tests/testthat/test-convert_rate.R
In januarharianto/respR: Import, Process, Analyse, and Calculate Rates from Respirometry Data
# library(testthat)
# testthat::test_file("tests/testthat/test-convert_rate.R")
# covr::file_coverage("R/convert_rate.R", "tests/testthat/test-convert_rate.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
capture.output({ ## stops printing outputs on assigning
test_that("convert_rate - works with default values", {
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")$rate.output),
36000)
})
test_that("convert_rate - accepts all allowed classes of 'x' input", {
# numeric
expect_error(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Numeric input detected. Converting all numeric rates.")
# calc_rate
cr_obj <- suppressWarnings(calc_rate(urchins.rd[,1:2], plot = F)) ## whole dataset
expect_error(suppressWarnings(convert_rate(cr_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(cr_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate' detected. Converting all rates in '\\$rate'.")
# calc_rate.int
dt <- intermittent.rd %>%
subset_data(from = 1) # removes first value at 0 time because of annoying messages during adjustments
dt.insp <- inspect(dt, plot = F)
sts <- c(1,2100,3899) # different from help file because first row removed above
cr.int_obj <- calc_rate.int(dt.insp,
starts = sts,
plot = F)
expect_error(suppressWarnings(convert_rate(cr.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(cr.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate.int' detected. Converting all rates in '\\$rate'.")
# auto_rate
ar_obj <- suppressWarnings(calc_rate(urchins.rd[,1:2], plot = F)) ## whole dataset
expect_error(suppressWarnings(convert_rate(ar_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(ar_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate' detected. Converting all rates in '\\$rate'.")
# auto_rate.int
ar.int_obj <- auto_rate.int(dt.insp,
starts = sts,
width = 100,
measure = 600,
plot = F)
expect_error(suppressWarnings(convert_rate(ar.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(ar.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'auto_rate.int' detected. Converting all rates in '\\$rate'.")
# adjust_rate - with numeric input
adj_rt_num <- adjust_rate(-0.01, -0.001)
expect_error(suppressWarnings(convert_rate(adj_rt_num, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_num, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with calc_rate input
adj_rt_cr <- adjust_rate(cr_obj, -0.005)
expect_error(suppressWarnings(convert_rate(adj_rt_cr, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_cr, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with calc_rate.int input
adj_rt_cr.int <- adjust_rate(cr.int_obj, -0.0001)
expect_error(suppressWarnings(convert_rate(adj_rt_cr.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_cr.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with auto_rate input
adj_rt_ar <- adjust_rate(ar_obj, -0.005)
expect_error(suppressWarnings(convert_rate(adj_rt_ar, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_ar, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with auto_rate.int input
adj_rt_ar.int <- adjust_rate(ar.int_obj, -0.0001)
expect_error(suppressWarnings(convert_rate(adj_rt_ar.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_ar.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# calc_rate.bg (incl with mass/area even tho wrong)
cr.bg.obj <- calc_rate.bg(urchins.rd, time = 1, oxygen = 18:19)
expect_error(suppressWarnings(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate.bg' detected. Converting all background rates in '\\$rate.bg'.")
expect_warning(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1),
"convert_rate: A 'calc_rate.bg' \\(i.e. background) object is being converted, and a 'mass' or 'area' has been entered. Are you sure you want to do this?")
expect_warning(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1),
"convert_rate: A 'calc_rate.bg' \\(i.e. background) object is being converted, and a 'mass' or 'area' has been entered. Are you sure you want to do this?")
# calc_rate.ft - invalid input
insp.ft.obj.outO2.1col.inO2.1col<- suppressWarnings(suppressMessages(inspect.ft(flowthrough_mult.rd, time = 1,
out.oxy = 2, in.oxy = 6, plot = F)))
crft.obj.1rate <- calc_rate.ft(insp.ft.obj.outO2.1col.inO2.1col,
from = 5, to = 900, by = "row",
flowrate = 2, plot = F)
expect_error(suppressWarnings(convert_rate(crft.obj.1rate, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate.ft' detected. \nPlease use 'convert_rate.ft' to convert the rate.")
# none of the above - invalid input
expect_error(suppressWarnings(convert_rate(urchins.rd, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: 'x' is not an accepted input.")
})
# use known warnings to do these checks
# maybe make this more specific later
test_that("convert_rate - falls back to default inputs properly", {
expect_warning(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l"),
"convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h'")
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")$output.unit),
"mgO2/hr")
expect_warning(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1),
"convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h/kg'")
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1)$output.unit),
"mgO2/hr/kg")
expect_warning(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1),
"convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h/m2'")
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1)$output.unit),
"mgO2/hr/m2")
})
#
test_that("convert_rate - (adjust_scale) produces valid output", {
expect_is(adjust_scale(10, "mg", "kg"), "numeric")
expect_is(adjust_scale(10, "ml", "l"), "numeric")
})
##
test_that("convert_rate - stops if 'oxy.unit' or 'time.unit' are NULL or numeric", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = NULL),
"convert_rate: The 'time.unit' of the original data is required.")
expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = 1.1),
"convert_rate: The 'time.unit' of the original data is required.")
expect_error(convert_rate(10, volume = 1, oxy.unit = NULL, time.unit = "s"),
"convert_rate: The 'oxy.unit' of the original data is required.")
expect_error(convert_rate(10, volume = 1, oxy.unit = 1.1, time.unit = "s"),
"convert_rate: The 'oxy.unit' of the original data is required.")
