tests/testthat/test_freqlist.R
In eheinzen/arsenal: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
## Tests for freqlist
context("Testing the freqlist output")
# "mdat" now defined in helper-data.R
TAB <- table(mdat[, c("Group", "Sex", "Phase")])
TAB.subset <- table(mdat[!(mdat$Group == "Low" & mdat$Sex == "Male"), c("Group", "Sex", "Phase")])
TAB.na <- table(mdat[, c("trt", "ethan")], useNA = 'a')
old.labs <- c(cumFreq = "cumFreq", freqPercent = "freqPercent", cumPercent = "cumPercent")
###########################################################################################################
#### Basic freqlist
###########################################################################################################
test_that("A basic freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB), labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 4.44| 4.44|",
"| | |II | 8| 12| 8.89| 13.33|",
"| | |III | 3| 15| 3.33| 16.67|",
"| |Male |I | 7| 22| 7.78| 24.44|",
"| | |II | 2| 24| 2.22| 26.67|",
"| | |III | 6| 30| 6.67| 33.33|",
"|Low |Female |I | 7| 37| 7.78| 41.11|",
"| | |II | 8| 45| 8.89| 50.00|",
"| | |III | 2| 47| 2.22| 52.22|",
"| |Male |I | 5| 52| 5.56| 57.78|",
"| | |II | 4| 56| 4.44| 62.22|",
"| | |III | 4| 60| 4.44| 66.67|",
"|Med |Female |II | 11| 71| 12.22| 78.89|",
"| | |III | 3| 74| 3.33| 82.22|",
"| |Male |II | 8| 82| 8.89| 91.11|",
"| | |III | 8| 90| 8.89| 100.00|"
)
)
})
test_that("strata option in freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB, strata = "Group"), single = FALSE, labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 13.33| 13.33|",
"| | |II | 8| 12| 26.67| 40.00|",
"| | |III | 3| 15| 10.00| 50.00|",
"| |Male |I | 7| 22| 23.33| 73.33|",
"| | |II | 2| 24| 6.67| 80.00|",
"| | |III | 6| 30| 20.00| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Low |Female |I | 7| 7| 23.33| 23.33|",
"| | |II | 8| 15| 26.67| 50.00|",
"| | |III | 2| 17| 6.67| 56.67|",
"| |Male |I | 5| 22| 16.67| 73.33|",
"| | |II | 4| 26| 13.33| 86.67|",
"| | |III | 4| 30| 13.33| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Med |Female |II | 11| 11| 36.67| 36.67|",
"| | |III | 3| 14| 10.00| 46.67|",
"| |Male |II | 8| 22| 26.67| 73.33|",
"| | |III | 8| 30| 26.67| 100.00|"
)
)
expect_error(freqlist(TAB, strata = "group"), "strata variable not found")
})
test_that("sparse option in freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB, sparse = TRUE), labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 4.44| 4.44|",
"| | |II | 8| 12| 8.89| 13.33|",
"| | |III | 3| 15| 3.33| 16.67|",
"| |Male |I | 7| 22| 7.78| 24.44|",
"| | |II | 2| 24| 2.22| 26.67|",
"| | |III | 6| 30| 6.67| 33.33|",
"|Low |Female |I | 7| 37| 7.78| 41.11|",
"| | |II | 8| 45| 8.89| 50.00|",
"| | |III | 2| 47| 2.22| 52.22|",
"| |Male |I | 5| 52| 5.56| 57.78|",
"| | |II | 4| 56| 4.44| 62.22|",
"| | |III | 4| 60| 4.44| 66.67|",
"|Med |Female |I | 0| 60| 0.00| 66.67|",
"| | |II | 11| 71| 12.22| 78.89|",
"| | |III | 3| 74| 3.33| 82.22|",
"| |Male |I | 0| 74| 0.00| 82.22|",
"| | |II | 8| 82| 8.89| 91.11|",
"| | |III | 8| 90| 8.89| 100.00|"
)
)
})
test_that("NA options in freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include"))),
c("|trt |ethan | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---|:-------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "showexclude"))),
c("|trt |ethan | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---|:-------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 19.54| 19.54|",
