tests/testthat/test-adjust_rate.ft.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.ft.R")
# covr::file_coverage("R/calc_rate.ft.R", "tests/testthat/test-adjust_rate.ft.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
capture.output({ ## stops printing outputs on assigning
# Create testing objects --------------------------------------------------
insp.ft_obj <- inspect.ft(flowthrough.rd, delta.oxy = 4, plot = FALSE)
## oxygen production data
insp.ft_obj_prod <- inspect.ft(cbind(flowthrough.rd[,1], -1*(flowthrough.rd[,4])),
time = 1, delta.oxy = 2, plot = FALSE)
# x objects
x1 <- calc_rate.ft(insp.ft_obj,
flowrate = 2, from = 200, to = 500,
by = NULL, width = NULL, plot = FALSE
)
xmany <- calc_rate.ft(insp.ft_obj,
flowrate = 2, from = 200:300, to = 500:600,
by = NULL, width = NULL, plot = FALSE
)
xwidth <- calc_rate.ft(insp.ft_obj,
flowrate = 2,
by = "row", width = 300, plot = FALSE
)
xprod <- calc_rate.ft(insp.ft_obj_prod,
flowrate = 2, from = 200, to = 500,
by = NULL, width = NULL, plot = FALSE
)
# by objects
by_val <- -0.7
by_vec <- seq(-0.75, -0.85, -0.01)
by_crft <- calc_rate.ft(suppressWarnings(inspect.ft(flowthrough_mult.rd, out.oxy = 4, in.oxy = 8, plot = FALSE)),
flowrate = 2, plot = FALSE)
by_crft_mult <- calc_rate.ft(suppressWarnings(inspect.ft(flowthrough_mult.rd, out.oxy = 4, in.oxy = 8, plot = FALSE)),
from = c(2000, 2500), to = c(2400, 2900), by = "row",
flowrate = 2, plot = FALSE)
# by_crft_nl <- calc_rate.ft(inspect.ft(flowthrough_sim.rd, out.oxy = 2, in.oxy = 3, plot = FALSE),
# flowrate = 2, plot = FALSE)
adj.ft_obj.insp.1 <- adjust_rate.ft(x1, by = by_val)
adj.ft_obj.insp.many <- adjust_rate.ft(xmany, by = by_val)
adj.ft_obj.insp.width <- adjust_rate.ft(xwidth, by = by_val)
adj.ft_obj.insp.prod <- adjust_rate.ft(xprod, by = 0.7)
adj.ft_obj.vec <- adjust_rate.ft(xmany$rate, by = by_val)
adj.ft_obj.val <- adjust_rate.ft(-1.5, by = by_val)
# validate 'x' inputs -----------------------------------------------------
test_that("adjust_rate.ft - stops if 'x' input not numeric or 'calc_rate.ft'", {
expect_error(adjust_rate.ft("string",
by = -0.7),
regexp = "adjust_rate.ft: 'x' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(as.data.frame(flowthrough.rd),
by = -0.7),
regexp = "adjust_rate.ft: 'x' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(inspect(flowthrough.rd, plot = FALSE),
by = -0.7),
regexp = "adjust_rate.ft: 'x' must be numeric or 'calc_rate.ft' object.")
})
# validate 'by' inputs ----------------------------------------------------
test_that("adjust_rate.ft - stops if 'by' input not numeric or 'calc_rate.ft'", {
expect_error(adjust_rate.ft(x1,
by = "string"),
regexp = "adjust_rate.ft: 'by' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(x1,
by = as.data.frame(flowthrough.rd)),
regexp = "adjust_rate.ft: 'by' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(x1,
by = inspect(flowthrough.rd, plot = FALSE)),
regexp = "adjust_rate.ft: 'by' must be numeric or 'calc_rate.ft' object.")
})
test_that("adjust_rate.ft - message if 'by' contains multiple rates", {
expect_message(adjust_rate.ft(x1,
by = c(23,34)),
regexp = "adjust_rate.ft: the 'by' input contains multiple background rates. The mean value will be used to perform adjustments.")
expect_message(adjust_rate.ft(x1,
by = xmany),
regexp = "adjust_rate.ft: the 'by' input contains multiple background rates. The mean value will be used to perform adjustments.")
