})
## These are tests of exact values we KNOW are correct - see various tests file for originals
test_that("adjust_rate: method = 'linear' - outputs KNOWN correct results.", {
## all negative
method <- "linear"
x <- -100
time_x <- 50
by <- 0
time_by <- 0
by2 <- -1
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
-99.5)
## all positive
method <- "linear"
x <- 100
time_x <- 50
by <- 0
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
99.5)
method <- "linear"
x <- 100
time_x <- 20
by <- 0
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
99.8)
method <- "linear"
x <- 100
time_x <- 50
by <- -1
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(suppressWarnings(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2))$rate.adjusted,
100)
method <- "linear"
x <- -100
time_x <- 50
by <- -1
time_by <- 0
by2 <- 1
time_by2 <- 100
expect_equal(suppressWarnings(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2))$rate.adjusted,
-100)
## numeric single inputs
expect_error(adjust_rate(x = -100, by = 0, by2 = -50, time_x = 50,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -100, by = 0, by2 = -50, time_x = 50,
time_by = 0, time_by2 = 100, method = "linear")$rate.adjusted,
-75)
## with calc_rate.bg for by, by2 and both
bg_obj1 <- suppressMessages(calc_rate.bg(urchins.rd[1:10,], 1, 18, plot = F))
bg_obj2 <- suppressMessages(calc_rate.bg(urchins.rd[250:271,], 1, 18, plot = F))
## by
expect_error(adjust_rate(x = -0.033, by = bg_obj1, by2 = -0.007030772, time_x = 15,
time_by = NULL, time_by2 = 43.25, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -0.033, by = bg_obj1, by2 = -0.007030772, time_x = 15,
time_by = NULL, time_by2 = 43.25, method = "linear")$adjustment,
-0.005878997)
## by2
expect_error(adjust_rate(x = -0.033, by = -0.005298013, by2 = bg_obj2, time_x = 15,
time_by = 0.75, time_by2 = NULL, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -0.033, by = -0.005298013, by2 = bg_obj2, time_x = 15,
time_by = 0.75, time_by2 = NULL, method = "linear")$adjustment,
-0.005878997)
## both
expect_error(adjust_rate(x = -0.033, by = bg_obj1, by2 = bg_obj2, time_x = 15,
time_by = NULL, time_by2 = NULL, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -0.033, by = bg_obj1, by2 = bg_obj2, time_x = 15,
time_by = NULL, time_by2 = NULL, method = "linear")$adjustment,
-0.005878997)
## numeric vector inputs
expect_error(adjust_rate(x = -c(100,110,120), by = 0, by2 = -50, time_x = c(50,60,70),
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
expect_equal(adjust_rate(x = -c(100,110,120), by = 0, by2 = -50, time_x = c(50,60,70),
time_by = 0, time_by2 = 100, method = "linear")$rate.adjusted,
c(-75, -80, -85))
## calc_rate input - one rate
cr_obj <- suppressWarnings(calc_rate(urchins.rd, plot = F)) ## whole dataset
## accepts calc_rate object
expect_error(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
## should apply exactly half of the by2 correction if over same time period
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$adjustment,
-0.01/2)
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$rate.adjusted,
-0.02282768)
## calc_rate input - multiples rates
cr_obj <- suppressWarnings(calc_rate(urchins.rd, from = c(0,10,20,30), to = c(10,20,30,40), plot = F))
## accepts calc_rate object
expect_error(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
## should apply a ninth to seven ninths of the by2 correction if over same time period
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$adjustment,
c(-0.01*1/9, -0.01*3/9, -0.01*5/9, -0.01*7/9))
expect_equal(adjust_rate(x = cr_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$rate.adjusted,
c(-0.03178548, -0.02555831, -0.02166402, -0.01793542))
## auto_rate input
ar_obj <- suppressWarnings(auto_rate(urchins.rd, plot = F))
## accepts auto_rate object
expect_error(adjust_rate(x = ar_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 100, method = "linear"),
regexp = NA)
## values
expect_equal(adjust_rate(x = ar_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$adjustment,
c(-0.003477778, -0.007422222, -0.001066667, -0.001222222))
expect_equal(adjust_rate(x = ar_obj, by = 0, by2 = -0.01,
time_by = 0, time_by2 = 45, method = "linear")$rate.adjusted,
c(-0.02578789, -0.01791415, -0.03132537, -0.03072295))
})
# method = "exponential" --------------------------------------------------
test_that("adjust_rate: method = 'exponential' - correct message", {
# if method = "mean" specified
expect_message(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: Rate adjustments applied using \"exponential\" method.",
fixed = TRUE)
})
test_that("adjust_rate: method = 'exponential' - stops if 'x' is not numeric, calc_rate, or auto_rate", {
expect_error(adjust_rate(x = NULL, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = "text", time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = crbg_df2col, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
expect_error(adjust_rate(x = urchins.rd, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'x' input must be a numeric value or vector, or an object of class 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int'.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'x' is numeric, and 'time_x' not also numeric, not entered or is unequal length", {
expect_error(adjust_rate(x = -0.03, time_x = NULL, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = c(20,21), method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = "text", method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = bg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
expect_error(adjust_rate(x = -0.03, time_x = crbg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'x' input, the 'time_x' must be a numeric input of the same length \\(i.e. timestamp\\(s\\) for all rates in 'x'\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'x' is calc_rate or auto_rate, and 'time_x' is not NULL", {
