tests/testthat/test-extra-agilent.R
In ethanbass/chromConverter: Chromatographic File Converter
# these tests rely on files included in the chromConverterExtraTests package,
# which is available on GitHub (https://github.com/ethanbass/chromConverterExtraTests).
test_that("read_chroms can read 'Agilent' MS files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
skip_if_not_installed("entab")
path <- system.file("chemstation_MSD.MS",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, parser = "entab", progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(95471, 3))
expect_equal(attr(x, "parser"), "entab")
expect_equal(attr(x, "data_format"), "long")
expect_equal(colnames(x), c("rt", "mz", "intensity"))
# export as mzML
tmp <- tempdir()
path_mzml <- fs::path(tmp, gsub(" ", "_", attr(x, "sample_name")),
ext = "mzML")
on.exit(unlink(path_mzml))
# chromConverter
x1 <- read_chroms(path, parser = "chromconverter", what = "MS1",
format_out = "data.table", data_format = "long",
progress_bar = FALSE,
export_format = "mzML", path_out = tmp, force = TRUE)[[1]]
expect_s3_class(x1, "data.table")
expect_equal(attr(x1, "format_out"), "data.table")
xx <- read_mzml(path_mzml, data_format="long")
expect_equal(xx$MS1[,-4], x1, ignore_attr = TRUE)
expect_equal(x1, as.data.frame(x), ignore_attr = TRUE)
expect_equal(attr(x1,"sample_name"), attr(x,"sample_name"))
expect_equal(attr(x1,"source_sha1"), attr(x,"source_sha1"))
expect_equal(attr(x1,"time_unit"), attr(x,"time_unit"))
# expect_equal(as.numeric(attr(x1,"run_datetime")),
# as.numeric(attr(x,"run_datetime"))) #timezone is wrong on entab
expect_equal(attr(x1,"operator"), attr(x,"operator"))
expect_equal(attr(x1,"method"), attr(x,"method"))
expect_equal(attr(x1,"detector"), attr(x,"detector"))
expect_equal(attr(x1, "data_format"), "long")
# rainbow
x2 <- read_chroms(path, parser = "rainbow",
progress_bar = FALSE, precision = 0)[[1]]
expect_equal(class(x2)[1], "matrix")
expect_equal(dim(x2), c(2534, 841))
expect_equal(attr(x2,"run_datetime"), attr(x1,"run_datetime"))
expect_equal(attr(x2, "method"), attr(x1, "method"))
expect_equal(attr(x2, "detector"), attr(x1, "detector"))
expect_equal(attr(x2, "data_format"), "wide")
x3 <- read_chroms(path, parser = "rainbow",
progress_bar = FALSE, data_format = "long",
format_out = "data.table",
precision = 0)[[1]]
expect_s3_class(x3, "data.table")
expect_equal(dim(x3), c(2131094, 3))
expect_equal(colnames(x3), c("rt", "mz", "intensity"))
expect_equal(attr(x3, "method"), attr(x2, "method"))
expect_equal(attr(x3, "detector"), attr(x2, "detector"))
expect_equal(attr(x3, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' version 30 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_30.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, parser = "chromconverter", progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(38405, 1))
expect_equal(head(get_times(x),1), -0.001333333, tolerance = .00001)
expect_equal(tail(get_times(x),1), 32.002, tolerance = .00001)
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "NVAC-6B1-S3R1")
expect_equal(attr(x, "detector"), "G1315B")
expect_equal(attr(x, "detector_y_unit"), "mAU")
expect_equal(attr(x, "method"), "JCMONO1.M")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
x1 <- read_chroms(path, parser = "chromconverter", format_out = "data.frame",
data_format = "long", progress_bar = FALSE)[[1]]
expect_equal(colnames(x1), c("rt","intensity"))
expect_s3_class(x1[1], "data.frame")
expect_equal(as.numeric(rownames(x)), x1[,1])
expect_equal(x[,1], x1[,2], ignore_attr = TRUE)
expect_equal(head(x1$rt, 1), -.00133333333333333, tolerance = .00001)
expect_equal(tail(x1$rt, 1), 32.002, tolerance = .00001)
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' 31 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
skip_if_not_installed("entab")
path <- system.file("chemstation_31.uv", package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE, parser = "chromconverter")[[1]]
x1 <- read_chroms(path, progress_bar = FALSE, parser = "entab")[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(class(x1)[1], "matrix")
expect_equal(dim(x), c(27659, 176))
expect_equal(dim(x1), c(27659, 177))
expect_equal(head(get_times(x), 1), 0.000333333333333333, tolerance = .00001)
expect_equal(head(get_times(x1), 1), 0.000333333333333333, tolerance = .00001)
expect_equal(tail(get_times(x), 1), 31.9911666666667, tolerance = .00001)
expect_equal(tail(get_times(x1), 1), 31.9911666666667, tolerance = .00001)
# check metadata
expect_equal(attr(x1, "parser"), "entab")
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "NVAC-6B1-S3R1")
expect_equal(attr(x, "sample_name"), attr(x1, "sample_name"))