})
test_that("convert_rate - stops if 'volume' is NULL or NOT numeric", {
expect_error(convert_rate(10, volume = NULL, oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g"),
"convert_rate: The 'volume' input is required.")
expect_error(convert_rate(10, volume = "text", oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g"),
"convert_rate: The 'volume' input is required.")
})
test_that("convert_rate - stops if both 'mass' and 'area' inputs are entered", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g",
mass = 1,
area = 1),
"convert_rate: Cannot have inputs for both 'mass' and 'area'.")
})
test_that("convert_rate - stops if 'output.unit' requires a 'mass' or 'area' input and neither is provided", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h/g",
mass = NULL, area = NULL),
"convert_rate: 'output.unit' requires a value for 'mass' or 'area'")
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h/cm2",
mass = NULL, area = NULL),
"convert_rate: 'output.unit' requires a value for 'mass' or 'area'")
})
test_that("convert_rate - stops if a 'mass' or 'area' input entered but output.unit is not mass- or area-specific", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h",
mass = 1, area = NULL),
"convert_rate: A 'mass' has been entered, but a mass-specific unit has not been specified in 'output.unit'.")
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h",
mass = NULL, area = 1),
"convert_rate: An 'area' has been entered, but an area-specific unit has not been specified in 'output.unit'.")
})
test_that("convert_rate - S3 generics work as expected", {
res_abs <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h",
volume = 0.0032245)
res_abs_mult <- convert_rate(c(-0.0001534657, -0.00015, -0.00016, -0.00017), oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h",
volume = 0.0032245)
res_ms <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/g",
volume = 0.0032245, mass = 0.00534)
res_as <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245, area = 0.000001429)
## summary
expect_output(summary(res_abs))
expect_output(summary(res_ms))
expect_output(summary(res_as))
expect_error(summary(res_abs, pos = 2),
"summary.convert_rate: Invalid 'pos' rank: only 1 rates found.")
expect_error(summary(res_abs, pos = 2:3),
"summary.convert_rate: Invalid 'pos' rank: only 1 rates found.")
expect_output(summary(res_abs_mult))
expect_output(summary(res_abs_mult, pos = 2:3))
expect_output(summary(res_abs_mult, pos = 2:3),
"Summary of converted rates from entered 'pos' rank\\(s)")
expect_is(summary(res_abs_mult, export = TRUE),
"data.table")
## print
expect_output(print(res_abs))
expect_error(print(res_abs, pos = 2),
"print.convert_rate: Invalid 'pos' rank: only 1 rates found.")
expect_error(print(res_abs, pos = 2:3),
"print.convert_rate: 'pos' must be a single value. To examine multiple results use summary().")
expect_output(print(res_ms))
expect_output(print(res_as))
## mean
## absolute
expect_output(suppressWarnings(mean(res_abs)))
expect_message(mean(res_abs),
"mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
expect_equal(suppressWarnings(mean(res_abs, export = TRUE)),
mean(res_abs$rate.output))
## mass-spec
expect_output(suppressWarnings(mean(res_ms)))
expect_message(mean(res_ms),
"mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
expect_equal(suppressWarnings(mean(res_ms, export = TRUE)),
mean(res_ms$rate.output))
## area-spec
expect_output(suppressWarnings(mean(res_as)))
expect_message(mean(res_as),
"mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
expect_equal(suppressWarnings(mean(res_as, export = TRUE)),
mean(res_as$rate.output))
## check multiple rates have correct mean
rate <- suppressWarnings(inspect(urchins.rd[,1:2], plot = F)) %>%
auto_rate(plot = F) %>%
convert_rate(oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245, area = 0.000001429)
expect_output(suppressWarnings(mean(rate)))
expect_equal(mean(rate, export = TRUE),
mean(rate$rate.output))
# mean and pos
expect_output(mean(rate, pos = 1:3),
"Mean of rate results from entered 'pos' ranks:")
expect_error(mean(rate, pos = 5:6),
"mean.convert_rate: Invalid 'pos' rank: only 4 rates found.")
})
test_that("convert_rate - stops if units require t, S and P", {
expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
area = 0.000001429),
"convert_rate: Input or output units require Salinity input")
expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
S = 35,
area = 0.000001429),
"convert_rate: Input or output units require Temperature input")
expect_message(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
S = 35, t = 31, P = NULL,
area = 0.000001429),
"convert_rate: Input or output units require Atmospheric Pressure input")
})