expect_error(adjust_rate(x = cr_obj_single, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = cr_obj_single, time_x = bg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = 20, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
expect_error(adjust_rate(x = ar_obj, time_x = bg_df2col, method = "exponential", by = -0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a 'calc_rate', 'calc_rate.int', 'auto_rate', or 'auto_rate.int' 'x' input, the 'time_x' input must be NULL.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = NULL, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = c(-0.001,-0.002), time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = "text", time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = ar_obj, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", the 'by' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' is a single numeric value, and 'time_by' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = NULL,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by' input, the 'time_by' input also requires a single numeric value \\(i.e. a timestamp for 'by' background rate\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' is dataframe, calc_rate.bg, or inspect, and 'time_by' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_df2col, time_by = crbg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = "text",
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = c(1,2),
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_bg_df2col, time_by = insp_bg_df2col,
by2 = -0.003, time_by2 = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by' input, the 'time_by' must be NULL.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by2' is not a single numeric value, or data.frame, inspect or calc_rate.bg", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = NULL, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = c(-0.001,-0.002), time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = "text", time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = ar_obj, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", the 'by2' input must be a single numeric value, or a 'data.frame', 'inspect', 'calc_rate.bg', or `calc_rate` object containing background time~oxygen data.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by2' is a single numeric value, and 'time_by2' is not entered or not also a single numeric", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = NULL,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = -0.002, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\" and a numeric 'by2' input, the 'time_by2' input also requires a single numeric value \\(i.e. a timestamp for 'by2' background rate\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by2' is dataframe, calc_rate.bg, or inspect, and 'time_by2' is not NULL", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = bg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = crbg_df2col, time_by2 = crbg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = 0,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = "text",
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = c(1,2),
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by2 = insp_bg_df2col, time_by2 = insp_bg_df2col,
by = -0.003, time_by = 40),
"adjust_rate: For method = \"exponential\", and a 'data.frame', 'inspect', 'calc_rate.bg', or 'calc_rate' 'by2' input, the 'time_by2' must be NULL.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'time_by' and 'time_by2' are wrong way round (either entered or extracted from objects)", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = -0.002, time_by = 40,
by2 = -0.003, time_by2 = 0),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = crbg_post_2col, time_by = NULL,
by2 = crbg_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = insp_post_2col, time_by = NULL,
by2 = insp_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = bgdf_post_2col, time_by = NULL,
by2 = bgdf_pre_2col, time_by2 = NULL),
"adjust_rate: Error in inputs. Timestamp for 'by2' is before timestamp for 'by' suggesting they are in the wrong order or come from different datasets.")
})
test_that("adjust_rate: method = 'exponential' - warns if any timestamps of 'x' rates are outside (i.e. before/after) the time_by' and 'time_by2' time range", {
# one rate outside
expect_warning(adjust_rate(x = -0.03, time_x = 10, method = "exponential", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, both outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,15), method = "exponential", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# two rates, one outside
expect_warning(adjust_rate(x = c(-0.03, -0.02), time_x = c(10,25), method = "exponential", by = -0.002, time_by = 20,
by2 = -0.003, time_by2 = 40),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
# using input objects
expect_warning(adjust_rate(x = cr_pre, time_x = NULL, method = "exponential", by = spec_insp, time_by = NULL,
by2 = insp_post_2col, time_by2 = NULL),
"adjust_rate: One or more of the timestamps for the rate\\(s\\) in 'x' do not lie between the timestamps for the 'by' and 'by2' background rates.")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' and 'by2' rate values have opposite sign", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential",
by = -0.002, time_by = 0,
by2 = 0.003, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when 'by' and 'by2' background rates are not the same sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0.002, time_by = 0,
by2 = -0.003, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when 'by' and 'by2' background rates are not the same sign \\(i.e. one is \\+ve, one is \\-ve\\).")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0.002, time_by = 0,
by2 = crbg_post_2col, time_by2 = NULL),
"adjust_rate: method = \"exponential\" cannot be used when 'by' and 'by2' background rates are not the same sign \\(i.e. one is \\+ve, one is \\-ve\\).")