"| |Heinzen | 16| 33| 18.39| 37.93|",
"| |NA | 3| NA| NA| NA|",
"|B |Ethan | 25| 58| 28.74| 66.67|",
"| |Heinzen | 29| 87| 33.33| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "remove"))),
c("|trt |ethan | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---|:-------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 19.54| 19.54|",
"| |Heinzen | 16| 33| 18.39| 37.93|",
"|B |Ethan | 25| 58| 28.74| 66.67|",
"| |Heinzen | 29| 87| 33.33| 100.00|"
)
)
})
test_that("Changing the labels on non-grouped freqlists", {
ref <- c(
"|Treatment |Ethan Rocks | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---------|:-----------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include"), labelTranslations = c(trt = "Treatment", ethan = "Ethan Rocks"))),
ref
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include", labelTranslations = list(trt = "Treatment", ethan = "Ethan Rocks")))),
ref
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include", labelTranslations = c(trt = "Treatment", ethan ="Ethan Rocks")))),
ref
)
expect_error(freqlist(TAB.na, labelTranslations = c("Treatment", "Ethan Rocks")), "Unnamed label")
expect_error(freqlist(TAB.na, labelTranslations = c(hi = "Treatment", ethan = "Ethan Rocks")), NA)
tmp <- freqlist(TAB.na, na.options = "include")
labels(tmp) <- c(trt = "Treatment", ethan = "Ethan Rocks")
expect_identical(
capture.kable(summary(tmp)),
ref
)
labels(tmp) <- NULL
expect_identical(
capture.kable(summary(tmp)),
c("|trt |ethan | Freq| cumFreq| freqPercent| cumPercent|",
"|:---|:-------|----:|-------:|-----------:|----------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
)
labels(tmp) <- c(ethan = "Ethan Rocks", trt = "Treatment", dummy = "Dummy")
expect_identical(
capture.kable(summary(tmp)),
c(
"|Treatment |Ethan Rocks | Freq| cumFreq| freqPercent| cumPercent|",
"|:---------|:-----------|----:|-------:|-----------:|----------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
)
})
test_that("Changing the labels on grouped freqlists", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include", strata = "ethan",
labelTranslations = c(trt = "Treatment", ethan = "Ethan", old.labs)))),
c("|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|Ethan |A | 17| 17| 40.48| 40.48|" ,
"| |B | 25| 42| 59.52| 100.00|" ,
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|",
"|:-------|:---------|----:|-------:|-----------:|----------:|",
"|Heinzen |A | 16| 16| 35.56| 35.56|",
"| |B | 29| 45| 64.44| 100.00|",
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|NA |A | 3| 3| 100.00| 100.00|"
)
)
})
test_that("dupLabels works", {
expect_identical(
capture.kable(summary(freqlist(TAB, labelTranslations = old.labs), dupLabels = TRUE)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 4.44| 4.44|",
"|High |Female |II | 8| 12| 8.89| 13.33|",
"|High |Female |III | 3| 15| 3.33| 16.67|",
"|High |Male |I | 7| 22| 7.78| 24.44|",
"|High |Male |II | 2| 24| 2.22| 26.67|",
"|High |Male |III | 6| 30| 6.67| 33.33|",
"|Low |Female |I | 7| 37| 7.78| 41.11|",
"|Low |Female |II | 8| 45| 8.89| 50.00|",
"|Low |Female |III | 2| 47| 2.22| 52.22|",
"|Low |Male |I | 5| 52| 5.56| 57.78|",
"|Low |Male |II | 4| 56| 4.44| 62.22|",
"|Low |Male |III | 4| 60| 4.44| 66.67|",
"|Med |Female |II | 11| 71| 12.22| 78.89|",
"|Med |Female |III | 3| 74| 3.33| 82.22|",
"|Med |Male |II | 8| 82| 8.89| 91.11|",