## Possibly update these in future with exact values we know are correct.
## For now, these just flag up if code changes cause output changes
test_that("convert_rate - outputs correct conversion values - absolute rates", {
res <- convert_rate(93.1, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 1, S = 35, t = 25, P = 1.013253)
expect_equal(res$rate.output, 22626.99, tolerance = 0.01) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 93.1)
expect_equal(res$inputs$oxy.unit, "%Air")
expect_equal(res$inputs$time.unit, "sec")
expect_equal(res$output.unit, "mgO2/hr")
expect_equal(res$summary$rate.input, 93.1)
expect_equal(res$summary$rate.output, 22626.99, tolerance = 0.01)
expect_equal(res$summary$rate.abs, 22626.99, tolerance = 0.01)
res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute", volume = 1, S = 35, t = 25, P = 1.013253)
expect_equal(res$rate.output, 0.05477929, tolerance = 0.00001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 4303)
expect_equal(res$inputs$oxy.unit, "ug/L")
expect_equal(res$inputs$time.unit, "hr")
expect_equal(res$output.unit, "mLO2/min")
expect_equal(res$summary$rate.input, 4303)
expect_equal(res$summary$rate.output, 0.05477929, tolerance = 0.00001)
expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min", volume = 1, S = 35, t = 25, P = 1.013253)
expect_equal(res$rate.output, 236.739, tolerance = 0.001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 234)
expect_equal(res$inputs$oxy.unit, "hPa")
expect_equal(res$inputs$time.unit, "min")
expect_equal(res$output.unit, "umolO2/min")
expect_equal(res$summary$rate.input, 234)
expect_equal(res$summary$rate.output, 236.739, tolerance = 0.001)
expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
# changing magnitude of inputs and outputs changes rate by right amount
rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
# sign of the rate
expect_equal(
convert_rate(-1*rate$rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output * -1
)
# time metric in output
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60*60
)
# time metric in input
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60*60
)
# volume
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 1, S = 35, t = 14, P = 1.013253)$rate.output*10
)
})
test_that("convert_rate - outputs correct conversion values - mass-specific rates", {
res <- convert_rate(93.1, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 1, S = 35, t = 25, P = 1.013253,
mass = 0.012)
expect_equal(res$rate.output, 1885.583, tolerance = 0.001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 93.1)
expect_equal(res$inputs$oxy.unit, "%Air")
expect_equal(res$inputs$time.unit, "sec")
expect_equal(res$output.unit, "mgO2/hr/g")
expect_equal(res$summary$rate.input, 93.1)
expect_equal(res$summary$rate.output, 1885.583, tolerance = 0.01)
expect_equal(res$summary$rate.abs, 22626.99, tolerance = 0.01)
expect_equal(res$summary$rate.m.spec, 1885.583, tolerance = 0.001)
res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute/kg", volume = 1, S = 35, t = 25, P = 1.013253,
mass = 0.012)
expect_equal(res$rate.output, 4.564941, tolerance = 0.00001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 4303)
expect_equal(res$inputs$oxy.unit, "ug/L")
expect_equal(res$inputs$time.unit, "hr")
expect_equal(res$output.unit, "mLO2/min/kg")
expect_equal(res$summary$rate.input, 4303)
expect_equal(res$summary$rate.output, 4.564941, tolerance = 0.00001)
expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
expect_equal(res$summary$rate.m.spec, 4.564941, tolerance = 0.00001)
res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min/ug", volume = 1, S = 35, t = 25, P = 1.013253,
mass = 0.012)
expect_equal(res$rate.output, 0.00001972825, tolerance = 0.000001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 234)
expect_equal(res$inputs$oxy.unit, "hPa")
expect_equal(res$inputs$time.unit, "min")
expect_equal(res$output.unit, "umolO2/min/ug")
expect_equal(res$summary$rate.input, 234)
expect_equal(res$summary$rate.output, 0.00001972825, tolerance = 0.000001)
expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
expect_equal(res$summary$rate.m.spec, 0.00001972825, tolerance = 0.000001)
# changing magnitude of inputs and outputs changes rate by right amount
rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
# sign of the rate
expect_equal(
convert_rate(-1*rate$rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output * -1
)
# time metric in output
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60*60
)
# time metric in input
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60*60
)
# volume
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 1, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*10
)
# mass
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/kg", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output/1000
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mg", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*1000
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/ug", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*1000000
)
})
## Kate Quigley data
## These values checked in Excel - first one is right
test_that("convert_rate - outputs correct conversion values - area-specific rates", {
res <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
S = 35, t = 31, P = 1.013253,
area = 0.000001429)
expect_equal(res$rate.output, -0.001246648) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, -0.0001534657)
expect_equal(res$inputs$oxy.unit, "mg/L")
expect_equal(res$inputs$time.unit, "sec")
expect_equal(res$output.unit, "mgO2/hr/mm2")
expect_equal(res$summary$rate.input, -0.0001534657)
expect_equal(res$summary$rate.output, -0.001246648)
expect_equal(res$summary$rate.abs, -0.001781461)
expect_equal(res$summary$rate.a.spec, -0.001246648)
## these made up
res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute/m2",
volume = 1, S = 35, t = 25, P = 1.013253,
area = 0.012)
expect_equal(res$rate.output, 4.564941, tolerance = 0.00001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 4303)
expect_equal(res$inputs$oxy.unit, "ug/L")
expect_equal(res$inputs$time.unit, "hr")
expect_equal(res$output.unit, "mLO2/min/m2")
expect_equal(res$summary$rate.input, 4303)
expect_equal(res$summary$rate.output, 4.564941, tolerance = 0.00001)
expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
expect_equal(res$summary$rate.a.spec, 4.564941, tolerance = 0.00001)
res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min/cm2",
volume = 1, S = 35, t = 25, P = 1.013253,
area = 0.012)
expect_equal(res$rate.output, 1.972825, tolerance = 0.000001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 234)
expect_equal(res$inputs$oxy.unit, "hPa")
expect_equal(res$inputs$time.unit, "min")
expect_equal(res$output.unit, "umolO2/min/cm2")
expect_equal(res$summary$rate.input, 234)
expect_equal(res$summary$rate.output, 1.972825, tolerance = 0.000001)
expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
expect_equal(res$summary$rate.a.spec, 1.972825, tolerance = 0.000001)
# changing magnitude of inputs and outputs changes rate by right amount
rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
# time metric in output
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60*60
)
