tests/testthat/test_lhs_tableby.R
In eheinzen/arsenal: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
## Tests for tableby
context("Testing the tableby strata and multiple LHS output")
# "mdat" now defined in helper-data.R
###########################################################################################################
#### Basic two-sided tableby
###########################################################################################################
test_that("A three-LHS tableby call", {
skip_if_not_installed("coin")
expect_identical(
capture.kable(summary(tableby(list(Group, trt, ethan) ~ Sex + time + dt + Phase, data = mdat), text = TRUE)),
c(
capture.kable(summary(tableby(Group ~ Sex + time + dt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(tableby(trt ~ Sex + time + dt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(tableby(ethan ~ Sex + time + dt + Phase, data = mdat), text = TRUE))
)
)
})
test_that("A tableby call with strata", {
skip_if_not_installed("coin")
expect_identical(
capture.kable(summary(tableby(Group ~ Age + time + Phase, data = mdat, strata = trt), text = TRUE)),
c("|Treatment Arm | | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:-------------|:------------|:---------------:|:---------------:|:---------------:|:---------------:|:-------:|",
"|A |Age in Years | | | | | 0.918 |",
"| |- Mean (SD) | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | |",
"| |- Range | 29.000 - 53.000 | 33.000 - 48.000 | 30.000 - 49.000 | 29.000 - 53.000 | |",
"| |time | | | | | 0.319 |",
"| |- Mean (SD) | 4.357 (1.865) | 3.273 (1.421) | 3.727 (1.954) | 3.833 (1.781) | |",
"| |- Range | 0.000 - 6.000 | 1.000 - 5.000 | 1.000 - 7.000 | 0.000 - 7.000 | |",
"| |Phase | | | | | 0.506 |",
"| |- I | 6 (42.9%) | 2 (18.2%) | 0 (0.0%) | 8 (22.2%) | |",
"| |- II | 3 (21.4%) | 6 (54.5%) | 8 (72.7%) | 17 (47.2%) | |",
"| |- III | 5 (35.7%) | 3 (27.3%) | 3 (27.3%) | 11 (30.6%) | |",
"|B |Age in Years | | | | | 0.960 |",
"| |- Mean (SD) | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | |",
"| |- Range | 30.000 - 49.000 | 32.000 - 47.000 | 30.000 - 52.000 | 30.000 - 52.000 | |",
"| |time | | | | | 0.081 |",
"| |- Mean (SD) | 4.750 (1.807) | 3.105 (2.355) | 3.895 (2.079) | 3.870 (2.172) | |",
"| |- Range | 1.000 - 7.000 | 0.000 - 6.000 | 1.000 - 7.000 | 0.000 - 7.000 | |",
"| |Phase | | | | | 0.005 |",
"| |- I | 5 (31.2%) | 10 (52.6%) | 0 (0.0%) | 15 (27.8%) | |",
"| |- II | 7 (43.8%) | 6 (31.6%) | 11 (57.9%) | 24 (44.4%) | |",
"| |- III | 4 (25.0%) | 3 (15.8%) | 8 (42.1%) | 15 (27.8%) | |"
)
)
expect_equal(
xtfrm(tableby(Group ~ Age + time + Phase, data = mdat, strata = trt)),
c(
xtfrm(tableby(Group ~ Age + time + Phase, data = mdat, subset = trt == "A")),
xtfrm(tableby(Group ~ Age + time + Phase, data = mdat, subset = trt == "B"))
)
)
})
test_that("strata levels are maintained", {
dat <- data.frame(a = c("A", "A", "A", "B", "A", "B"), b = c(1, 1, 1, 2, 2, 2), stringsAsFactors = FALSE)
expect_identical(
capture.kable(summary(tableby(~ a, strata = b, data = dat), text = TRUE)),
c("|b | | Overall (N=6) |",
"|:--|:----|:-------------:|",
"|1 |a | |",
"| |- A | 3 (100.0%) |",
"| |- B | 0 (0.0%) |",
"|2 |a | |",
"| |- A | 1 (33.3%) |",
"| |- B | 2 (66.7%) |"
)
)
})
###########################################################################################################
#### Change totals/p-values
###########################################################################################################
test_that("A two-LHS tableby call--no p-value, no total", {
expect_identical(
capture.kable(summary(tableby(list(Group, ethan) ~ Age + Sex, data = mdat, strata = trt), test = FALSE, total = FALSE, text = TRUE)),
capture.kable(summary(tableby(list(Group, ethan) ~ Age + Sex, data = mdat, strata = trt, test = FALSE, total = FALSE), text = TRUE))
)
})
###########################################################################################################