"|Med |Male |III | 8| 90| 8.89| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB, strata = "Group", labelTranslations = old.labs), single = FALSE, dupLabels = TRUE)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 13.33| 13.33|",
"|High |Female |II | 8| 12| 26.67| 40.00|",
"|High |Female |III | 3| 15| 10.00| 50.00|",
"|High |Male |I | 7| 22| 23.33| 73.33|",
"|High |Male |II | 2| 24| 6.67| 80.00|",
"|High |Male |III | 6| 30| 20.00| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Low |Female |I | 7| 7| 23.33| 23.33|",
"|Low |Female |II | 8| 15| 26.67| 50.00|",
"|Low |Female |III | 2| 17| 6.67| 56.67|",
"|Low |Male |I | 5| 22| 16.67| 73.33|",
"|Low |Male |II | 4| 26| 13.33| 86.67|",
"|Low |Male |III | 4| 30| 13.33| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Med |Female |II | 11| 11| 36.67| 36.67|",
"|Med |Female |III | 3| 14| 10.00| 46.67|",
"|Med |Male |II | 8| 22| 26.67| 73.33|",
"|Med |Male |III | 8| 30| 26.67| 100.00|"
)
)
})
test_that("Adding a title", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include", labelTranslations = c(trt = "Treatment", ethan = "Ethan", old.labs)),
dupLabels = TRUE, title = "Ethan Rocks")),
c("Table: Ethan Rocks" ,
"" ,
"|Treatment |Ethan | Freq| cumFreq| freqPercent| cumPercent|",
"|:---------|:-------|----:|-------:|-----------:|----------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"|A |Heinzen | 16| 33| 17.78| 36.67|",
"|A |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"|B |Heinzen | 29| 90| 32.22| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include", strata = "ethan",
labelTranslations = c(trt = "Treatment", ethan = "Ethan", old.labs)),
dupLabels = TRUE, title = "Ethan Rocks")),
c("Table: Ethan Rocks" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|Ethan |A | 17| 17| 40.48| 40.48|" ,
"|Ethan |B | 25| 42| 59.52| 100.00|" ,
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|",
"|:-------|:---------|----:|-------:|-----------:|----------:|",
"|Heinzen |A | 16| 16| 35.56| 35.56|",
"|Heinzen |B | 29| 45| 64.44| 100.00|",
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|NA |A | 3| 3| 100.00| 100.00|"
)
)
})
test_that("Formula method works", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include"), labelTranslations = c(trt = "Trt", ethan = "Ethan"))),
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), labelTranslations = c("addNA(ethan)" = "Ethan", trt = "Trt")))
)
if(getRversion() >= "3.4.0")
{
expect_identical(
capture.kable(summary(freqlist(~ trt + ethan, data = mdat, addNA = TRUE), labelTranslations = c(trt = "Trt", ethan = "Ethan"))),
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), labelTranslations = c("addNA(ethan)" = "Ethan", trt = "Trt")))
)
} else skip("R version isn't right to use 'addNA=TRUE'")
})
test_that("digits specification", {
expect_identical(
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), digits.pct = 1, digits.count = 1)),
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat, digits.pct = 1, digits.count = 1)))
)
expect_identical(
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), digits.pct = 1, digits.count = 1)),
c(
"|Treatment Arm |addNA(ethan) | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:-------------|:------------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17.0| 17.0| 18.9| 18.9|",
"| |Heinzen | 16.0| 33.0| 17.8| 36.7|",
"| |NA | 3.0| 36.0| 3.3| 40.0|",
"|B |Ethan | 25.0| 61.0| 27.8| 67.8|",
"| |Heinzen | 29.0| 90.0| 32.2| 100.0|"
)
)
})
###########################################################################################################