# time metric in input
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60*60
)
# volume
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 1, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*10
)
# area
# mm2 > cm2 > m2 > km2
# 1 x 100 x 10000 x 1000000
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output/100
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/m2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output/100/10000
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/km2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output/100/10000/1000000
)
})
test_that("convert_rate - changing 'time' inputs changes rates by correct magnitude multiplier", {
# Outputs
# s to m
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/m/kg',
volume = 1.2, mass = 0.5)$rate.output)
# s to h
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 60,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/h/kg',
volume = 1.2, mass = 0.5)$rate.output)
# s to d
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 60 * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
# If inut data was different time
# d to s
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 60 * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
# d to m
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/m/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
# d to h
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/h/kg',
volume = 1.2, mass = 0.5)$rate.output * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
})
test_that("convert_rate - different magnitudes of umol/mmol/mol changes rates by correct magnitude multiplier", {
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output*1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000/1000)
expect_equal(c(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000/1000),
rep(6.750253e-05, 5))
})
test_that("convert_rate - ml & ul oxygen output unit correct values ", {
# should be ml times 1000
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ul/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
})
test_that("convert_rate - mg & ug oxygen output unit correct values ", {
# should be mg times 1000
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ug/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
})
test_that("convert_rate - mm3 & cm3 (cc) oxygen output unit correct values ", {
# these are equivalent to ul and ml
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cc/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ul/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
})
# Plotting ----------------------------------------------------------------
test_that("convert_rate - plot is produced with converted auto_rate objects", {
ar_mult <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005)
)
expect_output(plot(ar_mult))
expect_output(plot(ar_mult, pos = 1:2))
expect_output(plot(ar_mult, pos = 1:2, type = "full"))
expect_output(plot(ar_mult, pos = 1:2, type = "full", highlight = 2))
expect_output(plot(ar_mult, pos = 1:2, type = "overlap"))
expect_output(plot(ar_mult, pos = 1:2, type = "overlap", highlight = 2))
expect_output(plot(ar_mult, pos = 1:2, type = "rate"))
expect_output(plot(ar_mult, pos = 1:2, type = "rate", highlight = 2))
expect_output(plot(ar_mult, type = "overlap", highlight = 2))
# adjusted
ar_mult_adj <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
adjust_rate(by = -0.005) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005))
expect_output(plot(ar_mult_adj))
})
test_that("convert_rate - plot is produced with converted calc_rate objects", {
cr <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_output(plot(cr))
})
test_that("convert_rate - plot pos and highlight correct messages", {
cr <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_message(plot(cr, pos = 50),
"convert_rate: One or more 'pos' inputs higher than number of rows in '\\$summary'. Applying default of all rows.")
expect_message(plot(cr, pos = 50, type = "overlap"),
"convert_rate: One or more 'pos' inputs higher than number of rows in '\\$summary'. Applying default of all rows.")
expect_message(plot(cr, highlight = 50, type = "overlap"),
"convert_rate: 'highlight' not within 'pos' input. Applying default of first 'pos' entry.")
})
test_that("convert_rate - plot errors with various disallowed inputs", {
num <- c(1,2,3) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09)
expect_error(plot(num),
"plot.convert_rate: Plot is not available for 'convert_rate' objects containing rates converted from numeric values.")
crbg <- suppressWarnings(urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate.bg(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_error(plot(crbg),
"plot.convert_rate: Plot is not available for converted 'calc_rate.bg' objects because rates may come from different columns of the dataframe.")
cr <- suppressWarnings(urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_error(plot(cr, type = "text"),
"plot.convert_rate: 'type' input not recognised.")
})
test_that("overlap.p - errors with various disallowed inputs", {
crbg <-
calc_rate.bg(urchins.rd[,1:2]) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09)
expect_error(overlap.p(crbg),
"overlap.p: Plot is not available for converted 'calc_rate.bg' objects because rates may come from different columns of the dataframe.")
crbg <-
calc_rate.bg(urchins.rd[,1:2])
expect_error(overlap.p(crbg),
"overlap.p: 'x' should be an 'auto_rate' or 'convert_rate' object.")
num <-
c(1,2,3) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09)
expect_error(overlap.p(num),
"overlap.p: Plot is not available for 'convert_rate' objects containing rates converted from numeric values.")
})
test_that("convert_rate - correct message when plot is called on objects with zero rates", {
# message with zero rates for both methods
ar_mult_no_rts <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005) %>%
select_rate("rate", c(-0.05, -0.06)))
expect_message(plot(ar_mult_no_rts),
"convert_rate: Nothing to plot! No rates found in object.")
expect_message(plot(ar_mult_no_rts, type = "overlap"),
"convert_rate: Nothing to plot! No rates found in object.")
})
test_that("convert_rate - plot defaults are correctly restored", {
# reset plotting first
dev.off()
# save par before
parb4 <- par(no.readonly = TRUE)
# now use a fn with plot
suppressWarnings(urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005,
plot = TRUE))
# 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)
})
}) ## end capture.output
januarharianto/respR documentation built on April 20, 2024, 4:34 p.m.
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# library(testthat)
# testthat::test_file("tests/testthat/test-convert_rate.R")
# covr::file_coverage("R/convert_rate.R", "tests/testthat/test-convert_rate.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)
capture.output({ ## stops printing outputs on assigning
test_that("convert_rate - works with default values", {
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")$rate.output),
36000)
})
test_that("convert_rate - accepts all allowed classes of 'x' input", {
# numeric
expect_error(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Numeric input detected. Converting all numeric rates.")
