tests/testthat/test-fcat.R
In dbosak01/fmtr: Easily Apply Formats to Data
context("Format Catalog Tests")
cdlst <- read.table(header = TRUE, text ='
CODELISTNAME RANK CODEDVALUE TRANSLATED
LBNRIND 1 H High
LBNRIND 2 L Low
LBNRIND 3 N Normal
LBTESTCD 1 ALB Albumin
LBTESTCD 2 ALP "Alkaline Phosphatase"
LBTESTCD 3 ALT "Alanine Aminotransferase"
LBTESTCD 4 AST "Aspartate Aminotransferase"
LBTESTCD 5 BILDIR "Direct Bilirubin"
LBTESTCD 6 BILI Bilirubin
LBTESTCD 7 GGT "Gamma Glutamyl Transferase"
LBTESTCD 8 HCT Hematocrit
LBTESTCD 9 HGB Hemoglobin
LBTESTCD 10 PROT Protein
LBTESTCD 11 GLUC Glucose
RACE 1 "BLACK OR AFRICAN AMERICAN" "Black or African American"
RACE 2 ASIAN Asian
RACE 3 WHITE White
SEX 1 F Female
SEX 2 M Male
SEX 3 U Unknown')
options("logr.output" = FALSE)
test_that("fcat1: fcat() function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other"))
)
expect_equal(class(c1)[1], "fcat")
expect_equal(length(c1), 2)
expect_equal(names(c1)[1], "lblA")
})
test_that("fcat2: as.data.frame.fcat() function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = 2),
condition(x == "B", "Label B", order = 1),
condition(TRUE, "Other", order = 3)),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other")),
lblC = "%d%b%Y",
lblD = function(x) format(x, big.mark = ","),
lblE = c(A = "Label A", B = "Label B")
)
dat <- as.data.frame(c1)
expect_equal(nrow(dat), 9)
expect_equal(as.character(dat[1, 1]), "lblA")
expect_equal(as.character(dat[4, 1]), "lblB")
expect_equal(as.character(dat[7, 1]), "lblC")
expect_equal(as.character(dat[7, 2]), "S")
})
test_that("fcat3: as.fcat.data.frame() function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = 2),
condition(x == "B", "Label B", order = 1),
condition(TRUE, "Other", order = 3)),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other")),
lblC = "%d%b%Y",
lblD = function(x) format(x, big.mark = ","),
lblE = c(A = "Label A", B = "Label B")
)
dat <- as.data.frame(c1)
dat
c2 <- as.fcat(dat)
# print(c1$lblA)
# print(dat)
# print(c2)
# print(c2[["lblA"]])
# print(fapply("B", c2[["lblA"]]))
# print(c2[["lblC"]])
expect_equal(length(c2), 5)
expect_equal(c2[["lblC"]], "%d%b%Y")
expect_equal(fapply("B", c2$lblA), "Label B")
expect_equal(fapply("B", c2$lblB), "Other")
expect_equal(fapply(as.Date("2020-10-05"), c2[["lblC"]]), "05Oct2020")
expect_equal(fapply(1000, c2[["lblD"]]), "1,000")
expect_equal(fapply("B", c2[["lblE"]]), "Label B")
})
test_that("fcat4: write.fcat and read.fcat functions work as expected.", {
fp <- tempdir()
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other"))
)
pth <- write.fcat(c1, fp)
c2 <- read.fcat(pth)
dat <- as.data.frame(c2)
expect_equal(nrow(dat), 6)
expect_equal(as.character(dat[1, 1]), "lblA")
expect_equal(as.character(dat[4, 1]), "lblB")
})
test_that("fcat5: is.fcat function work as expected.", {
c1 <- fcat(num_fmt = "%.1f",
label_fmt = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
date_fmt = "%d%b%Y")
expect_equal(is.fcat(c1), TRUE)
})
test_that("fcat6: fcat can be used for formatting vectors.", {
c1 <- fcat(num_fmt = "%.1f",
label_fmt = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
date_fmt = "%d%b%Y")
res <- c("Label A", "Label B", "Other")
expect_equal(fapply(2, c1[["num_fmt"]]), "2.0")
expect_equal(fapply(c("A", "B", "C"), c1[["label_fmt"]]), res)
expect_equal(fapply(as.Date("2020-05-16"), c1[["date_fmt"]]), "16May2020")
})
test_that("fcat7: fcat printing works as expected.", {
c1 <- fcat(num_fmt = "%.1f",
label_fmt = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
date_fmt = "%d%b%Y")
expect_output(print(c1, verbose = TRUE))
expect_output(print(c1))
})