expect_equal(attr(x, "detector"), "DAD")
expect_equal(attr(x, "detector_id"), "G1315B")
expect_equal(attr(x, "detector"), attr(x1, "detector"))
expect_equal(attr(x, "detector_range"), c(250, 600))
expect_equal(attr(x, "method"), "JCMONO1.M")
expect_equal(attr(x, "method"), attr(x1, "method"))
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "time_unit"), attr(x1, "time_unit"))
expect_equal(attr(x, "data_format"), "wide")
expect_equal(attr(x, "data_format"), attr(x1, "data_format"))
})
test_that("read_chroms can read 'Agilent ChemStation' version 81 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_81.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(dim(x), c(2699, 1))
expect_equal(head(get_times(x), 1), 3.00044479166667, tolerance = .00001)
expect_equal(tail(get_times(x), 1), 11.9971114583333, tolerance = .00001)
# check metadata
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(2699, 1))
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "detector_y_unit"), "pA")
expect_equal(attr(x, "detector_id"), "HP G1530A")
expect_equal(attr(x, "sample_name"), "5970 mix 10nG")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# long format
x1 <- read_chroms(path, progress_bar = FALSE,
format_out = "data.table", data_format = "long")[[1]]
expect_equal(colnames(x1), c("rt", "intensity"))
expect_s3_class(x1[1], "data.table")
expect_equal(dim(x1), c(2699, 2))
expect_equal(as.numeric(rownames(x)), x1[[1]])
expect_equal(x[,1], x1[[2]], ignore_attr = TRUE)
expect_equal(head(x1$rt, 1), 3.00044479166667, tolerance = .00001)
expect_equal(tail(x1$rt, 1), 11.9971114583333, tolerance = .00001)
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' version 130 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_130.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(12750, 1))
expect_equal(head(get_times(x),1), 0.00583333333333333, tolerance = .00001)
expect_equal(tail(get_times(x),1), 84.9991666666667, tolerance = .00001)
# check metadata
expect_equal(attr(x, "sample_name"), "0-CN-6-6-PU")
expect_equal(attr(x, "detector_y_unit"), "mAU")
expect_equal(attr(x, "method"), "Phenolics_new2.M")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# long format
x1 <- read_chroms(path, data_format = "long", format_out = "data.table",
progress_bar = FALSE)[[1]]
expect_equal(as.numeric(rownames(x)), x1[[1]])
expect_equal(x[,1], x1[[2]], ignore_attr = TRUE)
expect_s3_class(x1[1], c("data.table","data.frame"))
expect_equal(colnames(x1), c("rt", "intensity"))
expect_equal(dim(x1), c(12750, 2))
expect_equal(head(x1$rt,1), 0.00583333333333333, tolerance = .00001)
expect_equal(tail(x1$rt,1), 84.9991666666667, tolerance = .00001)
expect_equal(attr(x1, "sample_name"), "0-CN-6-6-PU")
expect_equal(attr(x1, "detector_y_unit"), "mAU")
expect_equal(attr(x1, "method"), "Phenolics_new2.M")
expect_equal(attr(x1, "time_unit"), "Minutes")
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent OpenLab' 179 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("openlab_179.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(10000, 1))
expect_equal(head(get_times(x),1), 0.001125, tolerance = .00001)
expect_equal(tail(get_times(x),1), 36, tolerance = .00001)
# check metadata
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "STD_1_1mM-1MKHCO3")
expect_equal(attr(x, "detector_y_unit"), "nRIU")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# long format
x1 <- read_chroms(path, progress_bar = FALSE,
format_out = "data.frame", data_format = "long")[[1]]
expect_equal(as.numeric(rownames(x)), x1[[1]])
expect_equal(x[,1], x1[[2]], ignore_attr = TRUE)
expect_s3_class(x1[1], "data.frame")
expect_equal(colnames(x1), c("rt", "intensity"))
expect_equal(as.numeric(rownames(x)), x1[,1])
expect_equal(x[,1], x1[,2], ignore_attr = TRUE)
expect_equal(head(x1$rt,1), 0.001125, tolerance = .00001)
expect_equal(tail(x1$rt,1), 36, tolerance = .00001)
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' 179 files (8-byte format)", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_179_mustang.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(54704, 1))
expect_equal(head(get_times(x),1), 0.000326049995422363, tolerance = .00001)
expect_equal(tail(get_times(x),1), 18.2346604166667, tolerance = .00001)
# check metadata
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "393006_A1_diol_Al")
expect_equal(attr(x, "detector_y_unit"), "pA")
expect_equal(attr(x, "software"), "Mustang ChemStation")
expect_equal(attr(x, "method"), "NGS Default Edit.M")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# test scale argument
x1 <- read_chroms(path, progress_bar = FALSE, scale=FALSE)[[1]]
expect_equal(x, x1*attr(x1,"intensity_multiplier"), ignore_attr = TRUE)
