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tests/testthat/test-inspect.ft.R
In respR: Import, Process, Analyse, and Calculate Rates from Respirometry Data
# rm(list=ls())
# library(testthat)
# test_file("tests/testthat/test-inspect.ft.R")
# covr::file_coverage("R/inspect.ft.R", "tests/testthat/test-inspect.ft.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
# covr::report(covr::package_coverage())
capture.output({ ## stops printing console outputs on assigning
if (!identical(Sys.getenv("NOT_CRAN"), "true")) return()
skip_on_cran()
# Create multicolumn dfs for testing --------------------------------------
{
## versions with various errors
## non-numeric in time
ft_mult_time_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_time_nonnum_1[432,1]
ft_mult_time_nonnum_1[432,1] <- "7.2"
## inf in time
ft_mult_time_inf_1 <- flowthrough_mult.rd
ft_mult_time_inf_1[431:433,1]
ft_mult_time_inf_1[432,1] <- Inf
ft_mult_time_inf_3 <- flowthrough_mult.rd
ft_mult_time_inf_3[431:433,1]
ft_mult_time_inf_3[432,1] <- Inf
ft_mult_time_inf_3[623:625,1]
ft_mult_time_inf_3[624,1] <- Inf
ft_mult_time_inf_3[723:725,1]
ft_mult_time_inf_3[724,1] <- Inf
## loads - more than 20 to check printing
ft_mult_time_inf_mult <- flowthrough_mult.rd
ft_mult_time_inf_mult[431:462,1]
ft_mult_time_inf_mult[432:461,1] <- Inf
ft_mult_time_inf_mult[621:672,1]
ft_mult_time_inf_mult[622:671,1] <- Inf
## versions with various errors
## NaN in time
ft_mult_time_nan_1 <- flowthrough_mult.rd
ft_mult_time_nan_1[431:433,1]
ft_mult_time_nan_1[432,1] <- NA
ft_mult_time_nan_3 <- flowthrough_mult.rd
ft_mult_time_nan_3[431:433,1]
ft_mult_time_nan_3[432,1] <- NA
ft_mult_time_nan_3[623:625,1]
ft_mult_time_nan_3[624,1] <- NA
ft_mult_time_nan_3[723:725,1]
ft_mult_time_nan_3[724,1] <- NA
## loads - more than 20 to check printing
ft_mult_time_nan_mult <- flowthrough_mult.rd
ft_mult_time_nan_mult[431:462,1]
ft_mult_time_nan_mult[432:461,1] <- NA
ft_mult_time_nan_mult[621:672,1]
ft_mult_time_nan_mult[622:671,1] <- NA
## non-sequential in time
ft_mult_time_nonseq_1 <- flowthrough_mult.rd
ft_mult_time_nonseq_1[431:433,1]
ft_mult_time_nonseq_1[432:433,1] <- c(432,431)
ft_mult_time_nonseq_3 <- flowthrough_mult.rd
ft_mult_time_nonseq_3[431:433,1]
ft_mult_time_nonseq_3[432:433,1] <- c(432,431)
ft_mult_time_nonseq_3[751:753,1]
ft_mult_time_nonseq_3[752:753,1] <- c(752,751)
ft_mult_time_nonseq_3[781:783,1]
ft_mult_time_nonseq_3[782:783,1] <- c(782,781)
ft_mult_time_nonseq_mult <- flowthrough_mult.rd
ft_mult_time_nonseq_mult[431:462,1]
ft_mult_time_nonseq_mult[432:461,1] <- ft_mult_time_nonseq_mult[461:432,1]
ft_mult_time_nonseq_mult[621:672,1]
ft_mult_time_nonseq_mult[622:671,1] <- ft_mult_time_nonseq_mult[671:622,1]
## duplicated in time
ft_mult_time_dupe_1 <- flowthrough_mult.rd
ft_mult_time_dupe_1[431:433,1]
ft_mult_time_dupe_1[432:433,1] <- c(431,431)
ft_mult_time_dupe_3 <- flowthrough_mult.rd
ft_mult_time_dupe_3[431:434,1]
ft_mult_time_dupe_3[432:434,1] <- c(431,431,431)
ft_mult_time_dupe_3[751:753,1]
ft_mult_time_dupe_3[752:753,1] <- c(752,752)
ft_mult_time_dupe_3[781:787,1]
ft_mult_time_dupe_3[782:787,1] <- c(781,781,781,781,781,781)
ft_mult_time_dupe_mult <- flowthrough_mult.rd
ft_mult_time_dupe_mult[431:462,1]
ft_mult_time_dupe_mult[432:461,1] <- 431
ft_mult_time_dupe_mult[621:672,1]
ft_mult_time_dupe_mult[622:671,1] <- 622
## unevenly spaced in time
ft_mult_time_uneven_1 <- flowthrough_mult.rd
ft_mult_time_uneven_1[431:433,1]
ft_mult_time_uneven_1 <- ft_mult_time_uneven_1[-432,]
ft_mult_time_uneven_3 <- flowthrough_mult.rd
ft_mult_time_uneven_3[431:434,1]
ft_mult_time_uneven_3 <- ft_mult_time_uneven_3[-432,]
ft_mult_time_uneven_3[751:753,1]
ft_mult_time_uneven_3 <- ft_mult_time_uneven_3[-752,]
ft_mult_time_uneven_3[781:787,1]
ft_mult_time_uneven_3 <- ft_mult_time_uneven_3[-782,]
ft_mult_time_uneven_mult <- flowthrough_mult.rd
ft_mult_time_uneven_mult[431:482,1]
ft_mult_time_uneven_mult <- ft_mult_time_uneven_mult[-seq(432, 472, 2),]
ft_mult_time_uneven_mult[831:882,1]
ft_mult_time_uneven_mult <- ft_mult_time_uneven_mult[-seq(832, 872, 2),]
## non-numeric in out.oxy
ft_mult_out.oxy_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_out.oxy_nonnum_1[432,2]
ft_mult_out.oxy_nonnum_1[432,2] <- "92.95885"
## non-numeric in in.oxy
ft_mult_in.oxy_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_in.oxy_nonnum_1[432,6]
ft_mult_in.oxy_nonnum_1[432,6] <- "97.19841"
## non-numeric in delta.oxy
ft_mult_delta.oxy_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_delta.oxy_nonnum_1[432,10]
ft_mult_delta.oxy_nonnum_1[432,10] <- "-4.239564"
## NaN in out.oxy
ft_mult_out.oxy_nan_1 <- flowthrough_mult.rd
ft_mult_out.oxy_nan_1[432,2] <- NA
ft_mult_out.oxy_nan_3 <- flowthrough_mult.rd
ft_mult_out.oxy_nan_3[432,2] <- NA
ft_mult_out.oxy_nan_3[624,2] <- NA
ft_mult_out.oxy_nan_3[724,2] <- NA
ft_mult_out.oxy_nan_3[624,3] <- NA
ft_mult_out.oxy_nan_3[724,3] <- NA
ft_mult_out.oxy_nan_mult <- flowthrough_mult.rd
ft_mult_out.oxy_nan_mult[432:461,2] <- NA
ft_mult_out.oxy_nan_mult[622:671,2] <- NA
## NaN in in.oxy
ft_mult_in.oxy_nan_1 <- flowthrough_mult.rd
ft_mult_in.oxy_nan_1[432,5] <- NA
ft_mult_in.oxy_nan_3 <- flowthrough_mult.rd
ft_mult_in.oxy_nan_3[432,5] <- NA
ft_mult_in.oxy_nan_3[624,5] <- NA
ft_mult_in.oxy_nan_3[724,5] <- NA
ft_mult_in.oxy_nan_3[624,6] <- NA
ft_mult_in.oxy_nan_3[724,6] <- NA
ft_mult_in.oxy_nan_mult <- flowthrough_mult.rd
ft_mult_in.oxy_nan_mult[432:461,5] <- NA
ft_mult_in.oxy_nan_mult[622:671,5] <- NA
## NaN in delta.oxy
ft_mult_delta.oxy_nan_1 <- flowthrough_mult.rd
ft_mult_delta.oxy_nan_1[432,8] <- NA
ft_mult_delta.oxy_nan_3 <- flowthrough_mult.rd
ft_mult_delta.oxy_nan_3[432,8] <- NA
ft_mult_delta.oxy_nan_3[624,8] <- NA
ft_mult_delta.oxy_nan_3[724,8] <- NA
ft_mult_delta.oxy_nan_3[624,9] <- NA
ft_mult_delta.oxy_nan_3[724,9] <- NA
ft_mult_delta.oxy_nan_mult <- flowthrough_mult.rd
ft_mult_delta.oxy_nan_mult[432:461,8] <- NA
ft_mult_delta.oxy_nan_mult[622:671,8] <- NA
## inf in out.oxy
ft_mult_out.oxy_inf_1 <- flowthrough_mult.rd
ft_mult_out.oxy_inf_1[432,2] <- Inf