})
test_that("adjust_rate.ft - stops if 'x' and 'by' are calc_rate.ft and have been determined using different 'flowrates'", {
expect_error(adjust_rate.ft(calc_rate.ft(insp.ft_obj,
flowrate = 2,
from = 200, to = 500, plot = FALSE),
by = calc_rate.ft(suppressWarnings(inspect.ft(flowthrough_mult.rd, out.oxy = 12, in.oxy = 13, plot = FALSE)),
flowrate = 1.5, plot = FALSE)),
regexp = "adjust_rate.ft: 'x' and by' input rates have been calculated using different 'flowrates'!")
})
# Verify adjustment -------------------------------------------------------
test_that("adjust_rate.ft - adjustment value correctly extracted from 'by'", {
expect_equal(adjust_rate.ft(x1,
by = by_val)$adjustment,
by_val)
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_vec))$adjustment,
mean(by_vec))
expect_equal(adjust_rate.ft(x1,
by = by_crft)$adjustment,
by_crft$rate)
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_crft_mult))$adjustment,
mean(by_crft_mult$rate))
})
test_that("adjust_rate.ft - adjustment value correctly applied", {
expect_equal(adjust_rate.ft(x1,
by = by_val)$rate.adjusted,
x1$rate - by_val)
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_vec))$rate.adjusted,
x1$rate - mean(by_vec))
expect_equal(adjust_rate.ft(x1,
by = by_crft)$rate.adjusted,
x1$rate - mean(by_crft$rate))
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_crft_mult))$rate.adjusted,
x1$rate - mean(by_crft_mult$rate))
expect_equal(adjust_rate.ft(xmany,
by = by_val)$rate.adjusted,
xmany$rate - by_val)
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_vec))$rate.adjusted,
xmany$rate - mean(by_vec))
expect_equal(adjust_rate.ft(xmany,
by = by_crft)$rate.adjusted,
xmany$rate - mean(by_crft$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_crft_mult))$rate.adjusted,
xmany$rate - mean(by_crft_mult$rate))
expect_equal(adjust_rate.ft(xwidth,
by = by_val)$rate.adjusted,
xwidth$rate - by_val)
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_vec))$rate.adjusted,
xwidth$rate - mean(by_vec))
expect_equal(adjust_rate.ft(xwidth,
by = by_crft)$rate.adjusted,
xwidth$rate - mean(by_crft$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_crft_mult))$rate.adjusted,
xwidth$rate - mean(by_crft_mult$rate))
})
test_that("adjust_rate.ft - adjustment value correctly applied with oxygen production rates", {
expect_equal(adjust_rate.ft(xprod,
by = -1*by_val)$rate.adjusted,
xprod$rate - (-1*by_val))
expect_equal(suppressWarnings(adjust_rate.ft(xprod,
by = -1*by_vec))$rate.adjusted,
xprod$rate -(-1*mean(by_vec)))
})
test_that("adjust_rate.ft - if multiple rates in 'by' the mean value is correctly applied", {
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_vec))$rate.adjusted,
x1$rate - mean(by_vec))
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_crft_mult))$rate.adjusted,
x1$rate - mean(by_crft_mult$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_vec))$rate.adjusted,
xmany$rate - mean(by_vec))
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_crft_mult))$rate.adjusted,
xmany$rate - mean(by_crft_mult$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_vec))$rate.adjusted,
xwidth$rate - mean(by_vec))
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_crft_mult))$rate.adjusted,
xwidth$rate - mean(by_crft_mult$rate))
})
# S3 Generics tests -------------------------------------------------------
test_that("adjust_rate.ft - objects can be printed.", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(print(adj.ft_obj.insp.1),
regexp = NA)
expect_output(print(adj.ft_obj.insp.1),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.insp.many),
regexp = NA)
expect_output(print(adj.ft_obj.insp.many),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.insp.width),
regexp = NA)
expect_output(print(adj.ft_obj.insp.width),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.insp.prod),
regexp = NA)
expect_output(print(adj.ft_obj.insp.prod),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.vec),
regexp = NA)
expect_output(print(adj.ft_obj.vec),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.val),
regexp = NA)
expect_output(print(adj.ft_obj.val),
regexp = "Adjusted Rate :")
})
test_that("adjust_rate.ft - objects can be printed with 'pos' input.", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(print(adj.ft_obj.insp.many, pos = 2),
regexp = NA)
expect_output(print(adj.ft_obj.insp.many, pos = 2),
regexp = "Rank 2 of 101 adjusted")
expect_error(print(adj.ft_obj.insp.width, pos = 100),
regexp = NA)
expect_output(print(adj.ft_obj.insp.width, pos = 100),
regexp = "Rank 100 of 636 adjusted")
expect_error(print(adj.ft_obj.vec, pos = 20),
regexp = NA)
expect_output(print(adj.ft_obj.vec, pos = 20),
regexp = "Rank 20 of 101 adjusted")
## to check Adjustment value is properly included in output
## previously caught some failures to do this when pos was > 1
expect_failure(expect_output(print(adj.ft_obj.vec, pos = 20),
regexp = "Adjustment : NA"))
})
test_that("adjust_rate.ft - print() stops with invalid 'pos' input.", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(print(adj.ft_obj.insp.1, pos = 2),
regexp = "print.adjust_rate.ft: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_error(print(adj.ft_obj.insp.many, pos = 2000),
regexp = "print.adjust_rate.ft: Invalid 'pos' rank: only 101 adjusted rates found.")