# calc_rate
cr_obj <- suppressWarnings(calc_rate(urchins.rd[,1:2], plot = F)) ## whole dataset
expect_error(suppressWarnings(convert_rate(cr_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(cr_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate' detected. Converting all rates in '\\$rate'.")
# calc_rate.int
dt <- intermittent.rd %>%
subset_data(from = 1) # removes first value at 0 time because of annoying messages during adjustments
dt.insp <- inspect(dt, plot = F)
sts <- c(1,2100,3899) # different from help file because first row removed above
cr.int_obj <- calc_rate.int(dt.insp,
starts = sts,
plot = F)
expect_error(suppressWarnings(convert_rate(cr.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(cr.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate.int' detected. Converting all rates in '\\$rate'.")
# auto_rate
ar_obj <- suppressWarnings(calc_rate(urchins.rd[,1:2], plot = F)) ## whole dataset
expect_error(suppressWarnings(convert_rate(ar_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(ar_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate' detected. Converting all rates in '\\$rate'.")
# auto_rate.int
ar.int_obj <- auto_rate.int(dt.insp,
starts = sts,
width = 100,
measure = 600,
plot = F)
expect_error(suppressWarnings(convert_rate(ar.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(ar.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'auto_rate.int' detected. Converting all rates in '\\$rate'.")
# adjust_rate - with numeric input
adj_rt_num <- adjust_rate(-0.01, -0.001)
expect_error(suppressWarnings(convert_rate(adj_rt_num, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_num, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with calc_rate input
adj_rt_cr <- adjust_rate(cr_obj, -0.005)
expect_error(suppressWarnings(convert_rate(adj_rt_cr, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_cr, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with calc_rate.int input
adj_rt_cr.int <- adjust_rate(cr.int_obj, -0.0001)
expect_error(suppressWarnings(convert_rate(adj_rt_cr.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_cr.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with auto_rate input
adj_rt_ar <- adjust_rate(ar_obj, -0.005)
expect_error(suppressWarnings(convert_rate(adj_rt_ar, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_ar, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# adjust_rate - with auto_rate.int input
adj_rt_ar.int <- adjust_rate(ar.int_obj, -0.0001)
expect_error(suppressWarnings(convert_rate(adj_rt_ar.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(adj_rt_ar.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")
# calc_rate.bg (incl with mass/area even tho wrong)
cr.bg.obj <- calc_rate.bg(urchins.rd, time = 1, oxygen = 18:19)
expect_error(suppressWarnings(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
NA)
expect_message(suppressWarnings(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate.bg' detected. Converting all background rates in '\\$rate.bg'.")
expect_warning(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1),
"convert_rate: A 'calc_rate.bg' \\(i.e. background) object is being converted, and a 'mass' or 'area' has been entered. Are you sure you want to do this?")
expect_warning(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1),
"convert_rate: A 'calc_rate.bg' \\(i.e. background) object is being converted, and a 'mass' or 'area' has been entered. Are you sure you want to do this?")
# calc_rate.ft - invalid input
insp.ft.obj.outO2.1col.inO2.1col<- suppressWarnings(suppressMessages(inspect.ft(flowthrough_mult.rd, time = 1,
out.oxy = 2, in.oxy = 6, plot = F)))
crft.obj.1rate <- calc_rate.ft(insp.ft.obj.outO2.1col.inO2.1col,
from = 5, to = 900, by = "row",
flowrate = 2, plot = F)
expect_error(suppressWarnings(convert_rate(crft.obj.1rate, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: Object of class 'calc_rate.ft' detected. \nPlease use 'convert_rate.ft' to convert the rate.")
# none of the above - invalid input
expect_error(suppressWarnings(convert_rate(urchins.rd, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
"convert_rate: 'x' is not an accepted input.")
})
# use known warnings to do these checks
# maybe make this more specific later
test_that("convert_rate - falls back to default inputs properly", {
expect_warning(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l"),
"convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h'")
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")$output.unit),
"mgO2/hr")
expect_warning(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1),
"convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h/kg'")
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1)$output.unit),
"mgO2/hr/kg")
expect_warning(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1),
"convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h/m2'")
expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1)$output.unit),
"mgO2/hr/m2")
})
#
test_that("convert_rate - (adjust_scale) produces valid output", {
expect_is(adjust_scale(10, "mg", "kg"), "numeric")
expect_is(adjust_scale(10, "ml", "l"), "numeric")
})
##
test_that("convert_rate - stops if 'oxy.unit' or 'time.unit' are NULL or numeric", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = NULL),
"convert_rate: The 'time.unit' of the original data is required.")
expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = 1.1),
"convert_rate: The 'time.unit' of the original data is required.")
expect_error(convert_rate(10, volume = 1, oxy.unit = NULL, time.unit = "s"),
"convert_rate: The 'oxy.unit' of the original data is required.")
expect_error(convert_rate(10, volume = 1, oxy.unit = 1.1, time.unit = "s"),
"convert_rate: The 'oxy.unit' of the original data is required.")
})
test_that("convert_rate - stops if 'volume' is NULL or NOT numeric", {
expect_error(convert_rate(10, volume = NULL, oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g"),
"convert_rate: The 'volume' input is required.")
expect_error(convert_rate(10, volume = "text", oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g"),
"convert_rate: The 'volume' input is required.")
})
test_that("convert_rate - stops if both 'mass' and 'area' inputs are entered", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g",
mass = 1,
area = 1),
"convert_rate: Cannot have inputs for both 'mass' and 'area'.")