ft_mult_out.oxy_inf_3 <- flowthrough_mult.rd
ft_mult_out.oxy_inf_3[432,2] <- Inf
ft_mult_out.oxy_inf_3[624,2] <- Inf
ft_mult_out.oxy_inf_3[724,2] <- Inf
ft_mult_out.oxy_inf_3[624,3] <- Inf
ft_mult_out.oxy_inf_3[724,3] <- Inf
ft_mult_out.oxy_inf_mult <- flowthrough_mult.rd
ft_mult_out.oxy_inf_mult[432:461,2] <- Inf
ft_mult_out.oxy_inf_mult[622:671,2] <- Inf
## inf in in.oxy
ft_mult_in.oxy_inf_1 <- flowthrough_mult.rd
ft_mult_in.oxy_inf_1[432,5] <- Inf
ft_mult_in.oxy_inf_3 <- flowthrough_mult.rd
ft_mult_in.oxy_inf_3[432,5] <- Inf
ft_mult_in.oxy_inf_3[624,5] <- Inf
ft_mult_in.oxy_inf_3[724,5] <- Inf
ft_mult_in.oxy_inf_3[624,6] <- Inf
ft_mult_in.oxy_inf_3[724,6] <- Inf
ft_mult_in.oxy_inf_mult <- flowthrough_mult.rd
ft_mult_in.oxy_inf_mult[432:461,5] <- Inf
ft_mult_in.oxy_inf_mult[622:671,5] <- Inf
## inf in delta.oxy
ft_mult_delta.oxy_inf_1 <- flowthrough_mult.rd
ft_mult_delta.oxy_inf_1[432,8] <- Inf
ft_mult_delta.oxy_inf_3 <- flowthrough_mult.rd
ft_mult_delta.oxy_inf_3[432,8] <- Inf
ft_mult_delta.oxy_inf_3[624,8] <- Inf
ft_mult_delta.oxy_inf_3[724,8] <- Inf
ft_mult_delta.oxy_inf_3[624,9] <- Inf
ft_mult_delta.oxy_inf_3[724,9] <- Inf
ft_mult_delta.oxy_inf_mult <- flowthrough_mult.rd
ft_mult_delta.oxy_inf_mult[432:461,8] <- Inf
ft_mult_delta.oxy_inf_mult[622:671,8] <- Inf
## 2 column input (i.e. time- and calculated delta)
insp.ft.obj <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 6, delta.oxy = NULL, plot = F))
## multi column input (i.e. time- and calculated delta)
insp.ft.mult.obj <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 6:8, delta.oxy = NULL, plot = F))
}
# inspect.ft(flowthrough_mult.rd, time = "num.time", out.oxy = 2,
# in.oxy = 6)
# tests -------------------------------------------------------------------
test_that("inspect.ft - works with NULL inputs and applies defaults correctly",{
## time = NULL
expect_message(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = NULL, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: Applying column default of 'time = 1")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = NULL, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = F)),
regexp = NA)
expect_equal(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = NULL, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = F))$data$time[[1]],
flowthrough_mult.rd[[1]])
# in.oxy = NULL & out.oxy = NULL & delta.oxy = NULL
expect_message(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: Applying column default of all non-time column\\(s\\) as 'delta.oxy'")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = NULL, plot = F)),
regexp = NA)
expect_equal(as.data.frame(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = NULL, plot = F)$data$delta.oxy)),
as.data.frame(flowthrough_mult.rd[,2:15]))
})
test_that("inspect.ft - stops if input column numbers found to conflict",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:6,
in.oxy = 5:9, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Input columns conflict.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = 1:10, plot = F),
regexp = "inspect.ft: Input columns conflict.")
})
test_that("inspect.ft - stops if out.oxy entered and neither or in.oxy or in.oxy.value have inputs",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:3,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: With 'out.oxy' data, paired 'in.oxy' columns or an 'in.oxy.value' is required.")
})
test_that("inspect.ft - stops if in.oxy entered and out.oxy does not have input",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: An 'in.oxy' input requires paired 'out.oxy' column\\(s\\).")
})
test_that("inspect.ft - stops if both or in.oxy and in.oxy.value have inputs",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:3,
in.oxy = 4, in.oxy.value = 5, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Only one of 'in.oxy' or 'in.oxy.value' can be entered.")
})
test_that("inspect.ft - correctly accepts and handles in.oxy.value input",{
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = NULL, in.oxy.value = 9, delta.oxy = NULL, plot = F))$dataframe$in.oxy.value,
regexp = NA)
expect_equal(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = NULL, in.oxy.value = 9, delta.oxy = NULL, plot = F))$dataframe$in.oxy.value,
rep(9, nrow(flowthrough_mult.rd)))
})
test_that("inspect.ft - stops if out.oxy and in.oxy entered, but in.oxy does not have same number of columns or a single column.",{
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:6, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: With 'out.oxy' data, 'in.oxy' must be a single column or an equal number of paired columns.")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:9, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: With 'out.oxy' data, 'in.oxy' must be a single column or an equal number of paired columns.")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 4, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = NA)
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 4:5, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = NA)
})
test_that("inspect.ft - stops if delta.oxy entered and out.oxy, in.oxy or in.oxy.value have inputs",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2,
in.oxy = NULL, in.oxy.value = 4, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2,
in.oxy = 4, in.oxy.value = NULL, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 4,
in.oxy = 5, in.oxy.value = NULL, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = 4, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
})
test_that("inspect.ft - stops if x not a dataframe", {
expect_error(inspect.ft(as.matrix(flowthrough.rd), time = 1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'x' must be data.frame object.")
expect_error(inspect.ft(flowthrough.rd[[1]], time = 1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'x' must be data.frame object.")
expect_error(inspect.ft("blah", time = 1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'x' must be data.frame object.")