expect_error(print(adj.ft_obj.insp.many, pos = 20:30),
regexp = "print.adjust_rate.ft: 'pos' must be a single value. To examine multiple results use summary().")
})
test_that("adjust_rate.ft - objects work with summary()", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.1),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.1),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.insp.many),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.many),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.insp.width),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.width),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.insp.prod),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.prod),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.vec),
regexp = NA)
expect_output(summary(adj.ft_obj.vec),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.val),
regexp = NA)
expect_output(summary(adj.ft_obj.val),
regexp = "rate.adjusted")
})
test_that("adjust_rate.ft - objects work with summary() and 'pos' input", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.many, pos = 2),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.many, pos = 2),
regexp = "rate.adjusted")
expect_equal(nrow(summary(adj.ft_obj.insp.many, pos = 2, export = TRUE)),
1)
expect_error(summary(adj.ft_obj.insp.many, pos = 2:10),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.many, pos = 2:10),
regexp = "rate.adjusted")
expect_equal(nrow(summary(adj.ft_obj.insp.many, pos = 2:10, export = TRUE)),
9)
expect_error(summary(adj.ft_obj.vec, pos = c(2,4,6,8)),
regexp = NA)
expect_output(summary(adj.ft_obj.vec, pos = c(2,4,6,8)),
regexp = "rate.adjusted")
expect_equal(nrow(summary(adj.ft_obj.vec, pos = c(2,4,6,8), export = TRUE)),
4)
expect_equal(summary(adj.ft_obj.vec, pos = c(2,4,6,8), export = TRUE)$rank,
c(2,4,6,8))
})
test_that("adjust_rate.ft - summary() stops with invalid 'pos' input", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.many, pos = 102),
regexp = "summary.adjust_rate.ft: Invalid 'pos' rank: only 101 rates found.")