#### Reported bugs for freqlist
###########################################################################################################
test_that("11/18/16: Emily Lundt's subsetted table and duplicate label problem", {
expect_identical(
capture.kable(summary(freqlist(TAB.subset), labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 5.19| 5.19|",
"| | |II | 8| 12| 10.39| 15.58|",
"| | |III | 3| 15| 3.90| 19.48|",
"| |Male |I | 7| 22| 9.09| 28.57|",
"| | |II | 2| 24| 2.60| 31.17|",
"| | |III | 6| 30| 7.79| 38.96|",
"|Low |Female |I | 7| 37| 9.09| 48.05|",
"| | |II | 8| 45| 10.39| 58.44|",
"| | |III | 2| 47| 2.60| 61.04|",
"|Med |Female |II | 11| 58| 14.29| 75.32|",
"| | |III | 3| 61| 3.90| 79.22|",
"| |Male |II | 8| 69| 10.39| 89.61|",
"| | |III | 8| 77| 10.39| 100.00|"
)
)
})
test_that("04/17/18: using 'method' in freqlist (#95)", {
dat <- data.frame(method = c(1, 1, 2, 2, 3, 3, 4, 4))
expect_identical(
capture.kable(summary(freqlist(~method, data = dat))),
c("|method | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:------|----:|---------------:|-------:|------------------:|",
"|1 | 2| 2| 25.00| 25.00|",
"|2 | 2| 4| 25.00| 50.00|",
"|3 | 2| 6| 25.00| 75.00|",
"|4 | 2| 8| 25.00| 100.00|"
)
)
})
test_that("02/26/19: don't drop labels with subset= argument (#184)", {
expect_identical(
capture.kable(summary(freqlist(~ age, data = mockstudy, subset = age > 80))),
c("|Age in Years | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:------------|----:|---------------:|-------:|------------------:|",
"|81 | 12| 12| 41.38| 41.38|",
"|82 | 6| 18| 20.69| 62.07|",
"|83 | 6| 24| 20.69| 82.76|",
"|84 | 1| 25| 3.45| 86.21|",
"|85 | 2| 27| 6.90| 93.10|",
"|88 | 2| 29| 6.90| 100.00|"
)
)
})
test_that("03/20/2019: freqlist still works with all zero counts (#194, #186).", {
tab0 <- table(factor(c(), levels = c("m", "f")))
expect_error(print(summary(freqlist(tab0))), "There wasn't anything")
expect_identical(
capture.kable(summary(freqlist(tab0), sparse = TRUE)),
c("|Var1 | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:----|----:|---------------:|-------:|------------------:|",
"|m | 0| 0| NA| NA|",
"|f | 0| 0| NA| NA|"
)
)
})
test_that("03/21/2019: freqlist doesn't lose labels when subsetting (#196)", {
expect_identical(
capture.kable(summary(freqlist(~ sex + ps + arm, data = mockstudy, strata = "arm",
subset = arm == "F: FOLFOX" & !is.na(ps))[c(1:2, 4)])),
c("|Treatment Arm |sex | Freq|",
"|:-------------|:------|----:|",
"|F: FOLFOX |Male | 168|",
"| | | 148|",
"| | | 16|",
"| |Female | 110|",
"| | | 95|",
"| | | 13|"
)
)
})
test_that("02/28/2020: freqlist.formula works without needing addNA AND na.option (#265)", {
expect_identical(
capture.kable(summary(freqlist(~ sex + ps, data = mockstudy))),
c("|sex |ps | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:------|:--|----:|---------------:|-------:|------------------:|",
"|Male |0 | 391| 391| 26.08| 26.08|",
"| |1 | 329| 720| 21.95| 48.03|",
"| |2 | 34| 754| 2.27| 50.30|",
"| |NA | 162| 916| 10.81| 61.11|",
"|Female |0 | 244| 1160| 16.28| 77.38|",
"| |1 | 202| 1362| 13.48| 90.86|",
"| |2 | 33| 1395| 2.20| 93.06|",
"| |NA | 104| 1499| 6.94| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(~ sex + ps, data = mockstudy, addNA = FALSE))),
capture.kable(summary(freqlist(~ sex + ps, data = mockstudy, na.options = "remove")))
)
})
eheinzen/arsenal documentation built on Sept. 11, 2022, 10:59 a.m.