#### Other warnings and tests and things...
###########################################################################################################
test_that("Certain functions don't work with multiple LHS or strata", {
expect_error(padjust(tableby(list(Group, ethan) ~ Age + Sex, data = mdat)), "with strata or multiple")
expect_error(padjust(tableby(Group ~ Age + Sex, data = mdat, strata = trt)), "with strata or multiple")
expect_error(sort(tableby(list(Group, ethan) ~ Age + Sex, data = mdat)), "with strata or multiple")
expect_error(sort(tableby(Group ~ Age + Sex, data = mdat, strata = trt)), "with strata or multiple")
})
test_that("Using cat.simplify", {
expect_identical(
capture.kable(summary(tableby(list(Group, ethan) ~ Sex + Age, data = mdat, cat.simplify = TRUE,
numeric.simplify = TRUE, numeric.stats = "meansd"), text = TRUE)),
c("| | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value|",
"|:------------|:--------------:|:--------------:|:--------------:|:--------------:|-------:|",
"|Sex | 15 (50.0%) | 13 (43.3%) | 16 (53.3%) | 44 (48.9%) | 0.733|",
"|Age in Years | 40.033 (6.217) | 39.633 (3.873) | 39.433 (5.569) | 39.700 (5.258) | 0.906|",
"" ,
"" ,
"| | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value|" ,
"|:------------|:--------------:|:--------------:|:--------------:|-------:|" ,
"|Sex | 24 (57.1%) | 18 (40.0%) | 42 (48.3%) | 0.110|" ,
"|Age in Years | 38.857 (5.201) | 40.200 (5.225) | 39.552 (5.227) | 0.233|"
)
)
expect_identical(
capture.kable(summary(tableby(list(Group, ethan) ~ Sex + Age, strata = trt, data = mdat, cat.simplify = TRUE,
numeric.simplify = TRUE, numeric.stats = "meansd"), text = TRUE)),
c("|Treatment Arm | | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:-------------|:------------|:--------------:|:--------------:|:--------------:|:--------------:|:-------:|",
"|A |Sex | 7 (50.0%) | 4 (36.4%) | 6 (54.5%) | 17 (47.2%) | 0.670 |",
"| |Age in Years | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | 0.918 |",
"|B |Sex | 8 (50.0%) | 9 (47.4%) | 10 (52.6%) | 27 (50.0%) | 0.949 |",
"| |Age in Years | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | 0.960 |",
"" ,
"" ,
"|Treatment Arm | | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value |" ,
"|:-------------|:------------|:--------------:|:--------------:|:--------------:|:-------:|" ,
"|A |Sex | 10 (58.8%) | 5 (31.2%) | 15 (45.5%) | 0.112 |" ,
"| |Age in Years | 37.647 (5.689) | 42.938 (3.924) | 40.212 (5.533) | 0.004 |" ,
"|B |Sex | 14 (56.0%) | 13 (44.8%) | 27 (50.0%) | 0.413 |" ,
"| |Age in Years | 39.680 (4.785) | 38.690 (5.292) | 39.148 (5.041) | 0.477 |"
)
)
})
test_that("Reordering variables and subsetting", {
tmp.tab <- tableby(list(Group, ethan) ~ fe(Sex) + dt + Age, strata = trt, data = mdat)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2), 2:1], text = TRUE)),
capture.kable(summary(tableby(list(ethan, Group) ~ Age + fe(Sex) + dt, strata = trt, data = mdat), text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2)], text = TRUE)),
capture.kable(summary(tmp.tab[c("Age", "Sex", "dt")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2:1], text = TRUE)),
capture.kable(summary(tmp.tab[, c("ethan", "Group")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[1:2], text = TRUE)),
capture.kable(summary(tmp.tab[c(TRUE, TRUE, FALSE)], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2], text = TRUE)),
capture.kable(summary(tmp.tab[, c(FALSE, TRUE)], text = TRUE))
)
expect_warning(tmp.tab[1:4], "Some indices not found")
expect_warning(tmp.tab[, 1:3], "Some indices not found")
expect_error(tmp.tab[TRUE], "Logical vector")
expect_error(tmp.tab[, TRUE], "Logical vector")
})
test_that("Merging tableby objects", {
skip_if_not_installed("coin")
tb1 <- tableby(list(Group, ethan) ~ Sex + Phase, strata = trt, data = mdat)
tb2 <- tableby(list(Group.fac, status) ~ Age, strata = trt, data = mdat)
tb3 <- tableby(list(Group, Group.fac, ethan) ~ Age + dt, strata = trt, data = mdat)
tb4 <- tableby(list(Group, ethan) ~ Sex + Phase + Age + dt, strata = trt, data = mdat)
expect_error(merge(tb1, tb2), "No terms in common")
expect_identical(
capture.kable(summary(merge(tb1, tb2, all = TRUE))),
c(capture.kable(summary(tb1)), "", "", capture.kable(summary(tb2)))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all.x = TRUE), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all = TRUE), text = TRUE)),
c(
capture.kable(summary(tb4, text = TRUE)), "", "",
capture.kable(summary(tableby(Group.fac ~ Age + dt, data = mdat, strata = trt), text = TRUE))