})
test_that("adjust_rate.ft - objects work with summary() and 'export' input", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.many, export = TRUE),
regexp = NA)
expect_equal(nrow(summary(adj.ft_obj.insp.many, export = TRUE)),
nrow(adj.ft_obj.insp.many$summary))
})
test_that("adjust_rate.ft - objects work with mean()", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(mean(adj.ft_obj.insp.1),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.1),
regexp = "Mean of 1 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.1, export = TRUE),
mean(adj.ft_obj.insp.1$rate.adjusted))
expect_message(mean(adj.ft_obj.insp.1),
regexp = "Only 1 rate found. Returning mean rate anyway")
expect_error(mean(adj.ft_obj.insp.many),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.many),
regexp = "Mean of 101 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.many, export = TRUE),
mean(adj.ft_obj.insp.many$rate.adjusted))
expect_error(mean(adj.ft_obj.insp.width),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.width),
regexp = "Mean of 636 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.width, export = TRUE),
mean(adj.ft_obj.insp.width$rate.adjusted))
expect_error(mean(adj.ft_obj.insp.prod),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.prod),
regexp = "Mean of 1 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.prod, export = TRUE),
mean(adj.ft_obj.insp.prod$rate.adjusted))
expect_error(mean(adj.ft_obj.vec),
regexp = NA)
expect_output(mean(adj.ft_obj.vec),
regexp = "Mean of 101 adjusted rates:")
expect_equal(mean(adj.ft_obj.vec, export = TRUE),
mean(adj.ft_obj.vec$rate.adjusted))
expect_error(mean(adj.ft_obj.val),
regexp = NA)
expect_output(mean(adj.ft_obj.val),
regexp = "Mean of 1 adjusted rates:")
expect_equal(mean(adj.ft_obj.val, export = TRUE),
mean(adj.ft_obj.val$rate.adjusted))
})
test_that("adjust_rate.ft - objects work with mean() and 'pos' input", {
expect_error(mean(adj.ft_obj.insp.many, pos = 1:10),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.many, pos = 1:10),
regexp = "Mean of adjusted rate results from entered 'pos' ranks:")
expect_equal(mean(adj.ft_obj.insp.many, pos = 1:10, export = TRUE),
mean(adj.ft_obj.insp.many$rate.adjusted[1:10]))
})
test_that("adjust_rate.ft - stops with mean() if 'pos' too high", {
expect_error(mean(adj.ft_obj.insp.many, pos = 200),
regexp = "mean.adjust_rate.ft: Invalid 'pos' rank: only 101 adjusted rates found.")
})
test_that("adjust_rate.ft - stops with plot()", {
expect_message(plot(adj.ft_obj.insp.many),
regexp = "adjust_rate.ft: plot\\(\\) is not available for 'adjust_rate.ft' objects.")
})
}) ## end capture.output
januarharianto/respR documentation built on April 20, 2024, 4:34 p.m.
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# library(testthat)
# rm(list=ls())
# testthat::test_file("tests/testthat/test-adjust_rate.ft.R")
# covr::file_coverage("R/calc_rate.ft.R", "tests/testthat/test-adjust_rate.ft.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
capture.output({ ## stops printing outputs on assigning
# Create testing objects --------------------------------------------------
insp.ft_obj <- inspect.ft(flowthrough.rd, delta.oxy = 4, plot = FALSE)
## oxygen production data
insp.ft_obj_prod <- inspect.ft(cbind(flowthrough.rd[,1], -1*(flowthrough.rd[,4])),
time = 1, delta.oxy = 2, plot = FALSE)
# x objects
x1 <- calc_rate.ft(insp.ft_obj,
flowrate = 2, from = 200, to = 500,
by = NULL, width = NULL, plot = FALSE
)
xmany <- calc_rate.ft(insp.ft_obj,
flowrate = 2, from = 200:300, to = 500:600,
by = NULL, width = NULL, plot = FALSE
)
xwidth <- calc_rate.ft(insp.ft_obj,
flowrate = 2,
by = "row", width = 300, plot = FALSE
)
xprod <- calc_rate.ft(insp.ft_obj_prod,
flowrate = 2, from = 200, to = 500,
by = NULL, width = NULL, plot = FALSE
)
# by objects
by_val <- -0.7
by_vec <- seq(-0.75, -0.85, -0.01)
by_crft <- calc_rate.ft(suppressWarnings(inspect.ft(flowthrough_mult.rd, out.oxy = 4, in.oxy = 8, plot = FALSE)),
flowrate = 2, plot = FALSE)
by_crft_mult <- calc_rate.ft(suppressWarnings(inspect.ft(flowthrough_mult.rd, out.oxy = 4, in.oxy = 8, plot = FALSE)),
from = c(2000, 2500), to = c(2400, 2900), by = "row",
flowrate = 2, plot = FALSE)
# by_crft_nl <- calc_rate.ft(inspect.ft(flowthrough_sim.rd, out.oxy = 2, in.oxy = 3, plot = FALSE),
# flowrate = 2, plot = FALSE)
adj.ft_obj.insp.1 <- adjust_rate.ft(x1, by = by_val)
adj.ft_obj.insp.many <- adjust_rate.ft(xmany, by = by_val)
adj.ft_obj.insp.width <- adjust_rate.ft(xwidth, by = by_val)
adj.ft_obj.insp.prod <- adjust_rate.ft(xprod, by = 0.7)
adj.ft_obj.vec <- adjust_rate.ft(xmany$rate, by = by_val)
adj.ft_obj.val <- adjust_rate.ft(-1.5, by = by_val)
# validate 'x' inputs -----------------------------------------------------
test_that("adjust_rate.ft - stops if 'x' input not numeric or 'calc_rate.ft'", {
expect_error(adjust_rate.ft("string",
by = -0.7),
regexp = "adjust_rate.ft: 'x' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(as.data.frame(flowthrough.rd),
by = -0.7),
regexp = "adjust_rate.ft: 'x' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(inspect(flowthrough.rd, plot = FALSE),
by = -0.7),
regexp = "adjust_rate.ft: 'x' must be numeric or 'calc_rate.ft' object.")
