Nothing

```
# rm(list=ls())
# library(testthat)
# test_file("tests/testthat/test-subset_data.R")
# covr::file_coverage("R/subset_data.R", "tests/testthat/test-subset_data.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
capture.output({ ## stops printing outputs on assigning
if (!identical(Sys.getenv("NOT_CRAN"), "true")) return()
skip_on_cran()
test_that("subset_data - works with data.frame input", {
# time
sub <- subset_data(sardine.rd, from = 2000, to = 3000, by = "time")
expect_is(sub,
"data.frame")
expect_is(sub,
"data.table")
expect_equal(nrow(sub),
1001)
expect_equal(c(sardine.rd[2001,]),
c(sub[1,]))
# row
sub <- subset_data(sardine.rd, from = 2000, to = 3000, by = "row")
expect_is(sub,
"data.frame")
expect_is(sub,
"data.table")
expect_equal(nrow(sub),
1001)
expect_equal(c(sardine.rd[2000,]),
c(sub[1,]))
})
test_that("subset_data - test some exact values", {
sub <- subset_data(sardine.rd, from = 2000, to = 3000, by = "time")
expect_equal(sub$Oxygen[1],
93.8)
expect_equal(tail(sub$Oxygen, 1),
93.1)
})
test_that("subset_data - works by row", {
sub <- subset_data(sardine.rd, from = 2000, to = 3000, by = "row")
expect_is(sub,
"data.frame")
})
test_that("subset_data - works by O2", {
sub <- subset_data(sardine.rd, from = 93, to = 92, by = "oxygen")
expect_is(sub,
"data.frame")
})
test_that("subset_data - works with variations of `by` input", {
invisible({
expect_error(subset_data(sardine.rd, from = 2000, to = 3000, by = "Time"), regexp = NA)
expect_error(subset_data(sardine.rd, from = 2000, to = 3000, by = "T"), regexp = NA)
expect_error(subset_data(sardine.rd, from = 2000, to = 3000, by = "Row"), regexp = NA)
expect_error(subset_data(sardine.rd, from = 2000, to = 3000, by = "r"), regexp = NA)
expect_error(subset_data(sardine.rd, from = 95, to = 94, by = "Oxygen"), regexp = NA)
expect_error(subset_data(sardine.rd, from = 95, to = 94, by = "oxygen"), regexp = NA)
})
})
test_that("subset_data - error with wrong by", {
expect_error(subset_data(sardine.rd, by = "tttimmmeee"),
"subset_data: 'by' input not valid or not recognised.")
})
test_that("subset_data - output can be printed", {
sub <- subset_data(sardine.rd, from = 2000, to = 3000, by = "time")
expect_output(print(sub))
})
test_that("subset_data - works with inspect objects for each method", {
urch <- suppressWarnings(inspect(urchins.rd, time = 1, oxygen = 14:15))
expect_error(subset_data(urch, from = 7.6, to = 7.4, by = "oxygen"),
regexp = NA)
expect_error(subset_data(urch, from = 10, to = 30, by = "time"),
regexp = NA)
expect_error(subset_data(urch, from = 70, to = 170, by = "row"),
regexp = NA)
})
test_that("subset_data - includes all columns when subsetting", {
urch <- suppressWarnings(inspect(urchins.rd, time = 1, oxygen = 10:15))
expect_equal(ncol((subset_data(urch, from = 7.6, to = 7.4, by = "oxygen"))$dataframe),
7)
expect_equal(ncol((subset_data(urch, from = 10, to = 30, by = "time"))$dataframe),
7)
expect_equal(ncol((subset_data(urch, from = 70, to = 170, by = "row"))$dataframe),
7)
})
test_that("subset_data - works with inspect.ft objects", {
fthr <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1,
delta.oxy = 10:12, plot = FALSE))
expect_error(subset_data(fthr, from = -3, to = -5, by = "oxygen"),
regexp = NA)
expect_output(subset_data(fthr, from = -3, to = -5, by = "oxygen", quiet = FALSE),
regexp = "Subset data:")
expect_equal(nrow(subset_data(fthr, from = -3, to = -5, by = "oxygen")$dataframe),
553)
expect_error(subset_data(fthr, from = 10, to = 20, by = "time"),
regexp = NA)
expect_output(subset_data(fthr, from = 10, to = 20, by = "time", quiet = FALSE),
regexp = "Subset data:")
expect_equal(nrow(subset_data(fthr, from = 10, to = 20, by = "time")$dataframe),
601)
expect_error(subset_data(fthr, from = 70, to = 170, by = "row"),
regexp = NA)
expect_output(subset_data(fthr, from = 70, to = 170, by = "row", quiet = FALSE),
regexp = "Subset data:")
expect_equal(nrow(subset_data(fthr, from = 70, to = 170, by = "row")$dataframe),
101)
})
test_that("subset_data - class retained in output", {
input <- sardine.rd
expect_is(subset_data(input, from = 7.6, to = 7.4, by = "oxygen"),
"data.frame")
input <- inspect(sardine.rd)
expect_is(subset_data(input, from = 7.6, to = 7.4, by = "oxygen"),
"inspect")
input <- inspect.ft(sardine.rd)
expect_is(subset_data(input, from = 7.6, to = 7.4, by = "oxygen"),
"inspect.ft")
})
test_that("subset_data - stops if 'from' or 'to' malformed", {
fthr <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1,
delta.oxy = 10:12, plot = FALSE))
expect_error(subset_data(fthr, from = 30, to = 20, by = "time"),
regexp = "subset_data: 'to' - one or more inputs are outside the range of allowed values.")