})
test_that("convert_rate - stops if 'output.unit' requires a 'mass' or 'area' input and neither is provided", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h/g",
mass = NULL, area = NULL),
"convert_rate: 'output.unit' requires a value for 'mass' or 'area'")
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h/cm2",
mass = NULL, area = NULL),
"convert_rate: 'output.unit' requires a value for 'mass' or 'area'")
})
test_that("convert_rate - stops if a 'mass' or 'area' input entered but output.unit is not mass- or area-specific", {
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h",
mass = 1, area = NULL),
"convert_rate: A 'mass' has been entered, but a mass-specific unit has not been specified in 'output.unit'.")
expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h",
mass = NULL, area = 1),
"convert_rate: An 'area' has been entered, but an area-specific unit has not been specified in 'output.unit'.")
})
test_that("convert_rate - S3 generics work as expected", {
res_abs <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h",
volume = 0.0032245)
res_abs_mult <- convert_rate(c(-0.0001534657, -0.00015, -0.00016, -0.00017), oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h",
volume = 0.0032245)
res_ms <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/g",
volume = 0.0032245, mass = 0.00534)
res_as <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245, area = 0.000001429)
## summary
expect_output(summary(res_abs))
expect_output(summary(res_ms))
expect_output(summary(res_as))
expect_error(summary(res_abs, pos = 2),
"summary.convert_rate: Invalid 'pos' rank: only 1 rates found.")
expect_error(summary(res_abs, pos = 2:3),
"summary.convert_rate: Invalid 'pos' rank: only 1 rates found.")
expect_output(summary(res_abs_mult))
expect_output(summary(res_abs_mult, pos = 2:3))
expect_output(summary(res_abs_mult, pos = 2:3),
"Summary of converted rates from entered 'pos' rank\\(s)")
expect_is(summary(res_abs_mult, export = TRUE),
"data.table")
## print
expect_output(print(res_abs))
expect_error(print(res_abs, pos = 2),
"print.convert_rate: Invalid 'pos' rank: only 1 rates found.")
expect_error(print(res_abs, pos = 2:3),
"print.convert_rate: 'pos' must be a single value. To examine multiple results use summary().")
expect_output(print(res_ms))
expect_output(print(res_as))
## mean
## absolute
expect_output(suppressWarnings(mean(res_abs)))
expect_message(mean(res_abs),
"mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
expect_equal(suppressWarnings(mean(res_abs, export = TRUE)),
mean(res_abs$rate.output))
## mass-spec
expect_output(suppressWarnings(mean(res_ms)))
expect_message(mean(res_ms),
"mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
expect_equal(suppressWarnings(mean(res_ms, export = TRUE)),
mean(res_ms$rate.output))
## area-spec
expect_output(suppressWarnings(mean(res_as)))
expect_message(mean(res_as),
"mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
expect_equal(suppressWarnings(mean(res_as, export = TRUE)),
mean(res_as$rate.output))
## check multiple rates have correct mean
rate <- suppressWarnings(inspect(urchins.rd[,1:2], plot = F)) %>%
auto_rate(plot = F) %>%
convert_rate(oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245, area = 0.000001429)
expect_output(suppressWarnings(mean(rate)))
expect_equal(mean(rate, export = TRUE),
mean(rate$rate.output))
# mean and pos
expect_output(mean(rate, pos = 1:3),
"Mean of rate results from entered 'pos' ranks:")
expect_error(mean(rate, pos = 5:6),
"mean.convert_rate: Invalid 'pos' rank: only 4 rates found.")
})
test_that("convert_rate - stops if units require t, S and P", {
expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
area = 0.000001429),
"convert_rate: Input or output units require Salinity input")
expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
S = 35,
area = 0.000001429),
"convert_rate: Input or output units require Temperature input")
expect_message(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
S = 35, t = 31, P = NULL,
area = 0.000001429),
"convert_rate: Input or output units require Atmospheric Pressure input")
})