})
test_that("inspect.ft - stops if column inputs malformed", {
## time
expect_error(inspect.ft(flowthrough.rd, time = 1.1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'time' - some column inputs are not integers.")
expect_error(inspect.ft(flowthrough.rd, time = 1:2, out.oxy = 3,
in.oxy = 4, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'time' - cannot enter more than 1 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 8, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'time' - one or more column inputs are out of range of allowed data columns.")
## out.oxy
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2.1,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - some column inputs are not integers")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 4:9,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - cannot enter more than 3 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 8:9,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - one or more column inputs are out of range of allowed data columns.")
## in.oxy
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2,
in.oxy = 3.1, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'in.oxy' - some column inputs are not integers.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 4:9,
in.oxy = 2, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - cannot enter more than 3 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:3,
in.oxy = 8:9, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'in.oxy' - one or more column inputs are out of range of allowed data columns.")
## delta.oxy
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 4.1, plot = F),
regexp = "inspect.ft: 'delta.oxy' - some column inputs are not integers")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 2:5, plot = F),
regexp = "inspect.ft: 'delta.oxy' - cannot enter more than 3 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 5, plot = F),
regexp = "inspect.ft: 'delta.oxy' - one or more column inputs are out of range of allowed data columns.")
})
test_that("inspect.ft - correctly identifies column name strings", {
# single time and oxygen columns work without error
expect_error(inspect.ft(flowthrough.rd, time = "time", out.oxy = "oxy.out", in.oxy = "oxy.in", plot = FALSE),
NA)
# delta data
expect_error(inspect.ft(flowthrough.rd, time = "time", delta.oxy = "oxy.delta", plot = FALSE),
NA)
# same as using numbers
# Everything except the $call should be the same
expect_equal(inspect.ft(flowthrough.rd, time = "time", out.oxy = "oxy.out", in.oxy = "oxy.in", plot = FALSE)[2:8],
inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, plot = FALSE)[2:8])
expect_equal(inspect.ft(flowthrough.rd, time = "time", delta.oxy = "oxy.delta", plot = FALSE)[2:8],
inspect.ft(flowthrough.rd, time = 1, delta.oxy = 4, plot = FALSE)[2:8])
# multiple oxygen columns
expect_error(inspect.ft(flowthrough.rd, time = "time", out.oxy = c("oxy.out","oxy.delta"), in.oxy = c("oxy.in"), plot = FALSE),
NA)
# same as using numbers
# Everything except the $call should be the same
expect_equal(inspect.ft(flowthrough.rd, time = "time", out.oxy = c("oxy.out","oxy.delta"), in.oxy = c("oxy.in"), plot = FALSE)[2:8],
inspect.ft(flowthrough.rd, time = 1, out.oxy = c(2,4), in.oxy = 3, plot = FALSE)[2:8])
# add.data
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, add.data = "oxy.delta", plot = FALSE),
NA)
# same as using numbers
# Everything except the $call should be the same
expect_equal(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, add.data = "oxy.delta", plot = FALSE)$add.data,
inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, add.data = 4, plot = FALSE)$add.data)
})
test_that("inspect.ft - outputs correct warnings", {
## time nonnum
expect_warning(inspect.ft(ft_mult_time_nonnum_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Time column not numeric. Other column checks skipped.")
## time Inf
expect_warning(inspect.ft(ft_mult_time_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Time column. Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_time_inf_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Time column. Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_time_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Time column. Remove or replace before proceeding.")
## time NA
expect_warning(inspect.ft(ft_mult_time_nan_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Time column.")
expect_warning(inspect.ft(ft_mult_time_nan_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Time column.")
expect_warning(inspect.ft(ft_mult_time_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Time column.")
## time non-seq
expect_warning(inspect.ft(ft_mult_time_nonseq_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Non-sequential Time values found.")
expect_warning(inspect.ft(ft_mult_time_nonseq_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Non-sequential Time values found.")
expect_warning(inspect.ft(ft_mult_time_nonseq_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Non-sequential Time values found.")
## time duplicates
expect_warning(inspect.ft(ft_mult_time_dupe_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Duplicate Time values found.")
expect_warning(inspect.ft(ft_mult_time_dupe_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Duplicate Time values found.")
expect_warning(inspect.ft(ft_mult_time_dupe_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Duplicate Time values found.")
## time uneven
expect_warning(inspect.ft(ft_mult_time_uneven_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Time values are not evenly-spaced")
expect_warning(inspect.ft(ft_mult_time_uneven_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Time values are not evenly-spaced")
expect_warning(inspect.ft(ft_mult_time_uneven_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Time values are not evenly-spaced.")
## out.oxy nonnum
expect_warning(inspect.ft(ft_mult_out.oxy_nonnum_1, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Oxygen column\\(s) not numeric. Other column checks skipped.")
## out.oxy Inf
expect_warning(inspect.ft(ft_mult_out.oxy_inf_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_out.oxy_inf_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_out.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
## out.oxy NA
expect_warning(inspect.ft(ft_mult_out.oxy_nan_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_out.oxy_nan_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
## out.oxy nonnum
expect_warning(inspect.ft(ft_mult_in.oxy_nonnum_1, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Oxygen column\\(s) not numeric. Other column checks skipped.")
## in.oxy Inf
expect_warning(inspect.ft(ft_mult_in.oxy_inf_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_in.oxy_inf_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_in.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
## in.oxy NA
expect_warning(inspect.ft(ft_mult_in.oxy_nan_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_in.oxy_nan_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_in.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
## delta.oxy non-numeric
expect_warning(inspect.ft(ft_mult_delta.oxy_nonnum_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Oxygen column\\(s) not numeric. Other column checks skipped.")