})
# validate 'by' inputs ----------------------------------------------------
test_that("adjust_rate.ft - stops if 'by' input not numeric or 'calc_rate.ft'", {
expect_error(adjust_rate.ft(x1,
by = "string"),
regexp = "adjust_rate.ft: 'by' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(x1,
by = as.data.frame(flowthrough.rd)),
regexp = "adjust_rate.ft: 'by' must be numeric or 'calc_rate.ft' object.")
expect_error(adjust_rate.ft(x1,
by = inspect(flowthrough.rd, plot = FALSE)),
regexp = "adjust_rate.ft: 'by' must be numeric or 'calc_rate.ft' object.")
})
test_that("adjust_rate.ft - message if 'by' contains multiple rates", {
expect_message(adjust_rate.ft(x1,
by = c(23,34)),
regexp = "adjust_rate.ft: the 'by' input contains multiple background rates. The mean value will be used to perform adjustments.")
expect_message(adjust_rate.ft(x1,
by = xmany),
regexp = "adjust_rate.ft: the 'by' input contains multiple background rates. The mean value will be used to perform adjustments.")
})
test_that("adjust_rate.ft - stops if 'x' and 'by' are calc_rate.ft and have been determined using different 'flowrates'", {
expect_error(adjust_rate.ft(calc_rate.ft(insp.ft_obj,
flowrate = 2,
from = 200, to = 500, plot = FALSE),
by = calc_rate.ft(suppressWarnings(inspect.ft(flowthrough_mult.rd, out.oxy = 12, in.oxy = 13, plot = FALSE)),
flowrate = 1.5, plot = FALSE)),
regexp = "adjust_rate.ft: 'x' and by' input rates have been calculated using different 'flowrates'!")
})
# Verify adjustment -------------------------------------------------------
test_that("adjust_rate.ft - adjustment value correctly extracted from 'by'", {
expect_equal(adjust_rate.ft(x1,
by = by_val)$adjustment,
by_val)
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_vec))$adjustment,
mean(by_vec))
expect_equal(adjust_rate.ft(x1,
by = by_crft)$adjustment,
by_crft$rate)
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_crft_mult))$adjustment,
mean(by_crft_mult$rate))
})
test_that("adjust_rate.ft - adjustment value correctly applied", {
expect_equal(adjust_rate.ft(x1,
by = by_val)$rate.adjusted,
x1$rate - by_val)
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_vec))$rate.adjusted,
x1$rate - mean(by_vec))
expect_equal(adjust_rate.ft(x1,
by = by_crft)$rate.adjusted,
x1$rate - mean(by_crft$rate))
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_crft_mult))$rate.adjusted,
x1$rate - mean(by_crft_mult$rate))
expect_equal(adjust_rate.ft(xmany,
by = by_val)$rate.adjusted,
xmany$rate - by_val)
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_vec))$rate.adjusted,
xmany$rate - mean(by_vec))
expect_equal(adjust_rate.ft(xmany,
by = by_crft)$rate.adjusted,
xmany$rate - mean(by_crft$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_crft_mult))$rate.adjusted,
xmany$rate - mean(by_crft_mult$rate))
expect_equal(adjust_rate.ft(xwidth,
by = by_val)$rate.adjusted,
xwidth$rate - by_val)
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_vec))$rate.adjusted,
xwidth$rate - mean(by_vec))
expect_equal(adjust_rate.ft(xwidth,
by = by_crft)$rate.adjusted,
xwidth$rate - mean(by_crft$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_crft_mult))$rate.adjusted,
xwidth$rate - mean(by_crft_mult$rate))
})