})
test_that("read_chroms can read 'Agilent ChemStation' 179 (4-byte format)", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_179_asterix.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(22800, 1))
expect_equal(head(get_times(x), 1), 0.00083331667582194, tolerance = .00001)
expect_equal(tail(get_times(x), 1), 19, tolerance = .00001)
expect_equal(attr(x, "data_format"), "wide")
# check metadata
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "NI cat")
expect_equal(attr(x, "detector_y_unit"), "pA")
expect_equal(attr(x, "software"), "Asterix ChemStation")
expect_equal(attr(x, "method"), "Sine14.M")
expect_equal(attr(x, "time_unit"), "Minutes")
})
test_that("read_chroms can read 'Agilent MassHunter' dad files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
skip_if_not_installed("entab")
path <- system.file("masshunter.d/AcqData/DAD1.sp",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "masshunter_dad", parser = "entab",
progress_bar = FALSE)[[1]]
x1 <- read_chroms(path, format_in = "masshunter_dad", parser = "aston",
progress_bar = FALSE)[[1]]
expect_equal(dim(x), c(240, 276))
expect_equal(class(x)[1], "matrix")
expect_equal(x, x1, ignore_attr = TRUE)
expect_equal(attr(x, "parser"), "entab")
expect_equal(attr(x1, "parser"), "aston")
expect_equal(attr(x, "data_format"), "wide")
expect_equal(attr(x1, "data_format"), "wide")
x <- read_chroms(path, format_in = "masshunter_dad", parser = "entab",
data_format = "long", format_out = "data.frame",
progress_bar = FALSE)[[1]]
x1 <- read_chroms(path, format_in = "masshunter_dad", parser = "aston",
data_format = "long", format_out = "data.frame",
progress_bar = FALSE)[[1]]
expect_equal(dim(x), c(66240, 3))
expect_equal(colnames(x), c("rt", "lambda", "intensity"))
expect_s3_class(x, "data.frame")
expect_equal(attr(x, "parser"), "entab")
expect_equal(attr(x1, "parser"), "aston")
expect_equal(colnames(x1), c("rt", "lambda", "intensity"))
expect_equal(attr(x, "data_format"), "long")
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' version 181 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_181.D",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "agilent_d", progress_bar = FALSE)[[1]]
expect_type(x, "list")
expect_equal(class(x[[1]]), c("matrix","array"))
expect_equal(dim(x[[2]]), c(5914, 1))
expect_equal(head(get_times(x$FID1A), 1), -.00181875, tolerance = .00001)
expect_equal(tail(get_times(x$FID1A), 1), 19.7048479166667, tolerance = .00001)
expect_equal(head(get_times(x$V181), 1), -.00126875, tolerance = .00001)
expect_equal(tail(get_times(x$V181), 1), 19.7053979166667, tolerance = .00001)
# check metadata
expect_equal(attr(x[[1]], "sample_name"), "blanc421")
expect_equal(attr(x[[1]], "file_version"), "181")
expect_equal(attr(x[[1]], "detector_y_unit"), "pA")
expect_equal(attr(x[[1]], "method"), "DET3300.M")
expect_equal(attr(x[[1]], "run_datetime"), as.POSIXct("2022-8-23 12:16:25",
tz = "UTC"))
expect_equal(attr(x[[1]], "time_unit"), "Minutes")
expect_equal(attr(x[[1]], "data_format"), "wide")
expect_equal(attr(x[[2]], "sample_name"), "140+H")
expect_equal(attr(x[[2]], "file_version"), "181")
expect_equal(attr(x[[2]], "detector_y_unit"), "pA")
expect_equal(attr(x[[2]], "method"), "DET3300.M")
expect_equal(attr(x[[2]], "run_datetime"), as.POSIXct("2022-8-23 12:48:20",
tz = "UTC"))
expect_equal(attr(x[[2]], "time_unit"), "Minutes")
# long format
x1 <- read_chroms(path, format_in="agilent_d", data_format = "long",
format_out = "data.table",
progress_bar = FALSE)[[1]]
expect_type(x1,"list")
expect_s3_class(x1[[1]],"data.table")
expect_equal(x[[1]][,1], x1[[1]][[2]], ignore_attr=TRUE)
expect_equal(as.numeric(rownames(x[[1]])), x1[[1]][[1]])
expect_equal(x[[2]][,1], x1[[2]][[2]], ignore_attr=TRUE)
expect_equal(colnames(x1[[1]]), c("rt","intensity"))
expect_equal(head(x1$FID1A$rt, 1), -.00181875, tolerance = .00001)
expect_equal(tail(x1$FID1A$rt, 1), 19.7048479166667, tolerance = .00001)
expect_equal(extract_metadata(x)[,c(1:8)], extract_metadata(x1)[,c(1:8)])
expect_equal(attr(x1[[1]], "data_format"), "long")
expect_warning(read_chroms(path, format_in = "agilent_d", what = "dad",
progress_bar = FALSE))
expect_error(read_agilent_d(path, what = "dad"))
})
test_that("read_chroms can read 'Agilent' .dx files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("agilent.dx", package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "agilent_dx", what = c("chroms", "instrument"),
progress_bar = FALSE)[[1]]
expect_equal(class(x$chroms)[1], "matrix")
expect_equal(colnames(x$chroms),"intensity")
expect_equal(dim(x$chroms), c(10000, 1))
expect_equal(attr(x$chroms, "parser"), "chromconverter")
expect_equal(attr(x$chroms, "data_format"), "wide")