## delta.oxy Inf
expect_warning(inspect.ft(ft_mult_delta.oxy_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_delta.oxy_inf_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_delta.oxy_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
## delta.oxy NA
expect_warning(inspect.ft(ft_mult_delta.oxy_nan_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_delta.oxy_nan_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_delta.oxy_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
})
test_that("inspect.ft works with 2-column data", {
expect_error(inspect.ft(sardine.rd[,1:2], plot = F),
regexp = NA)
expect_equal(ncol(inspect.ft(sardine.rd[,1:2], plot = F)$dataframe),
2)
})
test_that("inspect.ft works with multi-column data", {
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:7, plot = F)),
regexp = NA)
expect_equal(ncol(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:7, plot = F))$dataframe),
7 + 3) # 7 inputs, 3 delta calcs
})
test_that("inspect.ft outputs plot", {
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = T)),
regexp = NA)
expect_output(plot(insp.ft.obj))
expect_error(plot(insp.ft.obj),
regexp = NA)
expect_output(plot(insp.ft.mult.obj))
expect_error(plot(insp.ft.mult.obj),
regexp = NA)
})
test_that("inspect.ft outputs plot with 'add.data' input", {
expect_output(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, add.data = 15,
plot = T)))
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, add.data = 15,
plot = T)),
regexp = NA)
# multi cols
expect_message(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 5:6, delta.oxy = NULL, add.data = 15,
plot = T)),
"plot.inspect.ft: Additional data source cannot be plotted for multiple columns.")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 5:6, delta.oxy = NULL, add.data = 15,
plot = T)),
regexp = NA)
})
test_that("inspect.ft outputs plots with different 'wdith'", {
expect_output(plot(insp.ft.obj, width = 0.4))
expect_error(plot(insp.ft.obj, width = 0.4),
regexp = NA)
})
test_that("inspect.ft outputs plots when 'pos =' option is used", {
expect_output(plot(insp.ft.mult.obj, pos = 2))
expect_error(plot(insp.ft.mult.obj, pos = 2),
regexp = NA)
expect_output(plot(insp.ft.mult.obj, pos = 2))
expect_error(plot(insp.ft.mult.obj, pos = 2),
regexp = NA)
})
test_that("inspect.ft message with multiple plots and add.data", {
# object with multiple delta cols but also add.data
obj <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, delta.oxy = 10:12, plot = F, add.data = 15))
expect_message(plot(obj),
"plot.inspect.ft: Additional data source cannot be plotted for multiple columns.")
})
test_that("inspect.ft does not plot when 'pos =' input too large", {
expect_error(plot(insp.ft.obj, pos = 9),
regexp = "plot.inspect.ft: Invalid 'pos' input: only 1 data inputs found.")
expect_error(plot(insp.ft.mult.obj, pos = 9),
regexp = "inspect.ft: Invalid 'pos' input: only 3 data inputs found.")
})
test_that("inspect.ft - mean S3 returns message", {
expect_message(mean(insp.ft.obj),
"inspect.ft: mean\\() is not available for 'inspect.ft' objects.")
})
test_that("inspect.ft objects can be printed, including those which show warnings", {
## regular good data
expect_output(print(insp.ft.obj))
expect_error(print(insp.ft.obj),
regexp = NA)
expect_output(print(insp.ft.mult.obj))
expect_error(print(insp.ft.mult.obj),
regexp = NA)
## various errors/warnings
ob1 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob2 <- suppressWarnings(inspect.ft(ft_mult_time_nonseq_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob3 <- suppressWarnings(inspect.ft(ft_mult_time_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob4 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob5 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob6 <- suppressWarnings(inspect.ft(ft_mult_in.oxy_nan_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob7 <- suppressWarnings(inspect.ft(ft_mult_delta.oxy_nan_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F))
ob8 <- suppressWarnings(inspect.ft(ft_mult_time_dupe_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob8 <- suppressWarnings(inspect.ft(ft_mult_time_dupe_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob9 <- suppressWarnings(inspect.ft(ft_mult_time_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob10 <- suppressWarnings(inspect.ft(ft_mult_time_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob11 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_inf_1, time = 1, out.oxy = 2,
in.oxy = 6, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob12 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob13 <- suppressWarnings(inspect.ft(ft_mult_in.oxy_inf_1, time = 1, out.oxy = 2,
in.oxy = 6, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob14 <- suppressWarnings(inspect.ft(ft_mult_in.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob15 <- suppressWarnings(inspect.ft(ft_mult_delta.oxy_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8, plot = F))
ob16 <- suppressWarnings(inspect.ft(ft_mult_delta.oxy_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F))
expect_output(print(ob1))
expect_output(print(ob2))
expect_output(print(ob3))
expect_output(print(ob4))
expect_output(print(ob5))
expect_output(print(ob6))
expect_output(print(ob7))
expect_output(print(ob8))
expect_output(print(ob9))
expect_output(print(ob10))
expect_output(print(ob11))
expect_output(print(ob12))
expect_output(print(ob13))
expect_output(print(ob14))
expect_output(print(ob15))
expect_output(print(ob16))
expect_error(print(ob1),
regexp = NA)
expect_error(print(ob2),
regexp = NA)
expect_error(print(ob3),
regexp = NA)
expect_error(print(ob4),
regexp = NA)
expect_error(print(ob5),
regexp = NA)
expect_error(print(ob6),
regexp = NA)
expect_error(print(ob7),
regexp = NA)
expect_error(print(ob8),
regexp = NA)
expect_error(print(ob9),
regexp = NA)
expect_error(print(ob10),
regexp = NA)
expect_error(print(ob11),
regexp = NA)
expect_error(print(ob12),
regexp = NA)
expect_error(print(ob13),
regexp = NA)
expect_error(print(ob14),
regexp = NA)
expect_error(print(ob15),
regexp = NA)
expect_error(print(ob16),
regexp = NA)
expect_output(summary(ob1))
expect_output(summary(ob2))
expect_output(summary(ob3))
expect_output(summary(ob4))
expect_output(summary(ob5))
expect_output(summary(ob6))
expect_output(summary(ob7))
expect_output(summary(ob8))
expect_output(summary(ob9))
expect_output(summary(ob10))
expect_output(summary(ob11))
expect_output(summary(ob12))
expect_output(summary(ob13))
expect_output(summary(ob14))
expect_output(summary(ob15))
expect_output(summary(ob16))