test_that("fcat8: fcat can be applied to a data frame with formats function.", {
c1 <- fcat(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
dat <- data.frame(NAME = c("Fred", "Sally", "Sven"),
AGE = c(25.356, 84.345, 56.346),
CATEGORY = c("A", "B", "C"),
BDATE = c(as.Date("1995-04-24"),
as.Date("1940-02-11"),
as.Date("1964-11-12")))
formats(dat) <- c1
fdat <- fdata(dat)
expect_equal(as.character(fdat[1, "AGE"]), "25.4")
expect_equal(as.character(fdat[2, "CATEGORY"]), "Label B")
expect_equal(as.character(fdat[1, "AGE"]), "25.4")
})
test_that("fcat9: print.fcat works as expected.", {
c1 <- fcat(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y",
LKUP = c(A = 1, B = 2, C = 3),
FUNC = function(x) x + 1)
#print(c1)
c1
c1$CATEGORY
c1$AGE
c1$LKUP
c1$FUNC
#print(c1, verbose = TRUE)
expect_equal(TRUE, TRUE)
})
test_that("fcat10: as.fcat.fmt_lst works as expected.", {
f1 <- flist(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
c1 <- as.fcat(f1)
c1
expect_equal(is.fcat(c1), TRUE)
})
test_that("fcat11: as.fcat.list works as expected.", {
l1 <- list(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
c1 <- as.fcat(l1)
c1
expect_equal(is.fcat(c1), TRUE)
})
test_that("fcat12: as.fcat.tbl_df works as expected.", {
c1 <- fcat(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
df <- as.data.frame(c1)
tb <- tibble::as_tibble(df)
c2 <- as.fcat(tb)
c2
expect_equal(is.fcat(c2), TRUE)
})
test_that("fcat13: row_limit parameter works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = 2),
condition(x == "B", "Label B", order = 1),
condition(TRUE, "Other", order = 3)),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other")),
lblC = "%d%b%Y",
lblD = function(x) format(x, big.mark = ","),
lblE = c(A = "Label A", B = "Label B")
)
if (FALSE) {
print(c1)
print(c1, row_limit = NULL)
print(c1, row_limit = 3)
print(c1, row_limit = 7)
}
expect_equal(TRUE, TRUE)
})
test_that("fcat14: print.fcat function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = function(x) format(x, width = 4),
lblC = c(A = "Label A", B = "Label B")
)
expect_equal(class(c1)[1], "fcat")
expect_equal(length(c1), 3)
expect_equal(names(c1)[1], "lblA")
res <- capture.output(print(c1))
expect_equal(length(res) > 1, TRUE)
})
# This is a test of printing to console. No real test.
test_that("fcat15: log parameter works as expected.", {
# Prints to console
c1 <- fcat(lblA = c(A = 1, B = 2),
lblB = "%1.1f"
)
# Does not print to console
c1 <- fcat(lblA = c(A = 1, B = 2),
lblB = "%1.1f", log = FALSE
)
expect_equal(1, 1)
})
test_that("fcat16: import.fcat works as expected.", {
res <- import.fcat(cdlst, name = "CODELISTNAME",
value = "CODEDVALUE",
label = "TRANSLATED")
res
expect_equal(length(res), 4)
expect_equal(names(res), c("LBNRIND", "LBTESTCD", "RACE", "SEX"))
expect_equal(length(res$SEX), 3)
expect_equal(length(res$LBNRIND), 3)
expect_equal(length(res$LBTESTCD), 11)
expect_equal(length(res$RACE), 3)
res$SEX
res1 <- fapply(c("M", "F", "M"), res$SEX)
expect_equal(res1[1], "Male")
})
test_that("fcat17: write.fcat and read.fcat functions retain as.factor parameter.", {
fp <- tempdir()
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other"), as.factor = TRUE)
)
pth <- write.fcat(c1, fp)
c2 <- read.fcat(pth)
expect_equal(attr(c2$lblA, "as.factor"), FALSE)
expect_equal(attr(c2$lblB, "as.factor"), TRUE)
})
test_that("fcat18: as.fcat.data.frame() order works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = "2"),
condition(x == "B", "Label B", order = "1"),
condition(TRUE, "Other", order = "3"))
)
# Possible error
res <- fapply(c("A", "B", "C"), c1$lblA)
expect_equal(length(res), 3)
})
dbosak01/fmtr documentation built on May 11, 2024, 8:11 a.m.