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## Tests for freqlist
context("Testing the freqlist output")
# "mdat" now defined in helper-data.R
TAB <- table(mdat[, c("Group", "Sex", "Phase")])
TAB.subset <- table(mdat[!(mdat$Group == "Low" & mdat$Sex == "Male"), c("Group", "Sex", "Phase")])
TAB.na <- table(mdat[, c("trt", "ethan")], useNA = 'a')
old.labs <- c(cumFreq = "cumFreq", freqPercent = "freqPercent", cumPercent = "cumPercent")
###########################################################################################################
#### Basic freqlist
###########################################################################################################
test_that("A basic freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB), labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 4.44| 4.44|",
"| | |II | 8| 12| 8.89| 13.33|",
"| | |III | 3| 15| 3.33| 16.67|",
"| |Male |I | 7| 22| 7.78| 24.44|",
"| | |II | 2| 24| 2.22| 26.67|",
"| | |III | 6| 30| 6.67| 33.33|",
"|Low |Female |I | 7| 37| 7.78| 41.11|",
"| | |II | 8| 45| 8.89| 50.00|",
"| | |III | 2| 47| 2.22| 52.22|",
"| |Male |I | 5| 52| 5.56| 57.78|",
"| | |II | 4| 56| 4.44| 62.22|",
"| | |III | 4| 60| 4.44| 66.67|",
"|Med |Female |II | 11| 71| 12.22| 78.89|",
"| | |III | 3| 74| 3.33| 82.22|",
"| |Male |II | 8| 82| 8.89| 91.11|",
"| | |III | 8| 90| 8.89| 100.00|"
)
)
})
test_that("strata option in freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB, strata = "Group"), single = FALSE, labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 13.33| 13.33|",
"| | |II | 8| 12| 26.67| 40.00|",
"| | |III | 3| 15| 10.00| 50.00|",
"| |Male |I | 7| 22| 23.33| 73.33|",
"| | |II | 2| 24| 6.67| 80.00|",
"| | |III | 6| 30| 20.00| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Low |Female |I | 7| 7| 23.33| 23.33|",
"| | |II | 8| 15| 26.67| 50.00|",
"| | |III | 2| 17| 6.67| 56.67|",
"| |Male |I | 5| 22| 16.67| 73.33|",
"| | |II | 4| 26| 13.33| 86.67|",
"| | |III | 4| 30| 13.33| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Med |Female |II | 11| 11| 36.67| 36.67|",
"| | |III | 3| 14| 10.00| 46.67|",
"| |Male |II | 8| 22| 26.67| 73.33|",
"| | |III | 8| 30| 26.67| 100.00|"
)
)
expect_error(freqlist(TAB, strata = "group"), "strata variable not found")
})
test_that("sparse option in freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB, sparse = TRUE), labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 4.44| 4.44|",
"| | |II | 8| 12| 8.89| 13.33|",
"| | |III | 3| 15| 3.33| 16.67|",
"| |Male |I | 7| 22| 7.78| 24.44|",
"| | |II | 2| 24| 2.22| 26.67|",
"| | |III | 6| 30| 6.67| 33.33|",
"|Low |Female |I | 7| 37| 7.78| 41.11|",
"| | |II | 8| 45| 8.89| 50.00|",
"| | |III | 2| 47| 2.22| 52.22|",
"| |Male |I | 5| 52| 5.56| 57.78|",
"| | |II | 4| 56| 4.44| 62.22|",
"| | |III | 4| 60| 4.44| 66.67|",
"|Med |Female |I | 0| 60| 0.00| 66.67|",
"| | |II | 11| 71| 12.22| 78.89|",
"| | |III | 3| 74| 3.33| 82.22|",
"| |Male |I | 0| 74| 0.00| 82.22|",
"| | |II | 8| 82| 8.89| 91.11|",
"| | |III | 8| 90| 8.89| 100.00|"
)
)
})
test_that("NA options in freqlist call", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include"))),
c("|trt |ethan | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---|:-------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "showexclude"))),
c("|trt |ethan | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---|:-------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 19.54| 19.54|",
"| |Heinzen | 16| 33| 18.39| 37.93|",
"| |NA | 3| NA| NA| NA|",
"|B |Ethan | 25| 58| 28.74| 66.67|",