expect_error(summary(ob1),
regexp = NA)
expect_error(summary(ob2),
regexp = NA)
expect_error(summary(ob3),
regexp = NA)
expect_error(summary(ob4),
regexp = NA)
expect_error(summary(ob5),
regexp = NA)
expect_error(summary(ob6),
regexp = NA)
expect_error(summary(ob7),
regexp = NA)
expect_error(summary(ob8),
regexp = NA)
expect_error(summary(ob9),
regexp = NA)
expect_error(summary(ob10),
regexp = NA)
expect_error(summary(ob11),
regexp = NA)
expect_error(summary(ob12),
regexp = NA)
expect_error(summary(ob13),
regexp = NA)
expect_error(summary(ob14),
regexp = NA)
expect_error(summary(ob15),
regexp = NA)
expect_error(summary(ob16),
regexp = NA)
})
test_that("inspect.ft - plot defaults are correctly restored", {
# reset plotting first
dev.off()
# save par before
parb4 <- par(no.readonly = TRUE)
# now use a fn with plot
inspect.ft(flowthrough.rd, 1, 2, 3)
# save after
paraft <- par(no.readonly = TRUE)
# mai is something changed from the default,
# so if par settings not restored properly this should fail
expect_identical(parb4$mai,
paraft$mai)
})
}) ## turns console printing back on
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# rm(list=ls())
# library(testthat)
# test_file("tests/testthat/test-inspect.ft.R")
# covr::file_coverage("R/inspect.ft.R", "tests/testthat/test-inspect.ft.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
# covr::report(covr::package_coverage())
capture.output({ ## stops printing console outputs on assigning
if (!identical(Sys.getenv("NOT_CRAN"), "true")) return()
skip_on_cran()
# Create multicolumn dfs for testing --------------------------------------
{
## versions with various errors
## non-numeric in time
ft_mult_time_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_time_nonnum_1[432,1]
ft_mult_time_nonnum_1[432,1] <- "7.2"
## inf in time
ft_mult_time_inf_1 <- flowthrough_mult.rd
ft_mult_time_inf_1[431:433,1]
ft_mult_time_inf_1[432,1] <- Inf
ft_mult_time_inf_3 <- flowthrough_mult.rd
ft_mult_time_inf_3[431:433,1]
ft_mult_time_inf_3[432,1] <- Inf
ft_mult_time_inf_3[623:625,1]
ft_mult_time_inf_3[624,1] <- Inf
ft_mult_time_inf_3[723:725,1]
ft_mult_time_inf_3[724,1] <- Inf
## loads - more than 20 to check printing
ft_mult_time_inf_mult <- flowthrough_mult.rd
ft_mult_time_inf_mult[431:462,1]
ft_mult_time_inf_mult[432:461,1] <- Inf
ft_mult_time_inf_mult[621:672,1]
ft_mult_time_inf_mult[622:671,1] <- Inf
## versions with various errors
## NaN in time
ft_mult_time_nan_1 <- flowthrough_mult.rd
ft_mult_time_nan_1[431:433,1]
ft_mult_time_nan_1[432,1] <- NA
ft_mult_time_nan_3 <- flowthrough_mult.rd
ft_mult_time_nan_3[431:433,1]
ft_mult_time_nan_3[432,1] <- NA
ft_mult_time_nan_3[623:625,1]
ft_mult_time_nan_3[624,1] <- NA
ft_mult_time_nan_3[723:725,1]
ft_mult_time_nan_3[724,1] <- NA
## loads - more than 20 to check printing
ft_mult_time_nan_mult <- flowthrough_mult.rd
ft_mult_time_nan_mult[431:462,1]
ft_mult_time_nan_mult[432:461,1] <- NA
ft_mult_time_nan_mult[621:672,1]
ft_mult_time_nan_mult[622:671,1] <- NA
## non-sequential in time
ft_mult_time_nonseq_1 <- flowthrough_mult.rd
ft_mult_time_nonseq_1[431:433,1]
ft_mult_time_nonseq_1[432:433,1] <- c(432,431)
ft_mult_time_nonseq_3 <- flowthrough_mult.rd
ft_mult_time_nonseq_3[431:433,1]
ft_mult_time_nonseq_3[432:433,1] <- c(432,431)
ft_mult_time_nonseq_3[751:753,1]
ft_mult_time_nonseq_3[752:753,1] <- c(752,751)
ft_mult_time_nonseq_3[781:783,1]
ft_mult_time_nonseq_3[782:783,1] <- c(782,781)
ft_mult_time_nonseq_mult <- flowthrough_mult.rd
ft_mult_time_nonseq_mult[431:462,1]
ft_mult_time_nonseq_mult[432:461,1] <- ft_mult_time_nonseq_mult[461:432,1]
ft_mult_time_nonseq_mult[621:672,1]
ft_mult_time_nonseq_mult[622:671,1] <- ft_mult_time_nonseq_mult[671:622,1]
## duplicated in time
ft_mult_time_dupe_1 <- flowthrough_mult.rd
ft_mult_time_dupe_1[431:433,1]
ft_mult_time_dupe_1[432:433,1] <- c(431,431)
ft_mult_time_dupe_3 <- flowthrough_mult.rd
ft_mult_time_dupe_3[431:434,1]
ft_mult_time_dupe_3[432:434,1] <- c(431,431,431)
ft_mult_time_dupe_3[751:753,1]
ft_mult_time_dupe_3[752:753,1] <- c(752,752)
ft_mult_time_dupe_3[781:787,1]
ft_mult_time_dupe_3[782:787,1] <- c(781,781,781,781,781,781)
ft_mult_time_dupe_mult <- flowthrough_mult.rd
ft_mult_time_dupe_mult[431:462,1]
ft_mult_time_dupe_mult[432:461,1] <- 431
ft_mult_time_dupe_mult[621:672,1]
ft_mult_time_dupe_mult[622:671,1] <- 622
## unevenly spaced in time
ft_mult_time_uneven_1 <- flowthrough_mult.rd
ft_mult_time_uneven_1[431:433,1]
ft_mult_time_uneven_1 <- ft_mult_time_uneven_1[-432,]
ft_mult_time_uneven_3 <- flowthrough_mult.rd
ft_mult_time_uneven_3[431:434,1]
ft_mult_time_uneven_3 <- ft_mult_time_uneven_3[-432,]
ft_mult_time_uneven_3[751:753,1]
ft_mult_time_uneven_3 <- ft_mult_time_uneven_3[-752,]
ft_mult_time_uneven_3[781:787,1]
ft_mult_time_uneven_3 <- ft_mult_time_uneven_3[-782,]
ft_mult_time_uneven_mult <- flowthrough_mult.rd
ft_mult_time_uneven_mult[431:482,1]
ft_mult_time_uneven_mult <- ft_mult_time_uneven_mult[-seq(432, 472, 2),]
ft_mult_time_uneven_mult[831:882,1]
ft_mult_time_uneven_mult <- ft_mult_time_uneven_mult[-seq(832, 872, 2),]
## non-numeric in out.oxy
ft_mult_out.oxy_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_out.oxy_nonnum_1[432,2]
ft_mult_out.oxy_nonnum_1[432,2] <- "92.95885"
## non-numeric in in.oxy
ft_mult_in.oxy_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_in.oxy_nonnum_1[432,6]
ft_mult_in.oxy_nonnum_1[432,6] <- "97.19841"
## non-numeric in delta.oxy
ft_mult_delta.oxy_nonnum_1 <- as.data.frame(flowthrough_mult.rd)
ft_mult_delta.oxy_nonnum_1[432,10]
ft_mult_delta.oxy_nonnum_1[432,10] <- "-4.239564"
## NaN in out.oxy
ft_mult_out.oxy_nan_1 <- flowthrough_mult.rd
ft_mult_out.oxy_nan_1[432,2] <- NA
ft_mult_out.oxy_nan_3 <- flowthrough_mult.rd
ft_mult_out.oxy_nan_3[432,2] <- NA
ft_mult_out.oxy_nan_3[624,2] <- NA
ft_mult_out.oxy_nan_3[724,2] <- NA
ft_mult_out.oxy_nan_3[624,3] <- NA
ft_mult_out.oxy_nan_3[724,3] <- NA
ft_mult_out.oxy_nan_mult <- flowthrough_mult.rd
ft_mult_out.oxy_nan_mult[432:461,2] <- NA
ft_mult_out.oxy_nan_mult[622:671,2] <- NA
## NaN in in.oxy
ft_mult_in.oxy_nan_1 <- flowthrough_mult.rd
ft_mult_in.oxy_nan_1[432,5] <- NA
ft_mult_in.oxy_nan_3 <- flowthrough_mult.rd
ft_mult_in.oxy_nan_3[432,5] <- NA
ft_mult_in.oxy_nan_3[624,5] <- NA
ft_mult_in.oxy_nan_3[724,5] <- NA
ft_mult_in.oxy_nan_3[624,6] <- NA
ft_mult_in.oxy_nan_3[724,6] <- NA
ft_mult_in.oxy_nan_mult <- flowthrough_mult.rd
ft_mult_in.oxy_nan_mult[432:461,5] <- NA
ft_mult_in.oxy_nan_mult[622:671,5] <- NA
## NaN in delta.oxy
ft_mult_delta.oxy_nan_1 <- flowthrough_mult.rd
ft_mult_delta.oxy_nan_1[432,8] <- NA