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context("Format Catalog Tests")
cdlst <- read.table(header = TRUE, text ='
CODELISTNAME RANK CODEDVALUE TRANSLATED
LBNRIND 1 H High
LBNRIND 2 L Low
LBNRIND 3 N Normal
LBTESTCD 1 ALB Albumin
LBTESTCD 2 ALP "Alkaline Phosphatase"
LBTESTCD 3 ALT "Alanine Aminotransferase"
LBTESTCD 4 AST "Aspartate Aminotransferase"
LBTESTCD 5 BILDIR "Direct Bilirubin"
LBTESTCD 6 BILI Bilirubin
LBTESTCD 7 GGT "Gamma Glutamyl Transferase"
LBTESTCD 8 HCT Hematocrit
LBTESTCD 9 HGB Hemoglobin
LBTESTCD 10 PROT Protein
LBTESTCD 11 GLUC Glucose
RACE 1 "BLACK OR AFRICAN AMERICAN" "Black or African American"
RACE 2 ASIAN Asian
RACE 3 WHITE White
SEX 1 F Female
SEX 2 M Male
SEX 3 U Unknown')
options("logr.output" = FALSE)
test_that("fcat1: fcat() function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other"))
)
expect_equal(class(c1)[1], "fcat")
expect_equal(length(c1), 2)
expect_equal(names(c1)[1], "lblA")
})
test_that("fcat2: as.data.frame.fcat() function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = 2),
condition(x == "B", "Label B", order = 1),
condition(TRUE, "Other", order = 3)),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other")),
lblC = "%d%b%Y",
lblD = function(x) format(x, big.mark = ","),
lblE = c(A = "Label A", B = "Label B")
)
dat <- as.data.frame(c1)
expect_equal(nrow(dat), 9)
expect_equal(as.character(dat[1, 1]), "lblA")
expect_equal(as.character(dat[4, 1]), "lblB")
expect_equal(as.character(dat[7, 1]), "lblC")
expect_equal(as.character(dat[7, 2]), "S")
})
test_that("fcat3: as.fcat.data.frame() function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = 2),
condition(x == "B", "Label B", order = 1),
condition(TRUE, "Other", order = 3)),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other")),
lblC = "%d%b%Y",
lblD = function(x) format(x, big.mark = ","),
lblE = c(A = "Label A", B = "Label B")
)
dat <- as.data.frame(c1)
dat
c2 <- as.fcat(dat)
# print(c1$lblA)
# print(dat)
# print(c2)
# print(c2[["lblA"]])
# print(fapply("B", c2[["lblA"]]))
# print(c2[["lblC"]])
expect_equal(length(c2), 5)
expect_equal(c2[["lblC"]], "%d%b%Y")
expect_equal(fapply("B", c2$lblA), "Label B")
expect_equal(fapply("B", c2$lblB), "Other")
expect_equal(fapply(as.Date("2020-10-05"), c2[["lblC"]]), "05Oct2020")
expect_equal(fapply(1000, c2[["lblD"]]), "1,000")
expect_equal(fapply("B", c2[["lblE"]]), "Label B")
})
test_that("fcat4: write.fcat and read.fcat functions work as expected.", {
fp <- tempdir()
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other"))
)
pth <- write.fcat(c1, fp)
c2 <- read.fcat(pth)
dat <- as.data.frame(c2)
expect_equal(nrow(dat), 6)
expect_equal(as.character(dat[1, 1]), "lblA")
expect_equal(as.character(dat[4, 1]), "lblB")
})
test_that("fcat5: is.fcat function work as expected.", {
c1 <- fcat(num_fmt = "%.1f",
label_fmt = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
date_fmt = "%d%b%Y")
expect_equal(is.fcat(c1), TRUE)
})
test_that("fcat6: fcat can be used for formatting vectors.", {
c1 <- fcat(num_fmt = "%.1f",
label_fmt = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
date_fmt = "%d%b%Y")
res <- c("Label A", "Label B", "Other")
expect_equal(fapply(2, c1[["num_fmt"]]), "2.0")
expect_equal(fapply(c("A", "B", "C"), c1[["label_fmt"]]), res)
expect_equal(fapply(as.Date("2020-05-16"), c1[["date_fmt"]]), "16May2020")
})
test_that("fcat7: fcat printing works as expected.", {
c1 <- fcat(num_fmt = "%.1f",
label_fmt = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
date_fmt = "%d%b%Y")
expect_output(print(c1, verbose = TRUE))
expect_output(print(c1))
})
test_that("fcat8: fcat can be applied to a data frame with formats function.", {
c1 <- fcat(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