expect_error(subset_data(fthr, from = 80, to = 20, by = "time"),
regexp = "subset_data: 'from' - one or more inputs are outside the range of allowed values.")
expect_error(subset_data(fthr, from = 21:22, to = 30, by = "time"),
regexp = "subset_data: 'from' - only 1 inputs allowed.")
expect_error(subset_data(fthr, from = 3000.2, to = 2000, by = "row"),
regexp = "subset_data: 'from' - one or more inputs are not integers.")
expect_error(subset_data(fthr, from = 8000, to = 2000, by = "row"),
regexp = "subset_data: 'from' - one or more inputs are outside the range of allowed values.")
expect_error(subset_data(fthr, from = 2001:2002, to = 3000, by = "row"),
regexp = "subset_data: 'from' - only 1 inputs allowed.")
expect_error(subset_data(fthr, from = 2:3, to = 3800, by = "oxygen"),
regexp = "subset_data: 'from' - only 1 inputs allowed.")
})
# subset `inspect` and `inspect.ft` objects work as expected in subsequent functions
test_that("subset_data - `inspect` objects work as expected in subsequent functions.", {
urch <- suppressWarnings(inspect(urchins.rd, time = 1, oxygen = 4))
sub <- subset_data(urch, from = 7.6, to = 7.4, by = "oxygen")
expect_error(calc_rate(sub),
regexp = NA)
# rate from sub should be same as if sub was done in fn
expect_equal(calc_rate(urch, from = 7.6, to = 7.4, by = "oxygen")$rate,
calc_rate(sub)$rate)
urch <- suppressWarnings(inspect(urchins.rd, time = 1, oxygen = 4))
sub <- subset_data(urch, from = 10, to = 20, by = "time")
expect_error(calc_rate(sub),
regexp = NA)
# rate from sub should be same as if sub was done in fn
expect_equal(calc_rate(urch, from = 10, to = 20, by = "time")$rate,
calc_rate(sub)$rate)
expect_error(auto_rate(sub),
regexp = NA)
expect_equal(auto_rate(sub)$rate,
auto_rate(urchins.rd[61:121,c(1,4)])$rate)
})
test_that("subset_data - `inspect.ft` objects work as expected in subsequent functions.", {
fltr <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1,
out.oxy = 2, in.oxy = 6))
sub <- subset_data(fltr, from = 20, to = 30, by = "time")
expect_error(calc_rate.ft(sub, flowrate = 1.5),
regexp = NA)
# rate from sub should be same as if sub was done in fn
expect_equal(calc_rate.ft(fltr, flowrate = 1.5, from = 20, to = 30)$rate,
calc_rate.ft(sub, flowrate = 1.5)$rate)
})
test_that("subset_data - `inspect.ft` $dataframe and $inputs elements have both been subset correctly", {
fltr <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1,
out.oxy = 2, in.oxy = 6))
sub <- subset_data(fltr, from = 20, to = 30, by = "time")
dtt <- sapply(sub$data, function(z) rbind.data.frame(z))
dtt <- as.data.table(dtt)
names(dtt) <- names(sub$dataframe)
expect_identical(dtt,
sub$dataframe)
sub <- subset_data(fltr, from = 100, to = 867, by = "row")
dtt <- sapply(sub$data, function(z) rbind.data.frame(z))
dtt <- as.data.table(dtt)
names(dtt) <- names(sub$dataframe)
expect_identical(dtt,
sub$dataframe)
sub <- subset_data(fltr, from = 8.5, to = 8.2, by = "ox")
dtt <- sapply(sub$data, function(z) rbind.data.frame(z))
dtt <- as.data.table(dtt)
names(dtt) <- names(sub$dataframe)
expect_identical(dtt,
sub$dataframe)
fltr <- suppressWarnings(inspect.ft(flowthrough_mult.rd, time = 1,
delta.oxy = 8:10))
sub <- subset_data(fltr, from = 15, to = 32, by = "time")
dtt <- sapply(sub$data, function(z) rbind.data.frame(z))
dtt <- as.data.table(dtt)
names(dtt) <- names(sub$dataframe)
expect_identical(dtt,
sub$dataframe)
fltr <- suppressWarnings(inspect.ft(flowthrough.rd, time = 1,
out.oxy = 2, in.oxy = 3))
sub <- subset_data(fltr, from = 123, to = 654, by = "row")
dtt <- sapply(sub$data, function(z) rbind.data.frame(z))
dtt <- as.data.table(dtt)
names(dtt) <- names(sub$dataframe)
expect_identical(dtt,
sub$dataframe)
})