ft_mult_delta.oxy_nan_3 <- flowthrough_mult.rd
ft_mult_delta.oxy_nan_3[432,8] <- NA
ft_mult_delta.oxy_nan_3[624,8] <- NA
ft_mult_delta.oxy_nan_3[724,8] <- NA
ft_mult_delta.oxy_nan_3[624,9] <- NA
ft_mult_delta.oxy_nan_3[724,9] <- NA
ft_mult_delta.oxy_nan_mult <- flowthrough_mult.rd
ft_mult_delta.oxy_nan_mult[432:461,8] <- NA
ft_mult_delta.oxy_nan_mult[622:671,8] <- NA
## inf in out.oxy
ft_mult_out.oxy_inf_1 <- flowthrough_mult.rd
ft_mult_out.oxy_inf_1[432,2] <- Inf
ft_mult_out.oxy_inf_3 <- flowthrough_mult.rd
ft_mult_out.oxy_inf_3[432,2] <- Inf
ft_mult_out.oxy_inf_3[624,2] <- Inf
ft_mult_out.oxy_inf_3[724,2] <- Inf
ft_mult_out.oxy_inf_3[624,3] <- Inf
ft_mult_out.oxy_inf_3[724,3] <- Inf
ft_mult_out.oxy_inf_mult <- flowthrough_mult.rd
ft_mult_out.oxy_inf_mult[432:461,2] <- Inf
ft_mult_out.oxy_inf_mult[622:671,2] <- Inf
## inf in in.oxy
ft_mult_in.oxy_inf_1 <- flowthrough_mult.rd
ft_mult_in.oxy_inf_1[432,5] <- Inf
ft_mult_in.oxy_inf_3 <- flowthrough_mult.rd
ft_mult_in.oxy_inf_3[432,5] <- Inf
ft_mult_in.oxy_inf_3[624,5] <- Inf
ft_mult_in.oxy_inf_3[724,5] <- Inf
ft_mult_in.oxy_inf_3[624,6] <- Inf
ft_mult_in.oxy_inf_3[724,6] <- Inf
ft_mult_in.oxy_inf_mult <- flowthrough_mult.rd
ft_mult_in.oxy_inf_mult[432:461,5] <- Inf
ft_mult_in.oxy_inf_mult[622:671,5] <- Inf
## inf in delta.oxy
ft_mult_delta.oxy_inf_1 <- flowthrough_mult.rd
ft_mult_delta.oxy_inf_1[432,8] <- Inf
ft_mult_delta.oxy_inf_3 <- flowthrough_mult.rd
ft_mult_delta.oxy_inf_3[432,8] <- Inf
ft_mult_delta.oxy_inf_3[624,8] <- Inf
ft_mult_delta.oxy_inf_3[724,8] <- Inf
ft_mult_delta.oxy_inf_3[624,9] <- Inf
ft_mult_delta.oxy_inf_3[724,9] <- Inf
ft_mult_delta.oxy_inf_mult <- flowthrough_mult.rd
ft_mult_delta.oxy_inf_mult[432:461,8] <- Inf
ft_mult_delta.oxy_inf_mult[622:671,8] <- Inf
## 2 column input (i.e. time- and calculated delta)
insp.ft.obj <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 6, delta.oxy = NULL, plot = F))
## multi column input (i.e. time- and calculated delta)
insp.ft.mult.obj <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 6:8, delta.oxy = NULL, plot = F))
}
# inspect.ft(flowthrough_mult.rd, time = "num.time", out.oxy = 2,
# in.oxy = 6)
# tests -------------------------------------------------------------------
test_that("inspect.ft - works with NULL inputs and applies defaults correctly",{
## time = NULL
expect_message(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = NULL, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: Applying column default of 'time = 1")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = NULL, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = F)),
regexp = NA)
expect_equal(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = NULL, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = F))$data$time[[1]],
flowthrough_mult.rd[[1]])
# in.oxy = NULL & out.oxy = NULL & delta.oxy = NULL
expect_message(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: Applying column default of all non-time column\\(s\\) as 'delta.oxy'")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = NULL, plot = F)),
regexp = NA)
expect_equal(as.data.frame(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = NULL, plot = F)$data$delta.oxy)),
as.data.frame(flowthrough_mult.rd[,2:15]))
})
test_that("inspect.ft - stops if input column numbers found to conflict",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:6,
in.oxy = 5:9, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Input columns conflict.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, delta.oxy = 1:10, plot = F),
regexp = "inspect.ft: Input columns conflict.")
})
test_that("inspect.ft - stops if out.oxy entered and neither or in.oxy or in.oxy.value have inputs",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:3,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: With 'out.oxy' data, paired 'in.oxy' columns or an 'in.oxy.value' is required.")
})
test_that("inspect.ft - stops if in.oxy entered and out.oxy does not have input",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: An 'in.oxy' input requires paired 'out.oxy' column\\(s\\).")
})
test_that("inspect.ft - stops if both or in.oxy and in.oxy.value have inputs",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:3,
in.oxy = 4, in.oxy.value = 5, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Only one of 'in.oxy' or 'in.oxy.value' can be entered.")
})
test_that("inspect.ft - correctly accepts and handles in.oxy.value input",{
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = NULL, in.oxy.value = 9, delta.oxy = NULL, plot = F))$dataframe$in.oxy.value,
regexp = NA)
expect_equal(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = NULL, in.oxy.value = 9, delta.oxy = NULL, plot = F))$dataframe$in.oxy.value,
rep(9, nrow(flowthrough_mult.rd)))
})
test_that("inspect.ft - stops if out.oxy and in.oxy entered, but in.oxy does not have same number of columns or a single column.",{
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:6, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: With 'out.oxy' data, 'in.oxy' must be a single column or an equal number of paired columns.")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:9, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = "inspect.ft: With 'out.oxy' data, 'in.oxy' must be a single column or an equal number of paired columns.")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 4, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = NA)
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 4:5, in.oxy.value = NULL, delta.oxy = NULL, plot = F)),
regexp = NA)
})
test_that("inspect.ft - stops if delta.oxy entered and out.oxy, in.oxy or in.oxy.value have inputs",{
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2,
in.oxy = NULL, in.oxy.value = 4, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2,
in.oxy = 4, in.oxy.value = NULL, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 4,
in.oxy = 5, in.oxy.value = NULL, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = 4, delta.oxy = 3, plot = F),
regexp = "inspect.ft: With 'delta.oxy' data, 'out.oxy', 'in.oxy' and 'in.oxy.value' should be NULL.")
})
test_that("inspect.ft - stops if x not a dataframe", {
expect_error(inspect.ft(as.matrix(flowthrough.rd), time = 1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'x' must be data.frame object.")
expect_error(inspect.ft(flowthrough.rd[[1]], time = 1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'x' must be data.frame object.")
expect_error(inspect.ft("blah", time = 1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'x' must be data.frame object.")