"| |Heinzen | 29| 87| 33.33| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "remove"))),
c("|trt |ethan | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---|:-------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 19.54| 19.54|",
"| |Heinzen | 16| 33| 18.39| 37.93|",
"|B |Ethan | 25| 58| 28.74| 66.67|",
"| |Heinzen | 29| 87| 33.33| 100.00|"
)
)
})
test_that("Changing the labels on non-grouped freqlists", {
ref <- c(
"|Treatment |Ethan Rocks | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:---------|:-----------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include"), labelTranslations = c(trt = "Treatment", ethan = "Ethan Rocks"))),
ref
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include", labelTranslations = list(trt = "Treatment", ethan = "Ethan Rocks")))),
ref
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, na.options = "include", labelTranslations = c(trt = "Treatment", ethan ="Ethan Rocks")))),
ref
)
expect_error(freqlist(TAB.na, labelTranslations = c("Treatment", "Ethan Rocks")), "Unnamed label")
expect_error(freqlist(TAB.na, labelTranslations = c(hi = "Treatment", ethan = "Ethan Rocks")), NA)
tmp <- freqlist(TAB.na, na.options = "include")
labels(tmp) <- c(trt = "Treatment", ethan = "Ethan Rocks")
expect_identical(
capture.kable(summary(tmp)),
ref
)
labels(tmp) <- NULL
expect_identical(
capture.kable(summary(tmp)),
c("|trt |ethan | Freq| cumFreq| freqPercent| cumPercent|",
"|:---|:-------|----:|-------:|-----------:|----------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
)
labels(tmp) <- c(ethan = "Ethan Rocks", trt = "Treatment", dummy = "Dummy")
expect_identical(
capture.kable(summary(tmp)),
c(
"|Treatment |Ethan Rocks | Freq| cumFreq| freqPercent| cumPercent|",
"|:---------|:-----------|----:|-------:|-----------:|----------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"| |Heinzen | 16| 33| 17.78| 36.67|",
"| |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"| |Heinzen | 29| 90| 32.22| 100.00|"
)
)
})
test_that("Changing the labels on grouped freqlists", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include", strata = "ethan",
labelTranslations = c(trt = "Treatment", ethan = "Ethan", old.labs)))),
c("|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|Ethan |A | 17| 17| 40.48| 40.48|" ,
"| |B | 25| 42| 59.52| 100.00|" ,
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|",
"|:-------|:---------|----:|-------:|-----------:|----------:|",
"|Heinzen |A | 16| 16| 35.56| 35.56|",
"| |B | 29| 45| 64.44| 100.00|",
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|NA |A | 3| 3| 100.00| 100.00|"
)
)
})
test_that("dupLabels works", {
expect_identical(
capture.kable(summary(freqlist(TAB, labelTranslations = old.labs), dupLabels = TRUE)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 4.44| 4.44|",
"|High |Female |II | 8| 12| 8.89| 13.33|",
"|High |Female |III | 3| 15| 3.33| 16.67|",
"|High |Male |I | 7| 22| 7.78| 24.44|",
"|High |Male |II | 2| 24| 2.22| 26.67|",
"|High |Male |III | 6| 30| 6.67| 33.33|",
"|Low |Female |I | 7| 37| 7.78| 41.11|",
"|Low |Female |II | 8| 45| 8.89| 50.00|",
"|Low |Female |III | 2| 47| 2.22| 52.22|",
"|Low |Male |I | 5| 52| 5.56| 57.78|",
"|Low |Male |II | 4| 56| 4.44| 62.22|",
"|Low |Male |III | 4| 60| 4.44| 66.67|",
"|Med |Female |II | 11| 71| 12.22| 78.89|",
"|Med |Female |III | 3| 74| 3.33| 82.22|",
"|Med |Male |II | 8| 82| 8.89| 91.11|",
"|Med |Male |III | 8| 90| 8.89| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB, strata = "Group", labelTranslations = old.labs), single = FALSE, dupLabels = TRUE)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 13.33| 13.33|",