)
)
})
test_that("Changing labels", {
tb <- tableby(list(Group, ethan) ~ Sex + Age, strata = trt, data = mdat)
expect_warning(labels(tb) <- c(hi = "hi", Sex = "Sex label", Age = "Age at event", trt = "Trt Arm", ethan = "EthanH", Group = "Grp"), NA)
expect_identical(
capture.kable(summary(tb, text = TRUE, term.name = TRUE)),
c("|Trt Arm |Grp | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:-------|:------------|:---------------:|:---------------:|:---------------:|:---------------:|:-------:|",
"|A |Sex label | | | | | 0.670 |",
"| |- Female | 7 (50.0%) | 7 (63.6%) | 5 (45.5%) | 19 (52.8%) | |",
"| |- Male | 7 (50.0%) | 4 (36.4%) | 6 (54.5%) | 17 (47.2%) | |",
"| |Age at event | | | | | 0.918 |",
"| |- Mean (SD) | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | |",
"| |- Range | 29.000 - 53.000 | 33.000 - 48.000 | 30.000 - 49.000 | 29.000 - 53.000 | |",
"|B |Sex label | | | | | 0.949 |",
"| |- Female | 8 (50.0%) | 10 (52.6%) | 9 (47.4%) | 27 (50.0%) | |",
"| |- Male | 8 (50.0%) | 9 (47.4%) | 10 (52.6%) | 27 (50.0%) | |",
"| |Age at event | | | | | 0.960 |",
"| |- Mean (SD) | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | |",
"| |- Range | 30.000 - 49.000 | 32.000 - 47.000 | 30.000 - 52.000 | 30.000 - 52.000 | |",
"" ,
"" ,
"|Trt Arm |EthanH | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value |" ,
"|:-------|:------------|:---------------:|:---------------:|:---------------:|:-------:|" ,
"|A |Sex label | | | | 0.112 |" ,
"| |- Female | 7 (41.2%) | 11 (68.8%) | 18 (54.5%) | |" ,
"| |- Male | 10 (58.8%) | 5 (31.2%) | 15 (45.5%) | |" ,
"| |Age at event | | | | 0.004 |" ,
"| |- Mean (SD) | 37.647 (5.689) | 42.938 (3.924) | 40.212 (5.533) | |" ,
"| |- Range | 29.000 - 53.000 | 36.000 - 49.000 | 29.000 - 53.000 | |" ,
"|B |Sex label | | | | 0.413 |" ,
"| |- Female | 11 (44.0%) | 16 (55.2%) | 27 (50.0%) | |" ,
"| |- Male | 14 (56.0%) | 13 (44.8%) | 27 (50.0%) | |" ,
"| |Age at event | | | | 0.477 |" ,
"| |- Mean (SD) | 39.680 (4.785) | 38.690 (5.292) | 39.148 (5.041) | |" ,
"| |- Range | 30.000 - 48.000 | 30.000 - 52.000 | 30.000 - 52.000 | |"
)
)
labels(tb) <- NULL
expect_identical(
capture.kable(summary(tb, text = TRUE, term.name = TRUE)),
c("|trt |Group | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:---|:------------|:---------------:|:---------------:|:---------------:|:---------------:|:-------:|",
"|A |Sex | | | | | 0.670 |",
"| |- Female | 7 (50.0%) | 7 (63.6%) | 5 (45.5%) | 19 (52.8%) | |",
"| |- Male | 7 (50.0%) | 4 (36.4%) | 6 (54.5%) | 17 (47.2%) | |",
"| |Age | | | | | 0.918 |",
"| |- Mean (SD) | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | |",
"| |- Range | 29.000 - 53.000 | 33.000 - 48.000 | 30.000 - 49.000 | 29.000 - 53.000 | |",
"|B |Sex | | | | | 0.949 |",
"| |- Female | 8 (50.0%) | 10 (52.6%) | 9 (47.4%) | 27 (50.0%) | |",
"| |- Male | 8 (50.0%) | 9 (47.4%) | 10 (52.6%) | 27 (50.0%) | |",
"| |Age | | | | | 0.960 |",
"| |- Mean (SD) | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | |",
"| |- Range | 30.000 - 49.000 | 32.000 - 47.000 | 30.000 - 52.000 | 30.000 - 52.000 | |",
"" ,
"" ,
"|trt |ethan | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value |" ,
"|:---|:------------|:---------------:|:---------------:|:---------------:|:-------:|" ,
"|A |Sex | | | | 0.112 |" ,
"| |- Female | 7 (41.2%) | 11 (68.8%) | 18 (54.5%) | |" ,
"| |- Male | 10 (58.8%) | 5 (31.2%) | 15 (45.5%) | |" ,
"| |Age | | | | 0.004 |" ,
"| |- Mean (SD) | 37.647 (5.689) | 42.938 (3.924) | 40.212 (5.533) | |" ,
"| |- Range | 29.000 - 53.000 | 36.000 - 49.000 | 29.000 - 53.000 | |" ,
"|B |Sex | | | | 0.413 |" ,
"| |- Female | 11 (44.0%) | 16 (55.2%) | 27 (50.0%) | |" ,
"| |- Male | 14 (56.0%) | 13 (44.8%) | 27 (50.0%) | |" ,
"| |Age | | | | 0.477 |" ,
"| |- Mean (SD) | 39.680 (4.785) | 38.690 (5.292) | 39.148 (5.041) | |" ,
"| |- Range | 30.000 - 48.000 | 30.000 - 52.000 | 30.000 - 52.000 | |"
)
)
})
###########################################################################################################
#### Reported bugs for tableby
###########################################################################################################
test_that("02/23/2018: wrapping long labels (#59)", {
labs <- list(
Group = "This is a really long label for the Group variable",
time = "Another really long label. Can you believe how long this is",
dt = "ThisLabelHasNoSpacesSoLetsSeeHowItBehaves",
trt = NULL
)
expect_identical(