expect_equal(head(get_times(x$chroms),1), 0.001125, tolerance = .00001)
expect_equal(tail(get_times(x$chroms),1), 36, tolerance = .00001)
# auxiliary instrumental data
expect_equal(dim(x$instrument$`PMP1C,Solvent Ratio A`), c(43253, 1))
expect_true(all(
sapply(x$instrument, function(x) round(tail(get_times(x),1))) == 36)
)
expect_true(all(
sapply(x$instrument, function(x) round(head(get_times(x),1))) == 0)
)
expect_true(all(x$instrument$`PMP1C,Solvent Ratio A` == 100))
expect_true(all(x$instrument$`PMP1D,Solvent Ratio B` == 0))
expect_true(all(round(x$instrument$`THM1B,Right Temperature`) == 45))
expect_equal(head(names(x$instrument),5), c("RID1G,Board Temperature",
"RID1F,Diode 2",
"RID1E,Diode 1",
"RID1D,Polarity",
"RID1C,Diode Balance"))
expect_equal(sapply(x$instrument, function(xx) attr(xx, "detector_y_unit")),
c("\u00b0C","counts","counts","","","\u00b0C", "\u00b0C",
"\u00b0C","","%","%","%","%","mL/min","bar"),
ignore_attr = TRUE)
expect_equal(sapply(x$instrument, function(xx) attr(xx, "intensity_multiplier")),
c(1e-3, 1e-2, 1e-2, 1, 1e-6, 1e-3, 1e-3, 1e-3, 1e-5,1e-3,1e-3,
1e-3,1e-3,1e-6,5e-3),
ignore_attr = TRUE)
expect_true(all(
sapply(x$instrument, function(xx){
attr(xx, "run_datetime")
}) == 1636717143))
x1 <- read_chroms(path, format_in="agilent_dx", what = c("chroms","instrument"),
progress_bar = FALSE, data_format = "long",
format_out = "data.frame")[[1]]
expect_s3_class(x1$chroms[1], "data.frame")
expect_equal(dim(x1$chroms), c(10000, 2))
expect_equal(dim(x1$instrument[["PMP1C,Solvent Ratio A"]]), c(43253, 2))
expect_equal(attr(x1$chroms,"data_format"),"long")
expect_warning(read_chroms(path, format_in = "agilent_dx", what = "dad",
progress_bar = FALSE))
expect_error(read_agilent_dx(path, what = "dad"))
expect_equal(x1$instrument[[1]]$intensity, x$instrument[[1]][,1],
ignore_attr=TRUE)
expect_equal(x1$instrument[[1]]$rt, as.numeric(rownames(x$instrument[[1]])),
ignore_attr=TRUE)
expect_equal(x1$instrument[[2]]$intensity, x$instrument[[2]][,1],
ignore_attr=TRUE)
expect_equal(x1$instrument[[2]]$rt, as.numeric(rownames(x$instrument[[2]])),
ignore_attr=TRUE)
expect_equal(x1$instrument[[3]]$intensity, x$instrument[[3]][,1],
ignore_attr=TRUE)
expect_equal(x1$instrument[[3]]$rt, as.numeric(rownames(x$instrument[[3]])),
ignore_attr=TRUE)
})
test_that("read_chroms can read 'Agilent' .dx files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("MeOH1.dx", package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "agilent_dx", what = c("chroms","dad", "instrument"),
progress_bar = FALSE)[[1]]
expect_true(inherits(x$chroms, "list"))
expect_true(inherits(x$chroms[[1]], "matrix"))
expect_true(inherits(x$dad, "matrix"))
expect_true(inherits(x$instrument, "list"))
expect_true(inherits(x$instrument[[1]], "matrix"))
expect_equal(vapply(x$chroms, nrow, numeric(1), USE.NAMES = FALSE), rep(4050,5))
expect_equal(dim(x$dad), c(4050,156))
expect_equal(colnames(x$chroms[[1]]),"intensity")
expect_equal(dim(x$chroms[[1]]), c(4050, 1))
expect_equal(attr(x$chroms[[1]], "parser"), "chromconverter")
expect_equal(attr(x$chroms[[1]], "data_format"), "wide")
expect_equal(head(get_times(x$chroms),1), 0.00125, tolerance = .00001)
expect_equal(head(get_times(x$dad),1), 0.00125, tolerance = .00001)
expect_equal(tail(get_times(x$chroms),1), 27, tolerance = .00001)
expect_equal(tail(get_times(x$dad),1), 26.9946, tolerance = .00001)
# auxiliary instrumental data
expect_equal(dim(x$instrument$`PMP1C,Solvent Ratio A`), c(32440.0, 1))
expect_true(all(
sapply(x$instrument, function(x) round(tail(get_times(x),1))) == 27)
)
expect_true(all(
sapply(x$instrument, function(x) round(head(get_times(x),1))) == 0)
)
expect_true(all(head(x$instrument$`PMP1C,Solvent Ratio A`) == 92))
expect_true(all(tail(x$instrument$`PMP1C,Solvent Ratio A`) == 10))
expect_true(all(x$instrument$`PMP1D,Solvent Ratio C` == 0))
expect_true(all(round(x$instrument$`THM1B,Right Temperature`) == 20))
expect_equal(head(names(x$instrument), 5), c("WPS1A,Temperature",
"THM1B,Right Temperature",
"THM1A,Left Temperature",
"DAD1V,UV Lamp Anode Voltage",
"DAD1U,Optical Unit Temperature"))
expect_equal(sapply(x$instrument, function(xx) attr(xx, "detector_y_unit")),
c("\u00b0C", "\u00b0C", "\u00b0C", "V", "\u00b0C", "\u00b0C",
"", "%", "%", "%", "%", "mL/min", "bar", "counts"),
ignore_attr = TRUE)
expect_equal(sapply(x$instrument, function(xx) attr(xx, "intensity_multiplier")),
c(1e-3, 1e-3, 1e-3, 1e-6, 1e-2, 1e-2, 1e-5, 1e-3, 1e-3, 1e-3,
1e-3, 1e-6, 5e-3, 1e0),
ignore_attr = TRUE)
expect_true(all(
sapply(x$instrument, function(xx){
attr(xx, "run_datetime")
}) == 1749578656))
})
ethanbass/chromConverter documentation built on July 4, 2025, 12:08 p.m.