})
test_that("adjust_rate: method = 'exponential' - stops if 'by' or 'by2' rate values are zero", {
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0, time_by = 0,
by2 = 0.003, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when a 'by' or 'by2' background rate is zero.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0.002, time_by = 0,
by2 = 0, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when a 'by' or 'by2' background rate is zero.")
expect_error(adjust_rate(x = -0.03, time_x = 20, method = "exponential", by = 0, time_by = 0,
by2 = 0, time_by2 = 40),
"adjust_rate: method = \"exponential\" cannot be used when a 'by' or 'by2' background rate is zero.")
})
test_that("adjust_rate: method = 'exponential' - outputs KNOWN correct results.", {
## These values checked in Excel ¯\_(ツ)_/¯
## all negative
method <- "exponential"
x <- -100
time_x <- 50
by <- -1
time_by <- 0
by2 <- -2
time_by2 <- 100
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
-98.58579,
tolerance = 0.00001)
## all positive
method <- "exponential"
x <- 89.67
time_x <- 21.3
by <- 7.1
time_by <- 3
by2 <- 17.8
time_by2 <- 67
expect_equal(adjust_rate(x = x, time_x = time_x, method = method,
by = by, time_by = time_by,
by2 = by2, time_by2 = time_by2)$rate.adjusted,
80.43592,
tolerance = 0.00001)
})
# S3 tests ----------------------------------------------------------------
test_that("adjust_rate can be printed - if adjustment done to calc_rate or auto_rate object", {
cr <- suppressWarnings(adjust_rate(calc_rate(sardine.rd, plot = F), 0.001))
ar <- suppressWarnings(adjust_rate(auto_rate(sardine.rd, plot = F), 0.001))
expect_output(print(cr))
expect_output(print(ar))
})
test_that("adjust_rate can be printed - if adjustment done to numeric value", {
nr <- adjust_rate(0.1, 0.001)
expect_output(print(nr))
})
test_that("adjust_rate S3 generics work", {
cr <- suppressWarnings(adjust_rate(calc_rate(sardine.rd, plot = F), 0.001))
ar <- suppressWarnings(adjust_rate(auto_rate(sardine.rd, plot = F), 0.001))
nr <- suppressWarnings(adjust_rate(0.1, 0.001))
expect_output(summary(cr))
expect_output(summary(ar))
expect_output(summary(nr))
expect_is(summary(cr, export = TRUE),
"data.table")
expect_output(print(cr))
expect_output(print(ar))
expect_output(print(nr))
expect_output(suppressWarnings(mean(cr)))
expect_output(suppressWarnings(mean(ar)))
expect_output(suppressWarnings(mean(nr)))
expect_is(suppressWarnings(mean(cr, export = TRUE)),
"numeric")
# errors
expect_error(print(cr, pos = 2:3),
"print.adjust_rate: 'pos' must be a single value. To examine multiple results use summary().")
expect_error(print(cr, pos = 2),
"print.adjust_rate: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_output(summary(cr, pos = 1),
"Summary of rate results from entered 'pos' rank\\(s):")
expect_output(summary(cr, pos = 1),
"Adjustment was applied using 'mean' method.")
expect_error(summary(cr, pos = 2),
"summary.adjust_rate: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_error(mean(cr, pos = 2),
"mean.adjust_rate: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_output(mean(cr, pos = 1),
"Mean of adjusted rate results from entered 'pos' ranks:")
expect_message(mean(cr, pos = 1),
"Only 1 rate found. Returning mean rate anyway...")
})
test_that("adjust_rate applies mean method by default", {
## should adjust all by 4
ar <- adjust_rate(x = c(10,20,30,40,50), by = c(2,3,4,5,6))
expect_equal(ar$rate.adjusted,
c(6,16,26,36,46))
})
test_that("adjust_rate - stops with plot()", {
ar <- adjust_rate(x = c(10,20,30,40,50), by = c(2,3,4,5,6))
expect_message(plot(ar),
regexp = "adjust_rate: plot\\(\\) is not available for 'adjust_rate' objects.")
})
# })
}) ## end capture.output
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.