capture.kable(print(summary(tableby(Sex ~ Group + time + dt, strata = trt, data = set_labels(mdat, labs)), text = TRUE), width = 30)),
c("|trt | | Female (N=46) | Male (N=44) | Total (N=90) | p value |",
"|:---|:------------------------------|:-----------------------:|:-----------------------:|:-----------------------:|:-------:|",
"|A |This is a really long label | | | | 0.670 |",
"| |for the Group variable | | | | |",
"| |- High | 7 (36.8%) | 7 (41.2%) | 14 (38.9%) | |",
"| |- Low | 7 (36.8%) | 4 (23.5%) | 11 (30.6%) | |",
"| |- Med | 5 (26.3%) | 6 (35.3%) | 11 (30.6%) | |",
"| |Another really long label. | | | | 0.831 |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |- Mean (SD) | 3.895 (1.560) | 3.765 (2.047) | 3.833 (1.781) | |",
"| |- Range | 1.000 - 6.000 | 0.000 - 7.000 | 0.000 - 7.000 | |",
"| |ThisLabelHasNoSpacesSoLetsSeeH | | | | 0.669 |",
"| |owItBehaves | | | | |",
"| |- Median | 1949-11-01 | 1950-02-06 | 1949-12-19 | |",
"| |- Range | 1939-04-01 - 1959-09-06 | 1939-04-03 - 1968-05-14 | 1939-04-01 - 1968-05-14 | |",
"|B |This is a really long label | | | | 0.949 |",
"| |for the Group variable | | | | |",
"| |- High | 8 (29.6%) | 8 (29.6%) | 16 (29.6%) | |",
"| |- Low | 10 (37.0%) | 9 (33.3%) | 19 (35.2%) | |",
"| |- Med | 9 (33.3%) | 10 (37.0%) | 19 (35.2%) | |",
"| |Another really long label. | | | | 0.118 |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |- Mean (SD) | 3.407 (2.153) | 4.333 (2.130) | 3.870 (2.172) | |",
"| |- Range | 0.000 - 7.000 | 0.000 - 7.000 | 0.000 - 7.000 | |",
"| |ThisLabelHasNoSpacesSoLetsSeeH | | | | 0.102 |",
"| |owItBehaves | | | | |",
"| |- Median | 1948-05-31 | 1951-03-31 | 1949-09-09 | |",
"| |- Range | 1935-08-15 - 1957-08-15 | 1937-02-08 - 1958-07-30 | 1935-08-15 - 1958-07-30 | |"
)
)
})
test_that("strata with includeNA()", {
expect_identical(
capture.kable(summary(tableby(list(sex, arm) ~ age, data = mockstudy, strata = includeNA(mdquality.s, "NA")),
text = TRUE, labelTranslations = c('includeNA(mdquality.s, "NA")' = "QOL"))),
c("|QOL | | Male (N=916) | Female (N=583) | Total (N=1499) | p value |" ,
"|:---|:------------|:---------------:|:---------------:|:---------------:|:-------:|" ,
"|0 |Age in Years | | | | 0.648 |" ,
"| |- Mean (SD) | 59.714 (12.246) | 60.702 (10.634) | 60.089 (11.627) | |" ,
"| |- Range | 29.000 - 82.000 | 35.000 - 81.000 | 29.000 - 82.000 | |" ,
"|1 |Age in Years | | | | 0.013 |" ,
"| |- Mean (SD) | 60.445 (11.447) | 58.693 (11.611) | 59.763 (11.537) | |" ,
"| |- Range | 19.000 - 88.000 | 26.000 - 88.000 | 19.000 - 88.000 | |" ,
"|NA |Age in Years | | | | 0.933 |" ,
"| |- Mean (SD) | 60.876 (10.589) | 61.000 (12.557) | 60.925 (11.379) | |" ,
"| |- Range | 36.000 - 85.000 | 22.000 - 81.000 | 22.000 - 85.000 | |" ,
"" ,
"" ,
"|QOL | | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value |",
"|:---|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|:-------:|",
"|0 |Age in Years | | | | | 0.238 |",
"| |- Mean (SD) | 58.317 (11.869) | 62.154 (11.037) | 58.968 (12.098) | 60.089 (11.627) | |",
"| |- Range | 30.000 - 79.000 | 41.000 - 82.000 | 29.000 - 76.000 | 29.000 - 82.000 | |",
"|1 |Age in Years | | | | | 0.891 |",
"| |- Mean (SD) | 59.560 (11.279) | 59.944 (11.663) | 59.698 (11.647) | 59.763 (11.537) | |",
"| |- Range | 28.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |",
"|NA |Age in Years | | | | | 0.949 |",
"| |- Mean (SD) | 61.364 (11.522) | 60.788 (11.725) | 60.854 (10.009) | 60.925 (11.379) | |",
"| |- Range | 27.000 - 81.000 | 22.000 - 85.000 | 40.000 - 81.000 | 22.000 - 85.000 | |"
)
)
})
####################################################
test_that("01/31/2019: modpval.tableby (#174, #175)", {
tmp <- tableby(sex ~ age + arm, data = mockstudy, strata = fu.stat, test = FALSE)
expect_true(!any(c("test", "p.value") %in% names(as.data.frame(tmp))))
tmp <- modpval.tableby(tmp, data.frame(y = "sex", strata = c("1", "2"), x = c("age", "arm"), p = c(1, 0.5)), use.pname = TRUE)
expect_identical(
capture.kable(summary(tmp, pfootnote = TRUE, text = TRUE)),
c("|fu.stat | | Male (N=916) | Female (N=583) | Total (N=1499) | p |",
"|:-------|:-------------|:---------------:|:---------------:|:---------------:|:---------:|",
"|1 |Age in Years | | | | 1.000 (1) |",
"| |- Mean (SD) | 58.253 (12.048) | 61.018 (10.649) | 59.336 (11.561) | |",
"| |- Range | 32.000 - 85.000 | 35.000 - 80.000 | 32.000 - 85.000 | |",
"| |Treatment Arm | | | | |",
"| |- A: IFL | 14 (16.1%) | 4 (7.1%) | 18 (12.6%) | |",
"| |- F: FOLFOX | 56 (64.4%) | 43 (76.8%) | 99 (69.2%) | |",