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# these tests rely on files included in the chromConverterExtraTests package,
# which is available on GitHub (https://github.com/ethanbass/chromConverterExtraTests).
test_that("read_chroms can read 'Agilent' MS files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
skip_if_not_installed("entab")
path <- system.file("chemstation_MSD.MS",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, parser = "entab", progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(95471, 3))
expect_equal(attr(x, "parser"), "entab")
expect_equal(attr(x, "data_format"), "long")
expect_equal(colnames(x), c("rt", "mz", "intensity"))
# export as mzML
tmp <- tempdir()
path_mzml <- fs::path(tmp, gsub(" ", "_", attr(x, "sample_name")),
ext = "mzML")
on.exit(unlink(path_mzml))
# chromConverter
x1 <- read_chroms(path, parser = "chromconverter", what = "MS1",
format_out = "data.table", data_format = "long",
progress_bar = FALSE,
export_format = "mzML", path_out = tmp, force = TRUE)[[1]]
expect_s3_class(x1, "data.table")
expect_equal(attr(x1, "format_out"), "data.table")
xx <- read_mzml(path_mzml, data_format="long")
expect_equal(xx$MS1[,-4], x1, ignore_attr = TRUE)
expect_equal(x1, as.data.frame(x), ignore_attr = TRUE)
expect_equal(attr(x1,"sample_name"), attr(x,"sample_name"))
expect_equal(attr(x1,"source_sha1"), attr(x,"source_sha1"))
expect_equal(attr(x1,"time_unit"), attr(x,"time_unit"))
# expect_equal(as.numeric(attr(x1,"run_datetime")),
# as.numeric(attr(x,"run_datetime"))) #timezone is wrong on entab
expect_equal(attr(x1,"operator"), attr(x,"operator"))
expect_equal(attr(x1,"method"), attr(x,"method"))
expect_equal(attr(x1,"detector"), attr(x,"detector"))
expect_equal(attr(x1, "data_format"), "long")
# rainbow
x2 <- read_chroms(path, parser = "rainbow",
progress_bar = FALSE, precision = 0)[[1]]
expect_equal(class(x2)[1], "matrix")
expect_equal(dim(x2), c(2534, 841))
expect_equal(attr(x2,"run_datetime"), attr(x1,"run_datetime"))
expect_equal(attr(x2, "method"), attr(x1, "method"))
expect_equal(attr(x2, "detector"), attr(x1, "detector"))
expect_equal(attr(x2, "data_format"), "wide")
x3 <- read_chroms(path, parser = "rainbow",
progress_bar = FALSE, data_format = "long",
format_out = "data.table",
precision = 0)[[1]]
expect_s3_class(x3, "data.table")
expect_equal(dim(x3), c(2131094, 3))
expect_equal(colnames(x3), c("rt", "mz", "intensity"))
expect_equal(attr(x3, "method"), attr(x2, "method"))
expect_equal(attr(x3, "detector"), attr(x2, "detector"))
expect_equal(attr(x3, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' version 30 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_30.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, parser = "chromconverter", progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(38405, 1))
expect_equal(head(get_times(x),1), -0.001333333, tolerance = .00001)
expect_equal(tail(get_times(x),1), 32.002, tolerance = .00001)
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "NVAC-6B1-S3R1")
expect_equal(attr(x, "detector"), "G1315B")
expect_equal(attr(x, "detector_y_unit"), "mAU")
expect_equal(attr(x, "method"), "JCMONO1.M")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
x1 <- read_chroms(path, parser = "chromconverter", format_out = "data.frame",
data_format = "long", progress_bar = FALSE)[[1]]
expect_equal(colnames(x1), c("rt","intensity"))
expect_s3_class(x1[1], "data.frame")
expect_equal(as.numeric(rownames(x)), x1[,1])
expect_equal(x[,1], x1[,2], ignore_attr = TRUE)
expect_equal(head(x1$rt, 1), -.00133333333333333, tolerance = .00001)
expect_equal(tail(x1$rt, 1), 32.002, tolerance = .00001)
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' 31 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
skip_if_not_installed("entab")
path <- system.file("chemstation_31.uv", package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE, parser = "chromconverter")[[1]]
x1 <- read_chroms(path, progress_bar = FALSE, parser = "entab")[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(class(x1)[1], "matrix")
expect_equal(dim(x), c(27659, 176))
expect_equal(dim(x1), c(27659, 177))
expect_equal(head(get_times(x), 1), 0.000333333333333333, tolerance = .00001)
expect_equal(head(get_times(x1), 1), 0.000333333333333333, tolerance = .00001)
expect_equal(tail(get_times(x), 1), 31.9911666666667, tolerance = .00001)
expect_equal(tail(get_times(x1), 1), 31.9911666666667, tolerance = .00001)
# check metadata
expect_equal(attr(x1, "parser"), "entab")
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "NVAC-6B1-S3R1")
expect_equal(attr(x, "sample_name"), attr(x1, "sample_name"))
expect_equal(attr(x, "detector"), "DAD")
expect_equal(attr(x, "detector_id"), "G1315B")