"|High |Female |II | 8| 12| 26.67| 40.00|",
"|High |Female |III | 3| 15| 10.00| 50.00|",
"|High |Male |I | 7| 22| 23.33| 73.33|",
"|High |Male |II | 2| 24| 6.67| 80.00|",
"|High |Male |III | 6| 30| 20.00| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Low |Female |I | 7| 7| 23.33| 23.33|",
"|Low |Female |II | 8| 15| 26.67| 50.00|",
"|Low |Female |III | 2| 17| 6.67| 56.67|",
"|Low |Male |I | 5| 22| 16.67| 73.33|",
"|Low |Male |II | 4| 26| 13.33| 86.67|",
"|Low |Male |III | 4| 30| 13.33| 100.00|",
"" ,
"" ,
"|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|Med |Female |II | 11| 11| 36.67| 36.67|",
"|Med |Female |III | 3| 14| 10.00| 46.67|",
"|Med |Male |II | 8| 22| 26.67| 73.33|",
"|Med |Male |III | 8| 30| 26.67| 100.00|"
)
)
})
test_that("Adding a title", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include", labelTranslations = c(trt = "Treatment", ethan = "Ethan", old.labs)),
dupLabels = TRUE, title = "Ethan Rocks")),
c("Table: Ethan Rocks" ,
"" ,
"|Treatment |Ethan | Freq| cumFreq| freqPercent| cumPercent|",
"|:---------|:-------|----:|-------:|-----------:|----------:|",
"|A |Ethan | 17| 17| 18.89| 18.89|",
"|A |Heinzen | 16| 33| 17.78| 36.67|",
"|A |NA | 3| 36| 3.33| 40.00|",
"|B |Ethan | 25| 61| 27.78| 67.78|",
"|B |Heinzen | 29| 90| 32.22| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include", strata = "ethan",
labelTranslations = c(trt = "Treatment", ethan = "Ethan", old.labs)),
dupLabels = TRUE, title = "Ethan Rocks")),
c("Table: Ethan Rocks" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|Ethan |A | 17| 17| 40.48| 40.48|" ,
"|Ethan |B | 25| 42| 59.52| 100.00|" ,
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|",
"|:-------|:---------|----:|-------:|-----------:|----------:|",
"|Heinzen |A | 16| 16| 35.56| 35.56|",
"|Heinzen |B | 29| 45| 64.44| 100.00|",
"" ,
"" ,
"|Ethan |Treatment | Freq| cumFreq| freqPercent| cumPercent|" ,
"|:-----|:---------|----:|-------:|-----------:|----------:|" ,
"|NA |A | 3| 3| 100.00| 100.00|"
)
)
})
test_that("Formula method works", {
expect_identical(
capture.kable(summary(freqlist(TAB.na, options = "include"), labelTranslations = c(trt = "Trt", ethan = "Ethan"))),
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), labelTranslations = c("addNA(ethan)" = "Ethan", trt = "Trt")))
)
if(getRversion() >= "3.4.0")
{
expect_identical(
capture.kable(summary(freqlist(~ trt + ethan, data = mdat, addNA = TRUE), labelTranslations = c(trt = "Trt", ethan = "Ethan"))),
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), labelTranslations = c("addNA(ethan)" = "Ethan", trt = "Trt")))
)
} else skip("R version isn't right to use 'addNA=TRUE'")
})
test_that("digits specification", {
expect_identical(
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), digits.pct = 1, digits.count = 1)),
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat, digits.pct = 1, digits.count = 1)))
)
expect_identical(
capture.kable(summary(freqlist(~ trt + addNA(ethan), data = mdat), digits.pct = 1, digits.count = 1)),
c(
"|Treatment Arm |addNA(ethan) | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:-------------|:------------|----:|---------------:|-------:|------------------:|",
"|A |Ethan | 17.0| 17.0| 18.9| 18.9|",
"| |Heinzen | 16.0| 33.0| 17.8| 36.7|",
"| |NA | 3.0| 36.0| 3.3| 40.0|",
"|B |Ethan | 25.0| 61.0| 27.8| 67.8|",
"| |Heinzen | 29.0| 90.0| 32.2| 100.0|"
)
)
})
###########################################################################################################