"| |- G: IROX | 17 (19.5%) | 9 (16.1%) | 26 (18.2%) | |",
"|2 |Age in Years | | | | |",
"| |- Mean (SD) | 60.686 (11.278) | 59.059 (11.824) | 60.054 (11.516) | |",
"| |- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |",
"| |Treatment Arm | | | | 0.500 (1) |",
"| |- A: IFL | 263 (31.7%) | 147 (27.9%) | 410 (30.2%) | |",
"| |- F: FOLFOX | 355 (42.8%) | 237 (45.0%) | 592 (43.7%) | |",
"| |- G: IROX | 211 (25.5%) | 143 (27.1%) | 354 (26.1%) | |",
"1. Modified by user"
)
)
})
test_that("05/20/2019: non-alphabetical strata with missing values (#215)", {
dat <- data.frame(
strat = factor(rep(1:2, each = 5), levels = 2:1),
a = c("a", "a", "a", "b", NA, "b", "a", "b", "a", "b")
)
expect_identical(
capture.kable(summary(tableby(~ a, data = dat, strata = strat))),
c("|strat | | Overall (N=10) |",
"|:-----|:------------------------|:--------------:|",
"|2 |**a** | |",
"| | a | 2 (40.0%) |",
"| | b | 3 (60.0%) |",
"|1 |**a** | |",
"| | N-Miss | 1 |",
"| | a | 3 (75.0%) |",
"| | b | 1 (25.0%) |"
)
)
})
test_that("06/11/2019: retaining control.list with merge() (#221)", {
tab1 <- tableby(sex ~ age, data = mockstudy)
tab2 <- tableby(sex ~ anova(ps, digits = 0), data = mockstudy)
# this also doesn't work... I'm planning to fix this
expect_identical(
capture.kable(summary(merge(tab1, tab2))),
capture.kable(summary(merge(tab2, tab1)[2:1]))
)
expect_identical(
capture.kable(summary(merge(tab1, tab2), text = TRUE)),
c("| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|",
"|:------------|:---------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | 0.048|",
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |",
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |",
"|ps | | | | 0.345|",
"|- N-Miss | 162 | 104 | 266 | |",
"|- Mean (SD) | 1 (1) | 1 (1) | 1 (1) | |",
"|- Range | 0 - 2 | 0 - 2 | 0 - 2 | |"
)
)
})
test_that("Multiple labels work (#310)", {
tb <- tableby(list(sex, arm) ~ age, data = mockstudy)
expect_identical(
capture.kable(summary(tb, title = "Just one", text=TRUE)),
c("Table: Just one" ,
"" ,
"| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|" ,
"|:------------|:---------------:|:---------------:|:---------------:|-------:|" ,
"|Age in Years | | | | 0.048|" ,
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |" ,
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |" ,
"" ,
"" ,
"| | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value|",
"|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | | 0.614|",
"|- Mean (SD) | 59.673 (11.365) | 60.301 (11.632) | 59.763 (11.499) | 59.985 (11.519) | |",
"|- Range | 27.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |"
)
)
expect_identical(
capture.kable(summary(tb, title = c("Just one", "both"), text=TRUE)),
c("Table: Just one" ,
"" ,
"| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|" ,
"|:------------|:---------------:|:---------------:|:---------------:|-------:|" ,
"|Age in Years | | | | 0.048|" ,
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |" ,
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |" ,
"" ,
"" ,
"Table: both" ,
"" ,
"| | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value|",
"|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | | 0.614|",
"|- Mean (SD) | 59.673 (11.365) | 60.301 (11.632) | 59.763 (11.499) | 59.985 (11.519) | |",
"|- Range | 27.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |"
)
)
expect_identical(
capture.kable(summary(tb, title = list(NULL, "both"), text=TRUE)),
c("| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|" ,
"|:------------|:---------------:|:---------------:|:---------------:|-------:|" ,
"|Age in Years | | | | 0.048|" ,
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |" ,
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |" ,
"" ,
"" ,
"Table: both" ,
"" ,
"| | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value|",
"|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | | 0.614|",
"|- Mean (SD) | 59.673 (11.365) | 60.301 (11.632) | 59.763 (11.499) | 59.985 (11.519) | |",
"|- Range | 27.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |"
)
)
})
test_that("total.pos = 'before' (#320)", {
expect_identical(
capture.kable(summary(tableby(sex ~ age, data = mockstudy, strata = arm, total.pos = "before"), text = TRUE)),
c("|Treatment Arm | | Total (N=1499) | Male (N=916) | Female (N=583) | p value |",
"|:-------------|:------------|:---------------:|:---------------:|:---------------:|:-------:|",
"|A: IFL |Age in Years | | | | 0.572 |",
"| |- Mean (SD) | 59.673 (11.365) | 59.903 (11.347) | 59.252 (11.422) | |",