expect_equal(attr(x, "detector"), attr(x1, "detector"))
expect_equal(attr(x, "detector_range"), c(250, 600))
expect_equal(attr(x, "method"), "JCMONO1.M")
expect_equal(attr(x, "method"), attr(x1, "method"))
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "time_unit"), attr(x1, "time_unit"))
expect_equal(attr(x, "data_format"), "wide")
expect_equal(attr(x, "data_format"), attr(x1, "data_format"))
})
test_that("read_chroms can read 'Agilent ChemStation' version 81 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_81.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(dim(x), c(2699, 1))
expect_equal(head(get_times(x), 1), 3.00044479166667, tolerance = .00001)
expect_equal(tail(get_times(x), 1), 11.9971114583333, tolerance = .00001)
# check metadata
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(2699, 1))
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "detector_y_unit"), "pA")
expect_equal(attr(x, "detector_id"), "HP G1530A")
expect_equal(attr(x, "sample_name"), "5970 mix 10nG")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# long format
x1 <- read_chroms(path, progress_bar = FALSE,
format_out = "data.table", data_format = "long")[[1]]
expect_equal(colnames(x1), c("rt", "intensity"))
expect_s3_class(x1[1], "data.table")
expect_equal(dim(x1), c(2699, 2))
expect_equal(as.numeric(rownames(x)), x1[[1]])
expect_equal(x[,1], x1[[2]], ignore_attr = TRUE)
expect_equal(head(x1$rt, 1), 3.00044479166667, tolerance = .00001)
expect_equal(tail(x1$rt, 1), 11.9971114583333, tolerance = .00001)
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' version 130 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_130.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(12750, 1))
expect_equal(head(get_times(x),1), 0.00583333333333333, tolerance = .00001)
expect_equal(tail(get_times(x),1), 84.9991666666667, tolerance = .00001)
# check metadata
expect_equal(attr(x, "sample_name"), "0-CN-6-6-PU")
expect_equal(attr(x, "detector_y_unit"), "mAU")
expect_equal(attr(x, "method"), "Phenolics_new2.M")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# long format
x1 <- read_chroms(path, data_format = "long", format_out = "data.table",
progress_bar = FALSE)[[1]]
expect_equal(as.numeric(rownames(x)), x1[[1]])
expect_equal(x[,1], x1[[2]], ignore_attr = TRUE)
expect_s3_class(x1[1], c("data.table","data.frame"))
expect_equal(colnames(x1), c("rt", "intensity"))
expect_equal(dim(x1), c(12750, 2))
expect_equal(head(x1$rt,1), 0.00583333333333333, tolerance = .00001)
expect_equal(tail(x1$rt,1), 84.9991666666667, tolerance = .00001)
expect_equal(attr(x1, "sample_name"), "0-CN-6-6-PU")
expect_equal(attr(x1, "detector_y_unit"), "mAU")
expect_equal(attr(x1, "method"), "Phenolics_new2.M")
expect_equal(attr(x1, "time_unit"), "Minutes")
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent OpenLab' 179 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("openlab_179.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(10000, 1))
expect_equal(head(get_times(x),1), 0.001125, tolerance = .00001)
expect_equal(tail(get_times(x),1), 36, tolerance = .00001)
# check metadata
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "STD_1_1mM-1MKHCO3")
expect_equal(attr(x, "detector_y_unit"), "nRIU")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# long format
x1 <- read_chroms(path, progress_bar = FALSE,
format_out = "data.frame", data_format = "long")[[1]]
expect_equal(as.numeric(rownames(x)), x1[[1]])
expect_equal(x[,1], x1[[2]], ignore_attr = TRUE)
expect_s3_class(x1[1], "data.frame")
expect_equal(colnames(x1), c("rt", "intensity"))
expect_equal(as.numeric(rownames(x)), x1[,1])
expect_equal(x[,1], x1[,2], ignore_attr = TRUE)
expect_equal(head(x1$rt,1), 0.001125, tolerance = .00001)
expect_equal(tail(x1$rt,1), 36, tolerance = .00001)
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' 179 files (8-byte format)", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_179_mustang.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(54704, 1))
expect_equal(head(get_times(x),1), 0.000326049995422363, tolerance = .00001)
expect_equal(tail(get_times(x),1), 18.2346604166667, tolerance = .00001)
# check metadata
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "393006_A1_diol_Al")
expect_equal(attr(x, "detector_y_unit"), "pA")
expect_equal(attr(x, "software"), "Mustang ChemStation")
expect_equal(attr(x, "method"), "NGS Default Edit.M")
expect_equal(attr(x, "time_unit"), "Minutes")
expect_equal(attr(x, "data_format"), "wide")
# test scale argument
x1 <- read_chroms(path, progress_bar = FALSE, scale=FALSE)[[1]]
expect_equal(x, x1*attr(x1,"intensity_multiplier"), ignore_attr = TRUE)
})
test_that("read_chroms can read 'Agilent ChemStation' 179 (4-byte format)", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_179_asterix.ch",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, progress_bar = FALSE)[[1]]