test_that("adjust_rate.ft - adjustment value correctly applied with oxygen production rates", {
expect_equal(adjust_rate.ft(xprod,
by = -1*by_val)$rate.adjusted,
xprod$rate - (-1*by_val))
expect_equal(suppressWarnings(adjust_rate.ft(xprod,
by = -1*by_vec))$rate.adjusted,
xprod$rate -(-1*mean(by_vec)))
})
test_that("adjust_rate.ft - if multiple rates in 'by' the mean value is correctly applied", {
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_vec))$rate.adjusted,
x1$rate - mean(by_vec))
expect_equal(suppressWarnings(adjust_rate.ft(x1,
by = by_crft_mult))$rate.adjusted,
x1$rate - mean(by_crft_mult$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_vec))$rate.adjusted,
xmany$rate - mean(by_vec))
expect_equal(suppressWarnings(adjust_rate.ft(xmany,
by = by_crft_mult))$rate.adjusted,
xmany$rate - mean(by_crft_mult$rate))
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_vec))$rate.adjusted,
xwidth$rate - mean(by_vec))
expect_equal(suppressWarnings(adjust_rate.ft(xwidth,
by = by_crft_mult))$rate.adjusted,
xwidth$rate - mean(by_crft_mult$rate))
})
# S3 Generics tests -------------------------------------------------------
test_that("adjust_rate.ft - objects can be printed.", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(print(adj.ft_obj.insp.1),
regexp = NA)
expect_output(print(adj.ft_obj.insp.1),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.insp.many),
regexp = NA)
expect_output(print(adj.ft_obj.insp.many),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.insp.width),
regexp = NA)
expect_output(print(adj.ft_obj.insp.width),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.insp.prod),
regexp = NA)
expect_output(print(adj.ft_obj.insp.prod),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.vec),
regexp = NA)
expect_output(print(adj.ft_obj.vec),
regexp = "Adjusted Rate :")
expect_error(print(adj.ft_obj.val),
regexp = NA)
expect_output(print(adj.ft_obj.val),
regexp = "Adjusted Rate :")
})
test_that("adjust_rate.ft - objects can be printed with 'pos' input.", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(print(adj.ft_obj.insp.many, pos = 2),
regexp = NA)
expect_output(print(adj.ft_obj.insp.many, pos = 2),
regexp = "Rank 2 of 101 adjusted")
expect_error(print(adj.ft_obj.insp.width, pos = 100),
regexp = NA)
expect_output(print(adj.ft_obj.insp.width, pos = 100),
regexp = "Rank 100 of 636 adjusted")
expect_error(print(adj.ft_obj.vec, pos = 20),
regexp = NA)
expect_output(print(adj.ft_obj.vec, pos = 20),
regexp = "Rank 20 of 101 adjusted")
## to check Adjustment value is properly included in output
## previously caught some failures to do this when pos was > 1
expect_failure(expect_output(print(adj.ft_obj.vec, pos = 20),
regexp = "Adjustment : NA"))
})
test_that("adjust_rate.ft - print() stops with invalid 'pos' input.", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(print(adj.ft_obj.insp.1, pos = 2),
regexp = "print.adjust_rate.ft: Invalid 'pos' rank: only 1 adjusted rates found.")
expect_error(print(adj.ft_obj.insp.many, pos = 2000),
regexp = "print.adjust_rate.ft: Invalid 'pos' rank: only 101 adjusted rates found.")
expect_error(print(adj.ft_obj.insp.many, pos = 20:30),
regexp = "print.adjust_rate.ft: 'pos' must be a single value. To examine multiple results use summary().")