"| |- Range | 27.000 - 88.000 | 28.000 - 83.000 | 27.000 - 88.000 | |",
"|F: FOLFOX |Age in Years | | | | 0.286 |",
"| |- Mean (SD) | 60.301 (11.632) | 60.691 (11.598) | 59.729 (11.679) | |",
"| |- Range | 19.000 - 88.000 | 19.000 - 88.000 | 22.000 - 83.000 | |",
"|G: IROX |Age in Years | | | | 0.051 |",
"| |- Mean (SD) | 59.763 (11.499) | 60.702 (10.999) | 58.355 (12.113) | |",
"| |- Range | 26.000 - 85.000 | 29.000 - 85.000 | 26.000 - 82.000 | |"
)
)
})
test_that("cat.droplevels (#318)", {
d <- data.frame(
z = rep(LETTERS[1:3], each = 10),
x = rep(c("a", "b", "b"), each = 10),
y = rep(LETTERS[1:3], times = 10),
stringsAsFactors = FALSE
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = FALSE), text = TRUE)),
c("|z | | A (N=10) | B (N=10) | C (N=10) | Total (N=30) | p value |",
"|:--|:----|:----------:|:----------:|:----------:|:------------:|:-------:|",
"|A |x | | | | | |",
"| |- a | 4 (100.0%) | 3 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"| |- b | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |",
"|B |x | | | | | |",
"| |- a | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |",
"| |- b | 3 (100.0%) | 4 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"|C |x | | | | | |",
"| |- a | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |",
"| |- b | 3 (100.0%) | 3 (100.0%) | 4 (100.0%) | 10 (100.0%) | |"
)
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE), text = TRUE)),
c("|z | | A (N=10) | B (N=10) | C (N=10) | Total (N=30) | p value |",
"|:--|:----|:----------:|:----------:|:----------:|:------------:|:-------:|",
"|A |x | | | | | |",
"| |- a | 4 (100.0%) | 3 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"|B |x | | | | | |",
"| |- b | 3 (100.0%) | 4 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"|C |x | | | | | |",
"| |- b | 3 (100.0%) | 3 (100.0%) | 4 (100.0%) | 10 (100.0%) | |"
)
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE), text = TRUE)),
capture.kable(summary(tableby(y ~ chisq(x, cat.droplevels = TRUE), data = d, strata = z), text = TRUE))
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE, test.always = TRUE), text = TRUE)),
capture.kable(summary(tableby(y ~ chisq(x, cat.droplevels = TRUE), data = d, strata = z, test.always = TRUE), text = TRUE))
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE, test.always = TRUE), text = TRUE)),
capture.kable(summary(tableby(y ~ x, data = d, strata = z, test.always = TRUE), text = TRUE))[c(1:4, 6, 8:9, 11)]
)
})
eheinzen/arsenal documentation built on Sept. 11, 2022, 10:59 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## Tests for tableby
context("Testing the tableby strata and multiple LHS output")
# "mdat" now defined in helper-data.R
###########################################################################################################
#### Basic two-sided tableby
###########################################################################################################
test_that("A three-LHS tableby call", {
skip_if_not_installed("coin")
expect_identical(
capture.kable(summary(tableby(list(Group, trt, ethan) ~ Sex + time + dt + Phase, data = mdat), text = TRUE)),
c(
capture.kable(summary(tableby(Group ~ Sex + time + dt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(tableby(trt ~ Sex + time + dt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(tableby(ethan ~ Sex + time + dt + Phase, data = mdat), text = TRUE))
)
)
})
test_that("A tableby call with strata", {
skip_if_not_installed("coin")
expect_identical(
capture.kable(summary(tableby(Group ~ Age + time + Phase, data = mdat, strata = trt), text = TRUE)),
c("|Treatment Arm | | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:-------------|:------------|:---------------:|:---------------:|:---------------:|:---------------:|:-------:|",
"|A |Age in Years | | | | | 0.918 |",
"| |- Mean (SD) | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | |",
"| |- Range | 29.000 - 53.000 | 33.000 - 48.000 | 30.000 - 49.000 | 29.000 - 53.000 | |",
"| |time | | | | | 0.319 |",
"| |- Mean (SD) | 4.357 (1.865) | 3.273 (1.421) | 3.727 (1.954) | 3.833 (1.781) | |",
"| |- Range | 0.000 - 6.000 | 1.000 - 5.000 | 1.000 - 7.000 | 0.000 - 7.000 | |",
"| |Phase | | | | | 0.506 |",
"| |- I | 6 (42.9%) | 2 (18.2%) | 0 (0.0%) | 8 (22.2%) | |",
"| |- II | 3 (21.4%) | 6 (54.5%) | 8 (72.7%) | 17 (47.2%) | |",
"| |- III | 5 (35.7%) | 3 (27.3%) | 3 (27.3%) | 11 (30.6%) | |",
"|B |Age in Years | | | | | 0.960 |",