expect_equal(class(x)[1], "matrix")
expect_equal(dim(x), c(22800, 1))
expect_equal(head(get_times(x), 1), 0.00083331667582194, tolerance = .00001)
expect_equal(tail(get_times(x), 1), 19, tolerance = .00001)
expect_equal(attr(x, "data_format"), "wide")
# check metadata
expect_equal(attr(x, "parser"), "chromconverter")
expect_equal(attr(x, "sample_name"), "NI cat")
expect_equal(attr(x, "detector_y_unit"), "pA")
expect_equal(attr(x, "software"), "Asterix ChemStation")
expect_equal(attr(x, "method"), "Sine14.M")
expect_equal(attr(x, "time_unit"), "Minutes")
})
test_that("read_chroms can read 'Agilent MassHunter' dad files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
skip_if_not_installed("entab")
path <- system.file("masshunter.d/AcqData/DAD1.sp",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "masshunter_dad", parser = "entab",
progress_bar = FALSE)[[1]]
x1 <- read_chroms(path, format_in = "masshunter_dad", parser = "aston",
progress_bar = FALSE)[[1]]
expect_equal(dim(x), c(240, 276))
expect_equal(class(x)[1], "matrix")
expect_equal(x, x1, ignore_attr = TRUE)
expect_equal(attr(x, "parser"), "entab")
expect_equal(attr(x1, "parser"), "aston")
expect_equal(attr(x, "data_format"), "wide")
expect_equal(attr(x1, "data_format"), "wide")
x <- read_chroms(path, format_in = "masshunter_dad", parser = "entab",
data_format = "long", format_out = "data.frame",
progress_bar = FALSE)[[1]]
x1 <- read_chroms(path, format_in = "masshunter_dad", parser = "aston",
data_format = "long", format_out = "data.frame",
progress_bar = FALSE)[[1]]
expect_equal(dim(x), c(66240, 3))
expect_equal(colnames(x), c("rt", "lambda", "intensity"))
expect_s3_class(x, "data.frame")
expect_equal(attr(x, "parser"), "entab")
expect_equal(attr(x1, "parser"), "aston")
expect_equal(colnames(x1), c("rt", "lambda", "intensity"))
expect_equal(attr(x, "data_format"), "long")
expect_equal(attr(x1, "data_format"), "long")
})
test_that("read_chroms can read 'Agilent ChemStation' version 181 files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("chemstation_181.D",
package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "agilent_d", progress_bar = FALSE)[[1]]
expect_type(x, "list")
expect_equal(class(x[[1]]), c("matrix","array"))
expect_equal(dim(x[[2]]), c(5914, 1))
expect_equal(head(get_times(x$FID1A), 1), -.00181875, tolerance = .00001)
expect_equal(tail(get_times(x$FID1A), 1), 19.7048479166667, tolerance = .00001)
expect_equal(head(get_times(x$V181), 1), -.00126875, tolerance = .00001)
expect_equal(tail(get_times(x$V181), 1), 19.7053979166667, tolerance = .00001)
# check metadata
expect_equal(attr(x[[1]], "sample_name"), "blanc421")
expect_equal(attr(x[[1]], "file_version"), "181")
expect_equal(attr(x[[1]], "detector_y_unit"), "pA")
expect_equal(attr(x[[1]], "method"), "DET3300.M")
expect_equal(attr(x[[1]], "run_datetime"), as.POSIXct("2022-8-23 12:16:25",
tz = "UTC"))
expect_equal(attr(x[[1]], "time_unit"), "Minutes")
expect_equal(attr(x[[1]], "data_format"), "wide")
expect_equal(attr(x[[2]], "sample_name"), "140+H")
expect_equal(attr(x[[2]], "file_version"), "181")
expect_equal(attr(x[[2]], "detector_y_unit"), "pA")
expect_equal(attr(x[[2]], "method"), "DET3300.M")
expect_equal(attr(x[[2]], "run_datetime"), as.POSIXct("2022-8-23 12:48:20",
tz = "UTC"))
expect_equal(attr(x[[2]], "time_unit"), "Minutes")
# long format
x1 <- read_chroms(path, format_in="agilent_d", data_format = "long",
format_out = "data.table",
progress_bar = FALSE)[[1]]
expect_type(x1,"list")
expect_s3_class(x1[[1]],"data.table")
expect_equal(x[[1]][,1], x1[[1]][[2]], ignore_attr=TRUE)
expect_equal(as.numeric(rownames(x[[1]])), x1[[1]][[1]])
expect_equal(x[[2]][,1], x1[[2]][[2]], ignore_attr=TRUE)
expect_equal(colnames(x1[[1]]), c("rt","intensity"))
expect_equal(head(x1$FID1A$rt, 1), -.00181875, tolerance = .00001)
expect_equal(tail(x1$FID1A$rt, 1), 19.7048479166667, tolerance = .00001)
expect_equal(extract_metadata(x)[,c(1:8)], extract_metadata(x1)[,c(1:8)])
expect_equal(attr(x1[[1]], "data_format"), "long")
expect_warning(read_chroms(path, format_in = "agilent_d", what = "dad",
progress_bar = FALSE))
expect_error(read_agilent_d(path, what = "dad"))
})
test_that("read_chroms can read 'Agilent' .dx files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("agilent.dx", package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "agilent_dx", what = c("chroms", "instrument"),
progress_bar = FALSE)[[1]]
expect_equal(class(x$chroms)[1], "matrix")
expect_equal(colnames(x$chroms),"intensity")
expect_equal(dim(x$chroms), c(10000, 1))
expect_equal(attr(x$chroms, "parser"), "chromconverter")
expect_equal(attr(x$chroms, "data_format"), "wide")