dat <- data.frame(NAME = c("Fred", "Sally", "Sven"),
AGE = c(25.356, 84.345, 56.346),
CATEGORY = c("A", "B", "C"),
BDATE = c(as.Date("1995-04-24"),
as.Date("1940-02-11"),
as.Date("1964-11-12")))
formats(dat) <- c1
fdat <- fdata(dat)
expect_equal(as.character(fdat[1, "AGE"]), "25.4")
expect_equal(as.character(fdat[2, "CATEGORY"]), "Label B")
expect_equal(as.character(fdat[1, "AGE"]), "25.4")
})
test_that("fcat9: print.fcat works as expected.", {
c1 <- fcat(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y",
LKUP = c(A = 1, B = 2, C = 3),
FUNC = function(x) x + 1)
#print(c1)
c1
c1$CATEGORY
c1$AGE
c1$LKUP
c1$FUNC
#print(c1, verbose = TRUE)
expect_equal(TRUE, TRUE)
})
test_that("fcat10: as.fcat.fmt_lst works as expected.", {
f1 <- flist(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
c1 <- as.fcat(f1)
c1
expect_equal(is.fcat(c1), TRUE)
})
test_that("fcat11: as.fcat.list works as expected.", {
l1 <- list(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
c1 <- as.fcat(l1)
c1
expect_equal(is.fcat(c1), TRUE)
})
test_that("fcat12: as.fcat.tbl_df works as expected.", {
c1 <- fcat(AGE = "%.1f",
CATEGORY = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
BDATE = "%d%b%Y")
df <- as.data.frame(c1)
tb <- tibble::as_tibble(df)
c2 <- as.fcat(tb)
c2
expect_equal(is.fcat(c2), TRUE)
})
test_that("fcat13: row_limit parameter works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = 2),
condition(x == "B", "Label B", order = 1),
condition(TRUE, "Other", order = 3)),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other")),
lblC = "%d%b%Y",
lblD = function(x) format(x, big.mark = ","),
lblE = c(A = "Label A", B = "Label B")
)
if (FALSE) {
print(c1)
print(c1, row_limit = NULL)
print(c1, row_limit = 3)
print(c1, row_limit = 7)
}
expect_equal(TRUE, TRUE)
})
test_that("fcat14: print.fcat function works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = function(x) format(x, width = 4),
lblC = c(A = "Label A", B = "Label B")
)
expect_equal(class(c1)[1], "fcat")
expect_equal(length(c1), 3)
expect_equal(names(c1)[1], "lblA")
res <- capture.output(print(c1))
expect_equal(length(res) > 1, TRUE)
})
# This is a test of printing to console. No real test.
test_that("fcat15: log parameter works as expected.", {
# Prints to console
c1 <- fcat(lblA = c(A = 1, B = 2),
lblB = "%1.1f"
)
# Does not print to console
c1 <- fcat(lblA = c(A = 1, B = 2),
lblB = "%1.1f", log = FALSE
)
expect_equal(1, 1)
})
test_that("fcat16: import.fcat works as expected.", {
res <- import.fcat(cdlst, name = "CODELISTNAME",
value = "CODEDVALUE",
label = "TRANSLATED")
res
expect_equal(length(res), 4)
expect_equal(names(res), c("LBNRIND", "LBTESTCD", "RACE", "SEX"))
expect_equal(length(res$SEX), 3)
expect_equal(length(res$LBNRIND), 3)
expect_equal(length(res$LBTESTCD), 11)
expect_equal(length(res$RACE), 3)
res$SEX
res1 <- fapply(c("M", "F", "M"), res$SEX)
expect_equal(res1[1], "Male")
})
test_that("fcat17: write.fcat and read.fcat functions retain as.factor parameter.", {
fp <- tempdir()
c1 <- fcat(lblA = value(condition(x == "A", "Label A"),
condition(x == "B", "Label B"),
condition(TRUE, "Other")),
lblB = value(condition(x == "C", "Label C"),
condition(x == "D", "Label D"),
condition(TRUE, "Other"), as.factor = TRUE)
)
pth <- write.fcat(c1, fp)
c2 <- read.fcat(pth)
expect_equal(attr(c2$lblA, "as.factor"), FALSE)
expect_equal(attr(c2$lblB, "as.factor"), TRUE)
})
test_that("fcat18: as.fcat.data.frame() order works as expected", {
c1 <- fcat(lblA = value(condition(x == "A", "Label A", order = "2"),
condition(x == "B", "Label B", order = "1"),
condition(TRUE, "Other", order = "3"))
)
# Possible error
res <- fapply(c("A", "B", "C"), c1$lblA)
expect_equal(length(res), 3)
})
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