"| |- Mean (SD) | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | |",
"| |- Range | 30.000 - 49.000 | 32.000 - 47.000 | 30.000 - 52.000 | 30.000 - 52.000 | |",
"| |time | | | | | 0.081 |",
"| |- Mean (SD) | 4.750 (1.807) | 3.105 (2.355) | 3.895 (2.079) | 3.870 (2.172) | |",
"| |- Range | 1.000 - 7.000 | 0.000 - 6.000 | 1.000 - 7.000 | 0.000 - 7.000 | |",
"| |Phase | | | | | 0.005 |",
"| |- I | 5 (31.2%) | 10 (52.6%) | 0 (0.0%) | 15 (27.8%) | |",
"| |- II | 7 (43.8%) | 6 (31.6%) | 11 (57.9%) | 24 (44.4%) | |",
"| |- III | 4 (25.0%) | 3 (15.8%) | 8 (42.1%) | 15 (27.8%) | |"
)
)
expect_equal(
xtfrm(tableby(Group ~ Age + time + Phase, data = mdat, strata = trt)),
c(
xtfrm(tableby(Group ~ Age + time + Phase, data = mdat, subset = trt == "A")),
xtfrm(tableby(Group ~ Age + time + Phase, data = mdat, subset = trt == "B"))
)
)
})
test_that("strata levels are maintained", {
dat <- data.frame(a = c("A", "A", "A", "B", "A", "B"), b = c(1, 1, 1, 2, 2, 2), stringsAsFactors = FALSE)
expect_identical(
capture.kable(summary(tableby(~ a, strata = b, data = dat), text = TRUE)),
c("|b | | Overall (N=6) |",
"|:--|:----|:-------------:|",
"|1 |a | |",
"| |- A | 3 (100.0%) |",
"| |- B | 0 (0.0%) |",
"|2 |a | |",
"| |- A | 1 (33.3%) |",
"| |- B | 2 (66.7%) |"
)
)
})
###########################################################################################################
#### Change totals/p-values
###########################################################################################################
test_that("A two-LHS tableby call--no p-value, no total", {
expect_identical(
capture.kable(summary(tableby(list(Group, ethan) ~ Age + Sex, data = mdat, strata = trt), test = FALSE, total = FALSE, text = TRUE)),
capture.kable(summary(tableby(list(Group, ethan) ~ Age + Sex, data = mdat, strata = trt, test = FALSE, total = FALSE), text = TRUE))
)
})
###########################################################################################################
#### Other warnings and tests and things...
###########################################################################################################
test_that("Certain functions don't work with multiple LHS or strata", {
expect_error(padjust(tableby(list(Group, ethan) ~ Age + Sex, data = mdat)), "with strata or multiple")
expect_error(padjust(tableby(Group ~ Age + Sex, data = mdat, strata = trt)), "with strata or multiple")
expect_error(sort(tableby(list(Group, ethan) ~ Age + Sex, data = mdat)), "with strata or multiple")
expect_error(sort(tableby(Group ~ Age + Sex, data = mdat, strata = trt)), "with strata or multiple")
})
test_that("Using cat.simplify", {
expect_identical(
capture.kable(summary(tableby(list(Group, ethan) ~ Sex + Age, data = mdat, cat.simplify = TRUE,
numeric.simplify = TRUE, numeric.stats = "meansd"), text = TRUE)),
c("| | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value|",
"|:------------|:--------------:|:--------------:|:--------------:|:--------------:|-------:|",
"|Sex | 15 (50.0%) | 13 (43.3%) | 16 (53.3%) | 44 (48.9%) | 0.733|",
"|Age in Years | 40.033 (6.217) | 39.633 (3.873) | 39.433 (5.569) | 39.700 (5.258) | 0.906|",
"" ,
"" ,
"| | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value|" ,
"|:------------|:--------------:|:--------------:|:--------------:|-------:|" ,
"|Sex | 24 (57.1%) | 18 (40.0%) | 42 (48.3%) | 0.110|" ,
"|Age in Years | 38.857 (5.201) | 40.200 (5.225) | 39.552 (5.227) | 0.233|"
)
)
expect_identical(
capture.kable(summary(tableby(list(Group, ethan) ~ Sex + Age, strata = trt, data = mdat, cat.simplify = TRUE,
numeric.simplify = TRUE, numeric.stats = "meansd"), text = TRUE)),
c("|Treatment Arm | | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:-------------|:------------|:--------------:|:--------------:|:--------------:|:--------------:|:-------:|",
"|A |Sex | 7 (50.0%) | 4 (36.4%) | 6 (54.5%) | 17 (47.2%) | 0.670 |",
"| |Age in Years | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | 0.918 |",
"|B |Sex | 8 (50.0%) | 9 (47.4%) | 10 (52.6%) | 27 (50.0%) | 0.949 |",
"| |Age in Years | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | 0.960 |",
"" ,
"" ,
"|Treatment Arm | | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value |" ,
"|:-------------|:------------|:--------------:|:--------------:|:--------------:|:-------:|" ,
"|A |Sex | 10 (58.8%) | 5 (31.2%) | 15 (45.5%) | 0.112 |" ,
"| |Age in Years | 37.647 (5.689) | 42.938 (3.924) | 40.212 (5.533) | 0.004 |" ,
"|B |Sex | 14 (56.0%) | 13 (44.8%) | 27 (50.0%) | 0.413 |" ,