expect_equal(head(get_times(x$chroms),1), 0.001125, tolerance = .00001)
expect_equal(tail(get_times(x$chroms),1), 36, tolerance = .00001)
# auxiliary instrumental data
expect_equal(dim(x$instrument$`PMP1C,Solvent Ratio A`), c(43253, 1))
expect_true(all(
sapply(x$instrument, function(x) round(tail(get_times(x),1))) == 36)
)
expect_true(all(
sapply(x$instrument, function(x) round(head(get_times(x),1))) == 0)
)
expect_true(all(x$instrument$`PMP1C,Solvent Ratio A` == 100))
expect_true(all(x$instrument$`PMP1D,Solvent Ratio B` == 0))
expect_true(all(round(x$instrument$`THM1B,Right Temperature`) == 45))
expect_equal(head(names(x$instrument),5), c("RID1G,Board Temperature",
"RID1F,Diode 2",
"RID1E,Diode 1",
"RID1D,Polarity",
"RID1C,Diode Balance"))
expect_equal(sapply(x$instrument, function(xx) attr(xx, "detector_y_unit")),
c("\u00b0C","counts","counts","","","\u00b0C", "\u00b0C",
"\u00b0C","","%","%","%","%","mL/min","bar"),
ignore_attr = TRUE)
expect_equal(sapply(x$instrument, function(xx) attr(xx, "intensity_multiplier")),
c(1e-3, 1e-2, 1e-2, 1, 1e-6, 1e-3, 1e-3, 1e-3, 1e-5,1e-3,1e-3,
1e-3,1e-3,1e-6,5e-3),
ignore_attr = TRUE)
expect_true(all(
sapply(x$instrument, function(xx){
attr(xx, "run_datetime")
}) == 1636717143))
x1 <- read_chroms(path, format_in="agilent_dx", what = c("chroms","instrument"),
progress_bar = FALSE, data_format = "long",
format_out = "data.frame")[[1]]
expect_s3_class(x1$chroms[1], "data.frame")
expect_equal(dim(x1$chroms), c(10000, 2))
expect_equal(dim(x1$instrument[["PMP1C,Solvent Ratio A"]]), c(43253, 2))
expect_equal(attr(x1$chroms,"data_format"),"long")
expect_warning(read_chroms(path, format_in = "agilent_dx", what = "dad",
progress_bar = FALSE))
expect_error(read_agilent_dx(path, what = "dad"))
expect_equal(x1$instrument[[1]]$intensity, x$instrument[[1]][,1],
ignore_attr=TRUE)
expect_equal(x1$instrument[[1]]$rt, as.numeric(rownames(x$instrument[[1]])),
ignore_attr=TRUE)
expect_equal(x1$instrument[[2]]$intensity, x$instrument[[2]][,1],
ignore_attr=TRUE)
expect_equal(x1$instrument[[2]]$rt, as.numeric(rownames(x$instrument[[2]])),
ignore_attr=TRUE)
expect_equal(x1$instrument[[3]]$intensity, x$instrument[[3]][,1],
ignore_attr=TRUE)
expect_equal(x1$instrument[[3]]$rt, as.numeric(rownames(x$instrument[[3]])),
ignore_attr=TRUE)
})
test_that("read_chroms can read 'Agilent' .dx files", {
skip_on_cran()
skip_if_not_installed("chromConverterExtraTests")
path <- system.file("MeOH1.dx", package = "chromConverterExtraTests")
skip_if_not(file.exists(path))
x <- read_chroms(path, format_in = "agilent_dx", what = c("chroms","dad", "instrument"),
progress_bar = FALSE)[[1]]
expect_true(inherits(x$chroms, "list"))
expect_true(inherits(x$chroms[[1]], "matrix"))
expect_true(inherits(x$dad, "matrix"))
expect_true(inherits(x$instrument, "list"))
expect_true(inherits(x$instrument[[1]], "matrix"))
expect_equal(vapply(x$chroms, nrow, numeric(1), USE.NAMES = FALSE), rep(4050,5))
expect_equal(dim(x$dad), c(4050,156))
expect_equal(colnames(x$chroms[[1]]),"intensity")
expect_equal(dim(x$chroms[[1]]), c(4050, 1))
expect_equal(attr(x$chroms[[1]], "parser"), "chromconverter")
expect_equal(attr(x$chroms[[1]], "data_format"), "wide")
expect_equal(head(get_times(x$chroms),1), 0.00125, tolerance = .00001)
expect_equal(head(get_times(x$dad),1), 0.00125, tolerance = .00001)
expect_equal(tail(get_times(x$chroms),1), 27, tolerance = .00001)
expect_equal(tail(get_times(x$dad),1), 26.9946, tolerance = .00001)
# auxiliary instrumental data
expect_equal(dim(x$instrument$`PMP1C,Solvent Ratio A`), c(32440.0, 1))
expect_true(all(
sapply(x$instrument, function(x) round(tail(get_times(x),1))) == 27)
)
expect_true(all(
sapply(x$instrument, function(x) round(head(get_times(x),1))) == 0)
)
expect_true(all(head(x$instrument$`PMP1C,Solvent Ratio A`) == 92))
expect_true(all(tail(x$instrument$`PMP1C,Solvent Ratio A`) == 10))
expect_true(all(x$instrument$`PMP1D,Solvent Ratio C` == 0))
expect_true(all(round(x$instrument$`THM1B,Right Temperature`) == 20))
expect_equal(head(names(x$instrument), 5), c("WPS1A,Temperature",
"THM1B,Right Temperature",
"THM1A,Left Temperature",
"DAD1V,UV Lamp Anode Voltage",
"DAD1U,Optical Unit Temperature"))
expect_equal(sapply(x$instrument, function(xx) attr(xx, "detector_y_unit")),
c("\u00b0C", "\u00b0C", "\u00b0C", "V", "\u00b0C", "\u00b0C",
"", "%", "%", "%", "%", "mL/min", "bar", "counts"),
ignore_attr = TRUE)
expect_equal(sapply(x$instrument, function(xx) attr(xx, "intensity_multiplier")),
c(1e-3, 1e-3, 1e-3, 1e-6, 1e-2, 1e-2, 1e-5, 1e-3, 1e-3, 1e-3,
1e-3, 1e-6, 5e-3, 1e0),
ignore_attr = TRUE)
expect_true(all(
sapply(x$instrument, function(xx){
attr(xx, "run_datetime")
}) == 1749578656))
})
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