})
test_that("inspect.ft - stops if column inputs malformed", {
## time
expect_error(inspect.ft(flowthrough.rd, time = 1.1, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'time' - some column inputs are not integers.")
expect_error(inspect.ft(flowthrough.rd, time = 1:2, out.oxy = 3,
in.oxy = 4, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'time' - cannot enter more than 1 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 8, out.oxy = 2,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'time' - one or more column inputs are out of range of allowed data columns.")
## out.oxy
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2.1,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - some column inputs are not integers")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 4:9,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - cannot enter more than 3 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 8:9,
in.oxy = 3, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - one or more column inputs are out of range of allowed data columns.")
## in.oxy
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2,
in.oxy = 3.1, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'in.oxy' - some column inputs are not integers.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 4:9,
in.oxy = 2, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'out.oxy' - cannot enter more than 3 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2:3,
in.oxy = 8:9, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: 'in.oxy' - one or more column inputs are out of range of allowed data columns.")
## delta.oxy
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 4.1, plot = F),
regexp = "inspect.ft: 'delta.oxy' - some column inputs are not integers")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 2:5, plot = F),
regexp = "inspect.ft: 'delta.oxy' - cannot enter more than 3 column\\(s\\) with this input or this dataset.")
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 5, plot = F),
regexp = "inspect.ft: 'delta.oxy' - one or more column inputs are out of range of allowed data columns.")
})
test_that("inspect.ft - correctly identifies column name strings", {
# single time and oxygen columns work without error
expect_error(inspect.ft(flowthrough.rd, time = "time", out.oxy = "oxy.out", in.oxy = "oxy.in", plot = FALSE),
NA)
# delta data
expect_error(inspect.ft(flowthrough.rd, time = "time", delta.oxy = "oxy.delta", plot = FALSE),
NA)
# same as using numbers
# Everything except the $call should be the same
expect_equal(inspect.ft(flowthrough.rd, time = "time", out.oxy = "oxy.out", in.oxy = "oxy.in", plot = FALSE)[2:8],
inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, plot = FALSE)[2:8])
expect_equal(inspect.ft(flowthrough.rd, time = "time", delta.oxy = "oxy.delta", plot = FALSE)[2:8],
inspect.ft(flowthrough.rd, time = 1, delta.oxy = 4, plot = FALSE)[2:8])
# multiple oxygen columns
expect_error(inspect.ft(flowthrough.rd, time = "time", out.oxy = c("oxy.out","oxy.delta"), in.oxy = c("oxy.in"), plot = FALSE),
NA)
# same as using numbers
# Everything except the $call should be the same
expect_equal(inspect.ft(flowthrough.rd, time = "time", out.oxy = c("oxy.out","oxy.delta"), in.oxy = c("oxy.in"), plot = FALSE)[2:8],
inspect.ft(flowthrough.rd, time = 1, out.oxy = c(2,4), in.oxy = 3, plot = FALSE)[2:8])
# add.data
expect_error(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, add.data = "oxy.delta", plot = FALSE),
NA)
# same as using numbers
# Everything except the $call should be the same
expect_equal(inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, add.data = "oxy.delta", plot = FALSE)$add.data,
inspect.ft(flowthrough.rd, time = 1, out.oxy = 2, in.oxy = 3, add.data = 4, plot = FALSE)$add.data)
})
test_that("inspect.ft - outputs correct warnings", {
## time nonnum
expect_warning(inspect.ft(ft_mult_time_nonnum_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Time column not numeric. Other column checks skipped.")
## time Inf
expect_warning(inspect.ft(ft_mult_time_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Time column. Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_time_inf_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Time column. Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_time_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Time column. Remove or replace before proceeding.")
## time NA
expect_warning(inspect.ft(ft_mult_time_nan_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Time column.")
expect_warning(inspect.ft(ft_mult_time_nan_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Time column.")
expect_warning(inspect.ft(ft_mult_time_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Time column.")
## time non-seq
expect_warning(inspect.ft(ft_mult_time_nonseq_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Non-sequential Time values found.")
expect_warning(inspect.ft(ft_mult_time_nonseq_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Non-sequential Time values found.")
expect_warning(inspect.ft(ft_mult_time_nonseq_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Non-sequential Time values found.")
## time duplicates
expect_warning(inspect.ft(ft_mult_time_dupe_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Duplicate Time values found.")
expect_warning(inspect.ft(ft_mult_time_dupe_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Duplicate Time values found.")
expect_warning(inspect.ft(ft_mult_time_dupe_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Duplicate Time values found.")
## time uneven
expect_warning(inspect.ft(ft_mult_time_uneven_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Time values are not evenly-spaced")
expect_warning(inspect.ft(ft_mult_time_uneven_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Time values are not evenly-spaced")
expect_warning(inspect.ft(ft_mult_time_uneven_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "Time values are not evenly-spaced.")
## out.oxy nonnum
expect_warning(inspect.ft(ft_mult_out.oxy_nonnum_1, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Oxygen column\\(s) not numeric. Other column checks skipped.")
## out.oxy Inf
expect_warning(inspect.ft(ft_mult_out.oxy_inf_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_out.oxy_inf_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_out.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
## out.oxy NA
expect_warning(inspect.ft(ft_mult_out.oxy_nan_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_out.oxy_nan_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
## out.oxy nonnum
expect_warning(inspect.ft(ft_mult_in.oxy_nonnum_1, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Oxygen column\\(s) not numeric. Other column checks skipped.")
## in.oxy Inf
expect_warning(inspect.ft(ft_mult_in.oxy_inf_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_in.oxy_inf_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_in.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
## in.oxy NA
expect_warning(inspect.ft(ft_mult_in.oxy_nan_1, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_in.oxy_nan_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_in.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
## delta.oxy non-numeric
expect_warning(inspect.ft(ft_mult_delta.oxy_nonnum_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Oxygen column\\(s) not numeric. Other column checks skipped.")
## delta.oxy Inf
expect_warning(inspect.ft(ft_mult_delta.oxy_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_delta.oxy_inf_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
expect_warning(inspect.ft(ft_mult_delta.oxy_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "inspect.ft: Inf/-Inf values detected in Oxygen column\\(s). Remove or replace before proceeding.")
## delta.oxy NA
expect_warning(inspect.ft(ft_mult_delta.oxy_nan_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_delta.oxy_nan_3, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
expect_warning(inspect.ft(ft_mult_delta.oxy_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F),
regexp = "NA/NaN values detected in Oxygen column\\(s\\).")