# this should now be impossible...
# test_that("subset_data - warns if output is empty", {
# urch <- urchins.rd[20:200,]
# expect_warning(subset_data(urch, from = 0, to = 1, by = "time"),
# regexp = "subset_data: subsetting criteria result in empty dataset!")
# expect_warning(subset_data(inspect(urch), from = 0, to = 1, by = "time"),
# regexp = "subset_data: subsetting criteria result in empty dataset!")
# expect_warning(subset_data(inspect.ft(urch[,1:2]), from = 0, to = 1, by = "time"),
# regexp = "subset_data: subsetting criteria result in empty dataset!")
# })
test_that("subset_data - correctly handles 'from' NULL", {
urch <- urchins.rd[20:200,]
expect_error(subset_data(urch, from = NULL, to = 20, by = "time"),
regexp = NA)
expect_equal(as.numeric(subset_data(urch, from = NULL, to = 20, by = "time")[1,1]),
3.2)
expect_error(subset_data(urch, from = NULL, to = 20, by = "row"),
regexp = NA)
expect_equal(as.numeric(subset_data(urch, from = NULL, to = 20, by = "row")[1,1]),
3.2)
expect_error(subset_data(urch, from = NULL, to = 7, by = "oxygen"),
regexp = NA)
expect_equal(as.numeric(subset_data(urch, from = NULL, to = 20, by = "row")[1,2]),
7.75)
})
test_that("subset_data - correctly handles 'to' NULL", {
urch <- urchins.rd[20:200,]
expect_error(subset_data(urch, from = 5, to = NULL, by = "time"),
regexp = NA)
expect_equal(tail(subset_data(urch, from = 5, to = NULL, by = "time")[[1]], 1),
33.2)
expect_error(subset_data(urch, from = 5, to = NULL, by = "row"),
regexp = NA)
expect_equal(tail(subset_data(urch, from = 5, to = NULL, by = "row")[[1]], 1),
33.2)
expect_error(subset_data(urch, from = 7, to = NULL, by = "oxygen"),
regexp = NA)
expect_equal(tail(subset_data(urch, from = 5, to = NULL, by = "oxygen")[[2]], 1),
6.90)
})
test_that("subset_data - correctly handles 'from' and 'to' NULL", {
urch <- urchins.rd[20:200,]
# all NULL - deafults - applies by= "time"
expect_error(subset_data(urch),
regexp = NA)
expect_equal(subset_data(urch)[[1]][1],
urch[[1]][1])
expect_equal(tail(subset_data(urch)[[1]], 1),
urch[[1]][nrow(urch)])
expect_equal(subset_data(urch)[[2]][1],
urch[[2]][1])
expect_equal(tail(subset_data(urch)[[2]], 1),
urch[[2]][nrow(urch)])
# by "row"
expect_error(subset_data(urch, by = "row"),
regexp = NA)
expect_equal(subset_data(urch, by = "row")[[1]][1],
urch[[1]][1])
expect_equal(tail(subset_data(urch, by = "row")[[1]], 1),
urch[[1]][nrow(urch)])
expect_equal(subset_data(urch, by = "row")[[2]][1],
urch[[2]][1])
expect_equal(tail(subset_data(urch, by = "row")[[2]], 1),
urch[[2]][nrow(urch)])
# by "oxygen"
expect_error(subset_data(urch, by = "oxygen"),
regexp = NA)
expect_equal(subset_data(urch, by = "oxygen")[[1]][1],
urch[[1]][1])
expect_equal(tail(subset_data(urch, by = "oxygen")[[1]], 1),
urch[[1]][nrow(urch)])
expect_equal(subset_data(urch, by = "oxygen")[[2]][1],
urch[[2]][1])
expect_equal(tail(subset_data(urch, by = "oxygen")[[2]], 1),
urch[[2]][nrow(urch)])
})
}) ## end capture.output
```

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