## Possibly update these in future with exact values we know are correct.
## For now, these just flag up if code changes cause output changes
test_that("convert_rate - outputs correct conversion values - absolute rates", {
res <- convert_rate(93.1, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 1, S = 35, t = 25, P = 1.013253)
expect_equal(res$rate.output, 22626.99, tolerance = 0.01) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 93.1)
expect_equal(res$inputs$oxy.unit, "%Air")
expect_equal(res$inputs$time.unit, "sec")
expect_equal(res$output.unit, "mgO2/hr")
expect_equal(res$summary$rate.input, 93.1)
expect_equal(res$summary$rate.output, 22626.99, tolerance = 0.01)
expect_equal(res$summary$rate.abs, 22626.99, tolerance = 0.01)
res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute", volume = 1, S = 35, t = 25, P = 1.013253)
expect_equal(res$rate.output, 0.05477929, tolerance = 0.00001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 4303)
expect_equal(res$inputs$oxy.unit, "ug/L")
expect_equal(res$inputs$time.unit, "hr")
expect_equal(res$output.unit, "mLO2/min")
expect_equal(res$summary$rate.input, 4303)
expect_equal(res$summary$rate.output, 0.05477929, tolerance = 0.00001)
expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min", volume = 1, S = 35, t = 25, P = 1.013253)
expect_equal(res$rate.output, 236.739, tolerance = 0.001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 234)
expect_equal(res$inputs$oxy.unit, "hPa")
expect_equal(res$inputs$time.unit, "min")
expect_equal(res$output.unit, "umolO2/min")
expect_equal(res$summary$rate.input, 234)
expect_equal(res$summary$rate.output, 236.739, tolerance = 0.001)
expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
# changing magnitude of inputs and outputs changes rate by right amount
rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
# sign of the rate
expect_equal(
convert_rate(-1*rate$rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output * -1
)
# time metric in output
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60*60
)
# time metric in input
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60*60
)
# volume
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 1, S = 35, t = 14, P = 1.013253)$rate.output*10
)
})
test_that("convert_rate - outputs correct conversion values - mass-specific rates", {
res <- convert_rate(93.1, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 1, S = 35, t = 25, P = 1.013253,
mass = 0.012)
expect_equal(res$rate.output, 1885.583, tolerance = 0.001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 93.1)
expect_equal(res$inputs$oxy.unit, "%Air")
expect_equal(res$inputs$time.unit, "sec")
expect_equal(res$output.unit, "mgO2/hr/g")
expect_equal(res$summary$rate.input, 93.1)
expect_equal(res$summary$rate.output, 1885.583, tolerance = 0.01)
expect_equal(res$summary$rate.abs, 22626.99, tolerance = 0.01)
expect_equal(res$summary$rate.m.spec, 1885.583, tolerance = 0.001)
res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute/kg", volume = 1, S = 35, t = 25, P = 1.013253,
mass = 0.012)
expect_equal(res$rate.output, 4.564941, tolerance = 0.00001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 4303)
expect_equal(res$inputs$oxy.unit, "ug/L")
expect_equal(res$inputs$time.unit, "hr")
expect_equal(res$output.unit, "mLO2/min/kg")
expect_equal(res$summary$rate.input, 4303)
expect_equal(res$summary$rate.output, 4.564941, tolerance = 0.00001)
expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
expect_equal(res$summary$rate.m.spec, 4.564941, tolerance = 0.00001)
res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min/ug", volume = 1, S = 35, t = 25, P = 1.013253,
mass = 0.012)
expect_equal(res$rate.output, 0.00001972825, tolerance = 0.000001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 234)
expect_equal(res$inputs$oxy.unit, "hPa")
expect_equal(res$inputs$time.unit, "min")
expect_equal(res$output.unit, "umolO2/min/ug")
expect_equal(res$summary$rate.input, 234)
expect_equal(res$summary$rate.output, 0.00001972825, tolerance = 0.000001)
expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
expect_equal(res$summary$rate.m.spec, 0.00001972825, tolerance = 0.000001)
# changing magnitude of inputs and outputs changes rate by right amount
rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
# sign of the rate
expect_equal(
convert_rate(-1*rate$rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output * -1
)
# time metric in output
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60*60
)
# time metric in input
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*60*60
)
# volume
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 1, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*10
)
# mass
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/kg", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output/1000
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mg", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*1000
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/ug", volume = 10, S = 35, t = 14, P = 1.013253,
mass = 0.012)$rate.output*1000000
)
})
## Kate Quigley data
## These values checked in Excel - first one is right
test_that("convert_rate - outputs correct conversion values - area-specific rates", {
res <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
volume = 0.0032245,
S = 35, t = 31, P = 1.013253,
area = 0.000001429)
expect_equal(res$rate.output, -0.001246648) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, -0.0001534657)
expect_equal(res$inputs$oxy.unit, "mg/L")
expect_equal(res$inputs$time.unit, "sec")
expect_equal(res$output.unit, "mgO2/hr/mm2")
expect_equal(res$summary$rate.input, -0.0001534657)
expect_equal(res$summary$rate.output, -0.001246648)
expect_equal(res$summary$rate.abs, -0.001781461)
expect_equal(res$summary$rate.a.spec, -0.001246648)
## these made up
res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute/m2",
volume = 1, S = 35, t = 25, P = 1.013253,
area = 0.012)
expect_equal(res$rate.output, 4.564941, tolerance = 0.00001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 4303)
expect_equal(res$inputs$oxy.unit, "ug/L")
expect_equal(res$inputs$time.unit, "hr")
expect_equal(res$output.unit, "mLO2/min/m2")
expect_equal(res$summary$rate.input, 4303)
expect_equal(res$summary$rate.output, 4.564941, tolerance = 0.00001)
expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
expect_equal(res$summary$rate.a.spec, 4.564941, tolerance = 0.00001)
res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min/cm2",
volume = 1, S = 35, t = 25, P = 1.013253,
area = 0.012)
expect_equal(res$rate.output, 1.972825, tolerance = 0.000001) # exact value
## inputs and outputs are saved in object correctly
expect_equal(res$rate.input, 234)
expect_equal(res$inputs$oxy.unit, "hPa")
expect_equal(res$inputs$time.unit, "min")
expect_equal(res$output.unit, "umolO2/min/cm2")
expect_equal(res$summary$rate.input, 234)
expect_equal(res$summary$rate.output, 1.972825, tolerance = 0.000001)
expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
expect_equal(res$summary$rate.a.spec, 1.972825, tolerance = 0.000001)
# changing magnitude of inputs and outputs changes rate by right amount
rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
# time metric in output
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60*60