})
test_that("adjust_rate.ft - objects work with summary()", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.1),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.1),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.insp.many),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.many),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.insp.width),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.width),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.insp.prod),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.prod),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.vec),
regexp = NA)
expect_output(summary(adj.ft_obj.vec),
regexp = "rate.adjusted")
expect_error(summary(adj.ft_obj.val),
regexp = NA)
expect_output(summary(adj.ft_obj.val),
regexp = "rate.adjusted")
})
test_that("adjust_rate.ft - objects work with summary() and 'pos' input", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.many, pos = 2),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.many, pos = 2),
regexp = "rate.adjusted")
expect_equal(nrow(summary(adj.ft_obj.insp.many, pos = 2, export = TRUE)),
1)
expect_error(summary(adj.ft_obj.insp.many, pos = 2:10),
regexp = NA)
expect_output(summary(adj.ft_obj.insp.many, pos = 2:10),
regexp = "rate.adjusted")
expect_equal(nrow(summary(adj.ft_obj.insp.many, pos = 2:10, export = TRUE)),
9)
expect_error(summary(adj.ft_obj.vec, pos = c(2,4,6,8)),
regexp = NA)
expect_output(summary(adj.ft_obj.vec, pos = c(2,4,6,8)),
regexp = "rate.adjusted")
expect_equal(nrow(summary(adj.ft_obj.vec, pos = c(2,4,6,8), export = TRUE)),
4)
expect_equal(summary(adj.ft_obj.vec, pos = c(2,4,6,8), export = TRUE)$rank,
c(2,4,6,8))
})
test_that("adjust_rate.ft - summary() stops with invalid 'pos' input", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.many, pos = 102),
regexp = "summary.adjust_rate.ft: Invalid 'pos' rank: only 101 rates found.")
})
test_that("adjust_rate.ft - objects work with summary() and 'export' input", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(summary(adj.ft_obj.insp.many, export = TRUE),
regexp = NA)
expect_equal(nrow(summary(adj.ft_obj.insp.many, export = TRUE)),
nrow(adj.ft_obj.insp.many$summary))
})
test_that("adjust_rate.ft - objects work with mean()", {
# # objects
# adj.ft_obj.insp.1
# adj.ft_obj.insp.many
# adj.ft_obj.insp.width
# adj.ft_obj.insp.prod
# adj.ft_obj.vec
# adj.ft_obj.val
expect_error(mean(adj.ft_obj.insp.1),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.1),
regexp = "Mean of 1 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.1, export = TRUE),
mean(adj.ft_obj.insp.1$rate.adjusted))
expect_message(mean(adj.ft_obj.insp.1),
regexp = "Only 1 rate found. Returning mean rate anyway")
expect_error(mean(adj.ft_obj.insp.many),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.many),
regexp = "Mean of 101 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.many, export = TRUE),
mean(adj.ft_obj.insp.many$rate.adjusted))
expect_error(mean(adj.ft_obj.insp.width),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.width),
regexp = "Mean of 636 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.width, export = TRUE),
mean(adj.ft_obj.insp.width$rate.adjusted))
expect_error(mean(adj.ft_obj.insp.prod),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.prod),
regexp = "Mean of 1 adjusted rates:")
expect_equal(mean(adj.ft_obj.insp.prod, export = TRUE),
mean(adj.ft_obj.insp.prod$rate.adjusted))
expect_error(mean(adj.ft_obj.vec),
regexp = NA)
expect_output(mean(adj.ft_obj.vec),
regexp = "Mean of 101 adjusted rates:")
expect_equal(mean(adj.ft_obj.vec, export = TRUE),
mean(adj.ft_obj.vec$rate.adjusted))
expect_error(mean(adj.ft_obj.val),
regexp = NA)
expect_output(mean(adj.ft_obj.val),
regexp = "Mean of 1 adjusted rates:")
expect_equal(mean(adj.ft_obj.val, export = TRUE),
mean(adj.ft_obj.val$rate.adjusted))
})
test_that("adjust_rate.ft - objects work with mean() and 'pos' input", {
expect_error(mean(adj.ft_obj.insp.many, pos = 1:10),
regexp = NA)
expect_output(mean(adj.ft_obj.insp.many, pos = 1:10),
regexp = "Mean of adjusted rate results from entered 'pos' ranks:")
expect_equal(mean(adj.ft_obj.insp.many, pos = 1:10, export = TRUE),
mean(adj.ft_obj.insp.many$rate.adjusted[1:10]))
})
test_that("adjust_rate.ft - stops with mean() if 'pos' too high", {
expect_error(mean(adj.ft_obj.insp.many, pos = 200),
regexp = "mean.adjust_rate.ft: Invalid 'pos' rank: only 101 adjusted rates found.")
})
test_that("adjust_rate.ft - stops with plot()", {
expect_message(plot(adj.ft_obj.insp.many),
regexp = "adjust_rate.ft: plot\\(\\) is not available for 'adjust_rate.ft' objects.")
})
}) ## end capture.output
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