})
test_that("inspect.ft works with 2-column data", {
expect_error(inspect.ft(sardine.rd[,1:2], plot = F),
regexp = NA)
expect_equal(ncol(inspect.ft(sardine.rd[,1:2], plot = F)$dataframe),
2)
})
test_that("inspect.ft works with multi-column data", {
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:7, plot = F)),
regexp = NA)
expect_equal(ncol(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:4,
in.oxy = 5:7, plot = F))$dataframe),
7 + 3) # 7 inputs, 3 delta calcs
})
test_that("inspect.ft outputs plot", {
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, plot = T)),
regexp = NA)
expect_output(plot(insp.ft.obj))
expect_error(plot(insp.ft.obj),
regexp = NA)
expect_output(plot(insp.ft.mult.obj))
expect_error(plot(insp.ft.mult.obj),
regexp = NA)
})
test_that("inspect.ft outputs plot with 'add.data' input", {
expect_output(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, add.data = 15,
plot = T)))
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2,
in.oxy = 5, delta.oxy = NULL, add.data = 15,
plot = T)),
regexp = NA)
# multi cols
expect_message(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 5:6, delta.oxy = NULL, add.data = 15,
plot = T)),
"plot.inspect.ft: Additional data source cannot be plotted for multiple columns.")
expect_error(suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, out.oxy = 2:3,
in.oxy = 5:6, delta.oxy = NULL, add.data = 15,
plot = T)),
regexp = NA)
})
test_that("inspect.ft outputs plots with different 'wdith'", {
expect_output(plot(insp.ft.obj, width = 0.4))
expect_error(plot(insp.ft.obj, width = 0.4),
regexp = NA)
})
test_that("inspect.ft outputs plots when 'pos =' option is used", {
expect_output(plot(insp.ft.mult.obj, pos = 2))
expect_error(plot(insp.ft.mult.obj, pos = 2),
regexp = NA)
expect_output(plot(insp.ft.mult.obj, pos = 2))
expect_error(plot(insp.ft.mult.obj, pos = 2),
regexp = NA)
})
test_that("inspect.ft message with multiple plots and add.data", {
# object with multiple delta cols but also add.data
obj <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1, delta.oxy = 10:12, plot = F, add.data = 15))
expect_message(plot(obj),
"plot.inspect.ft: Additional data source cannot be plotted for multiple columns.")
})
test_that("inspect.ft does not plot when 'pos =' input too large", {
expect_error(plot(insp.ft.obj, pos = 9),
regexp = "plot.inspect.ft: Invalid 'pos' input: only 1 data inputs found.")
expect_error(plot(insp.ft.mult.obj, pos = 9),
regexp = "inspect.ft: Invalid 'pos' input: only 3 data inputs found.")
})
test_that("inspect.ft - mean S3 returns message", {
expect_message(mean(insp.ft.obj),
"inspect.ft: mean\\() is not available for 'inspect.ft' objects.")
})
test_that("inspect.ft objects can be printed, including those which show warnings", {
## regular good data
expect_output(print(insp.ft.obj))
expect_error(print(insp.ft.obj),
regexp = NA)
expect_output(print(insp.ft.mult.obj))
expect_error(print(insp.ft.mult.obj),
regexp = NA)
## various errors/warnings
ob1 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob2 <- suppressWarnings(inspect.ft(ft_mult_time_nonseq_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob3 <- suppressWarnings(inspect.ft(ft_mult_time_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob4 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob5 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_nan_mult, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob6 <- suppressWarnings(inspect.ft(ft_mult_in.oxy_nan_3, time = 1, out.oxy = 2:4,
in.oxy = 5:7, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob7 <- suppressWarnings(inspect.ft(ft_mult_delta.oxy_nan_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F))
ob8 <- suppressWarnings(inspect.ft(ft_mult_time_dupe_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob8 <- suppressWarnings(inspect.ft(ft_mult_time_dupe_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob9 <- suppressWarnings(inspect.ft(ft_mult_time_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob10 <- suppressWarnings(inspect.ft(ft_mult_time_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob11 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_inf_1, time = 1, out.oxy = 2,
in.oxy = 6, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob12 <- suppressWarnings(inspect.ft(ft_mult_out.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob13 <- suppressWarnings(inspect.ft(ft_mult_in.oxy_inf_1, time = 1, out.oxy = 2,
in.oxy = 6, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob14 <- suppressWarnings(inspect.ft(ft_mult_in.oxy_inf_mult, time = 1, out.oxy = 2:4,
in.oxy = 6:8, in.oxy.value = NULL, delta.oxy = NULL, plot = F))
ob15 <- suppressWarnings(inspect.ft(ft_mult_delta.oxy_inf_1, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8, plot = F))
ob16 <- suppressWarnings(inspect.ft(ft_mult_delta.oxy_inf_mult, time = 1, out.oxy = NULL,
in.oxy = NULL, in.oxy.value = NULL, delta.oxy = 8:10, plot = F))
expect_output(print(ob1))
expect_output(print(ob2))
expect_output(print(ob3))
expect_output(print(ob4))
expect_output(print(ob5))
expect_output(print(ob6))
expect_output(print(ob7))
expect_output(print(ob8))
expect_output(print(ob9))
expect_output(print(ob10))
expect_output(print(ob11))
expect_output(print(ob12))
expect_output(print(ob13))
expect_output(print(ob14))
expect_output(print(ob15))
expect_output(print(ob16))
expect_error(print(ob1),
regexp = NA)
expect_error(print(ob2),
regexp = NA)
expect_error(print(ob3),
regexp = NA)
expect_error(print(ob4),
regexp = NA)
expect_error(print(ob5),
regexp = NA)
expect_error(print(ob6),
regexp = NA)
expect_error(print(ob7),
regexp = NA)
expect_error(print(ob8),
regexp = NA)
expect_error(print(ob9),
regexp = NA)
expect_error(print(ob10),
regexp = NA)
expect_error(print(ob11),
regexp = NA)
expect_error(print(ob12),
regexp = NA)
expect_error(print(ob13),
regexp = NA)
expect_error(print(ob14),
regexp = NA)
expect_error(print(ob15),
regexp = NA)
expect_error(print(ob16),
regexp = NA)
expect_output(summary(ob1))
expect_output(summary(ob2))
expect_output(summary(ob3))
expect_output(summary(ob4))
expect_output(summary(ob5))
expect_output(summary(ob6))
expect_output(summary(ob7))
expect_output(summary(ob8))
expect_output(summary(ob9))
expect_output(summary(ob10))
expect_output(summary(ob11))
expect_output(summary(ob12))
expect_output(summary(ob13))
expect_output(summary(ob14))
expect_output(summary(ob15))
expect_output(summary(ob16))
expect_error(summary(ob1),
regexp = NA)
expect_error(summary(ob2),
regexp = NA)
expect_error(summary(ob3),
regexp = NA)
expect_error(summary(ob4),
regexp = NA)
expect_error(summary(ob5),
regexp = NA)
expect_error(summary(ob6),
regexp = NA)
expect_error(summary(ob7),
regexp = NA)
expect_error(summary(ob8),
regexp = NA)
expect_error(summary(ob9),
regexp = NA)
expect_error(summary(ob10),
regexp = NA)
expect_error(summary(ob11),
regexp = NA)
expect_error(summary(ob12),
regexp = NA)
expect_error(summary(ob13),
regexp = NA)
expect_error(summary(ob14),
regexp = NA)
expect_error(summary(ob15),
regexp = NA)
expect_error(summary(ob16),
regexp = NA)
})
test_that("inspect.ft - plot defaults are correctly restored", {
# reset plotting first
dev.off()
# save par before
parb4 <- par(no.readonly = TRUE)
# now use a fn with plot
inspect.ft(flowthrough.rd, 1, 2, 3)
# save after
paraft <- par(no.readonly = TRUE)
# mai is something changed from the default,
# so if par settings not restored properly this should fail
expect_identical(parb4$mai,
paraft$mai)
})
}) ## turns console printing back on
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