#### Reported bugs for freqlist
###########################################################################################################
test_that("11/18/16: Emily Lundt's subsetted table and duplicate label problem", {
expect_identical(
capture.kable(summary(freqlist(TAB.subset), labelTranslations = old.labs)),
c("|Group |Sex |Phase | Freq| cumFreq| freqPercent| cumPercent|",
"|:-----|:------|:-----|----:|-------:|-----------:|----------:|",
"|High |Female |I | 4| 4| 5.19| 5.19|",
"| | |II | 8| 12| 10.39| 15.58|",
"| | |III | 3| 15| 3.90| 19.48|",
"| |Male |I | 7| 22| 9.09| 28.57|",
"| | |II | 2| 24| 2.60| 31.17|",
"| | |III | 6| 30| 7.79| 38.96|",
"|Low |Female |I | 7| 37| 9.09| 48.05|",
"| | |II | 8| 45| 10.39| 58.44|",
"| | |III | 2| 47| 2.60| 61.04|",
"|Med |Female |II | 11| 58| 14.29| 75.32|",
"| | |III | 3| 61| 3.90| 79.22|",
"| |Male |II | 8| 69| 10.39| 89.61|",
"| | |III | 8| 77| 10.39| 100.00|"
)
)
})
test_that("04/17/18: using 'method' in freqlist (#95)", {
dat <- data.frame(method = c(1, 1, 2, 2, 3, 3, 4, 4))
expect_identical(
capture.kable(summary(freqlist(~method, data = dat))),
c("|method | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:------|----:|---------------:|-------:|------------------:|",
"|1 | 2| 2| 25.00| 25.00|",
"|2 | 2| 4| 25.00| 50.00|",
"|3 | 2| 6| 25.00| 75.00|",
"|4 | 2| 8| 25.00| 100.00|"
)
)
})
test_that("02/26/19: don't drop labels with subset= argument (#184)", {
expect_identical(
capture.kable(summary(freqlist(~ age, data = mockstudy, subset = age > 80))),
c("|Age in Years | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:------------|----:|---------------:|-------:|------------------:|",
"|81 | 12| 12| 41.38| 41.38|",
"|82 | 6| 18| 20.69| 62.07|",
"|83 | 6| 24| 20.69| 82.76|",
"|84 | 1| 25| 3.45| 86.21|",
"|85 | 2| 27| 6.90| 93.10|",
"|88 | 2| 29| 6.90| 100.00|"
)
)
})
test_that("03/20/2019: freqlist still works with all zero counts (#194, #186).", {
tab0 <- table(factor(c(), levels = c("m", "f")))
expect_error(print(summary(freqlist(tab0))), "There wasn't anything")
expect_identical(
capture.kable(summary(freqlist(tab0), sparse = TRUE)),
c("|Var1 | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:----|----:|---------------:|-------:|------------------:|",
"|m | 0| 0| NA| NA|",
"|f | 0| 0| NA| NA|"
)
)
})
test_that("03/21/2019: freqlist doesn't lose labels when subsetting (#196)", {
expect_identical(
capture.kable(summary(freqlist(~ sex + ps + arm, data = mockstudy, strata = "arm",
subset = arm == "F: FOLFOX" & !is.na(ps))[c(1:2, 4)])),
c("|Treatment Arm |sex | Freq|",
"|:-------------|:------|----:|",
"|F: FOLFOX |Male | 168|",
"| | | 148|",
"| | | 16|",
"| |Female | 110|",
"| | | 95|",
"| | | 13|"
)
)
})
test_that("02/28/2020: freqlist.formula works without needing addNA AND na.option (#265)", {
expect_identical(
capture.kable(summary(freqlist(~ sex + ps, data = mockstudy))),
c("|sex |ps | Freq| Cumulative Freq| Percent| Cumulative Percent|",
"|:------|:--|----:|---------------:|-------:|------------------:|",
"|Male |0 | 391| 391| 26.08| 26.08|",
"| |1 | 329| 720| 21.95| 48.03|",
"| |2 | 34| 754| 2.27| 50.30|",
"| |NA | 162| 916| 10.81| 61.11|",
"|Female |0 | 244| 1160| 16.28| 77.38|",
"| |1 | 202| 1362| 13.48| 90.86|",
"| |2 | 33| 1395| 2.20| 93.06|",
"| |NA | 104| 1499| 6.94| 100.00|"
)
)
expect_identical(
capture.kable(summary(freqlist(~ sex + ps, data = mockstudy, addNA = FALSE))),
capture.kable(summary(freqlist(~ sex + ps, data = mockstudy, na.options = "remove")))
)
})
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