)
# time metric in input
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*60*60
)
# volume
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 1, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output*10
)
# area
# mm2 > cm2 > m2 > km2
# 1 x 100 x 10000 x 1000000
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output/100
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/m2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output/100/10000
)
expect_equal(
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output,
convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/km2", volume = 10, S = 35, t = 14, P = 1.013253,
area = 0.012)$rate.output/100/10000/1000000
)
})
test_that("convert_rate - changing 'time' inputs changes rates by correct magnitude multiplier", {
# Outputs
# s to m
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/m/kg',
volume = 1.2, mass = 0.5)$rate.output)
# s to h
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 60,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/h/kg',
volume = 1.2, mass = 0.5)$rate.output)
# s to d
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 60 * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
# If inut data was different time
# d to s
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/s/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 60 * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
# d to m
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/m/kg',
volume = 1.2, mass = 0.5)$rate.output * 60 * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
# d to h
expect_equal(
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/h/kg',
volume = 1.2, mass = 0.5)$rate.output * 24,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
volume = 1.2, mass = 0.5)$rate.output)
})
test_that("convert_rate - different magnitudes of umol/mmol/mol changes rates by correct magnitude multiplier", {
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output*1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000000)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000/1000)
expect_equal(c(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
volume = 1.2, mass = 0.5)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000/1000),
rep(6.750253e-05, 5))
})
test_that("convert_rate - ml & ul oxygen output unit correct values ", {
# should be ml times 1000
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ul/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
})
test_that("convert_rate - mg & ug oxygen output unit correct values ", {
# should be mg times 1000
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ug/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
})
test_that("convert_rate - mm3 & cm3 (cc) oxygen output unit correct values ", {
# these are equivalent to ul and ml
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cc/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mm3/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ul/h/kg',
volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
})
# Plotting ----------------------------------------------------------------
test_that("convert_rate - plot is produced with converted auto_rate objects", {
ar_mult <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005)
)
expect_output(plot(ar_mult))
expect_output(plot(ar_mult, pos = 1:2))
expect_output(plot(ar_mult, pos = 1:2, type = "full"))
expect_output(plot(ar_mult, pos = 1:2, type = "full", highlight = 2))
expect_output(plot(ar_mult, pos = 1:2, type = "overlap"))
expect_output(plot(ar_mult, pos = 1:2, type = "overlap", highlight = 2))
expect_output(plot(ar_mult, pos = 1:2, type = "rate"))
expect_output(plot(ar_mult, pos = 1:2, type = "rate", highlight = 2))
expect_output(plot(ar_mult, type = "overlap", highlight = 2))
# adjusted
ar_mult_adj <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
adjust_rate(by = -0.005) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005))
expect_output(plot(ar_mult_adj))
})
test_that("convert_rate - plot is produced with converted calc_rate objects", {
cr <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_output(plot(cr))
})
test_that("convert_rate - plot pos and highlight correct messages", {
cr <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_message(plot(cr, pos = 50),
"convert_rate: One or more 'pos' inputs higher than number of rows in '\\$summary'. Applying default of all rows.")
expect_message(plot(cr, pos = 50, type = "overlap"),
"convert_rate: One or more 'pos' inputs higher than number of rows in '\\$summary'. Applying default of all rows.")
expect_message(plot(cr, highlight = 50, type = "overlap"),
"convert_rate: 'highlight' not within 'pos' input. Applying default of first 'pos' entry.")
})
test_that("convert_rate - plot errors with various disallowed inputs", {
num <- c(1,2,3) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09)
expect_error(plot(num),
"plot.convert_rate: Plot is not available for 'convert_rate' objects containing rates converted from numeric values.")
crbg <- suppressWarnings(urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate.bg(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_error(plot(crbg),
"plot.convert_rate: Plot is not available for converted 'calc_rate.bg' objects because rates may come from different columns of the dataframe.")
cr <- suppressWarnings(urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
calc_rate(plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09))
expect_error(plot(cr, type = "text"),
"plot.convert_rate: 'type' input not recognised.")
})
test_that("overlap.p - errors with various disallowed inputs", {
crbg <-
calc_rate.bg(urchins.rd[,1:2]) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09)
expect_error(overlap.p(crbg),
"overlap.p: Plot is not available for converted 'calc_rate.bg' objects because rates may come from different columns of the dataframe.")
crbg <-
calc_rate.bg(urchins.rd[,1:2])
expect_error(overlap.p(crbg),
"overlap.p: 'x' should be an 'auto_rate' or 'convert_rate' object.")
num <-
c(1,2,3) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h",
volume = 1.09)
expect_error(overlap.p(num),
"overlap.p: Plot is not available for 'convert_rate' objects containing rates converted from numeric values.")
})
test_that("convert_rate - correct message when plot is called on objects with zero rates", {
# message with zero rates for both methods
ar_mult_no_rts <-
suppressWarnings(
urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005) %>%
select_rate("rate", c(-0.05, -0.06)))
expect_message(plot(ar_mult_no_rts),
"convert_rate: Nothing to plot! No rates found in object.")
expect_message(plot(ar_mult_no_rts, type = "overlap"),
"convert_rate: Nothing to plot! No rates found in object.")
})
test_that("convert_rate - plot defaults are correctly restored", {
# reset plotting first
dev.off()
# save par before
parb4 <- par(no.readonly = TRUE)
# now use a fn with plot
suppressWarnings(urchins.rd %>%
inspect(1,2, plot = FALSE) %>%
auto_rate(width = 0.2, plot = FALSE) %>%
convert_rate(oxy.unit = "mg/l",
time.unit = "min",
output.unit = "mg/h/g",
volume = 1.09,
mass = 0.005,
plot = TRUE))
# 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)
})
}) ## end capture.output
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