"| |Age in Years | 39.680 (4.785) | 38.690 (5.292) | 39.148 (5.041) | 0.477 |"
)
)
})
test_that("Reordering variables and subsetting", {
tmp.tab <- tableby(list(Group, ethan) ~ fe(Sex) + dt + Age, strata = trt, data = mdat)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2), 2:1], text = TRUE)),
capture.kable(summary(tableby(list(ethan, Group) ~ Age + fe(Sex) + dt, strata = trt, data = mdat), text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2)], text = TRUE)),
capture.kable(summary(tmp.tab[c("Age", "Sex", "dt")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2:1], text = TRUE)),
capture.kable(summary(tmp.tab[, c("ethan", "Group")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[1:2], text = TRUE)),
capture.kable(summary(tmp.tab[c(TRUE, TRUE, FALSE)], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2], text = TRUE)),
capture.kable(summary(tmp.tab[, c(FALSE, TRUE)], text = TRUE))
)
expect_warning(tmp.tab[1:4], "Some indices not found")
expect_warning(tmp.tab[, 1:3], "Some indices not found")
expect_error(tmp.tab[TRUE], "Logical vector")
expect_error(tmp.tab[, TRUE], "Logical vector")
})
test_that("Merging tableby objects", {
skip_if_not_installed("coin")
tb1 <- tableby(list(Group, ethan) ~ Sex + Phase, strata = trt, data = mdat)
tb2 <- tableby(list(Group.fac, status) ~ Age, strata = trt, data = mdat)
tb3 <- tableby(list(Group, Group.fac, ethan) ~ Age + dt, strata = trt, data = mdat)
tb4 <- tableby(list(Group, ethan) ~ Sex + Phase + Age + dt, strata = trt, data = mdat)
expect_error(merge(tb1, tb2), "No terms in common")
expect_identical(
capture.kable(summary(merge(tb1, tb2, all = TRUE))),
c(capture.kable(summary(tb1)), "", "", capture.kable(summary(tb2)))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all.x = TRUE), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all = TRUE), text = TRUE)),
c(
capture.kable(summary(tb4, text = TRUE)), "", "",
capture.kable(summary(tableby(Group.fac ~ Age + dt, data = mdat, strata = trt), text = TRUE))
)
)
})
test_that("Changing labels", {
tb <- tableby(list(Group, ethan) ~ Sex + Age, strata = trt, data = mdat)
expect_warning(labels(tb) <- c(hi = "hi", Sex = "Sex label", Age = "Age at event", trt = "Trt Arm", ethan = "EthanH", Group = "Grp"), NA)
expect_identical(
capture.kable(summary(tb, text = TRUE, term.name = TRUE)),
c("|Trt Arm |Grp | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:-------|:------------|:---------------:|:---------------:|:---------------:|:---------------:|:-------:|",
"|A |Sex label | | | | | 0.670 |",
"| |- Female | 7 (50.0%) | 7 (63.6%) | 5 (45.5%) | 19 (52.8%) | |",
"| |- Male | 7 (50.0%) | 4 (36.4%) | 6 (54.5%) | 17 (47.2%) | |",
"| |Age at event | | | | | 0.918 |",
"| |- Mean (SD) | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | |",
"| |- Range | 29.000 - 53.000 | 33.000 - 48.000 | 30.000 - 49.000 | 29.000 - 53.000 | |",
"|B |Sex label | | | | | 0.949 |",
"| |- Female | 8 (50.0%) | 10 (52.6%) | 9 (47.4%) | 27 (50.0%) | |",
"| |- Male | 8 (50.0%) | 9 (47.4%) | 10 (52.6%) | 27 (50.0%) | |",
"| |Age at event | | | | | 0.960 |",
"| |- Mean (SD) | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | |",
"| |- Range | 30.000 - 49.000 | 32.000 - 47.000 | 30.000 - 52.000 | 30.000 - 52.000 | |",
"" ,
"" ,
"|Trt Arm |EthanH | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value |" ,
"|:-------|:------------|:---------------:|:---------------:|:---------------:|:-------:|" ,
"|A |Sex label | | | | 0.112 |" ,
"| |- Female | 7 (41.2%) | 11 (68.8%) | 18 (54.5%) | |" ,
"| |- Male | 10 (58.8%) | 5 (31.2%) | 15 (45.5%) | |" ,
"| |Age at event | | | | 0.004 |" ,
"| |- Mean (SD) | 37.647 (5.689) | 42.938 (3.924) | 40.212 (5.533) | |" ,
"| |- Range | 29.000 - 53.000 | 36.000 - 49.000 | 29.000 - 53.000 | |" ,
"|B |Sex label | | | | 0.413 |" ,
"| |- Female | 11 (44.0%) | 16 (55.2%) | 27 (50.0%) | |" ,
"| |- Male | 14 (56.0%) | 13 (44.8%) | 27 (50.0%) | |" ,
"| |Age at event | | | | 0.477 |" ,
"| |- Mean (SD) | 39.680 (4.785) | 38.690 (5.292) | 39.148 (5.041) | |" ,
"| |- Range | 30.000 - 48.000 | 30.000 - 52.000 | 30.000 - 52.000 | |"
)
)
labels(tb) <- NULL
expect_identical(
capture.kable(summary(tb, text = TRUE, term.name = TRUE)),
c("|trt |Group | High (N=30) | Low (N=30) | Med (N=30) | Total (N=90) | p value |",
"|:---|:------------|:---------------:|:---------------:|:---------------:|:---------------:|:-------:|",
"|A |Sex | | | | | 0.670 |",
"| |- Female | 7 (50.0%) | 7 (63.6%) | 5 (45.5%) | 19 (52.8%) | |",
"| |- Male | 7 (50.0%) | 4 (36.4%) | 6 (54.5%) | 17 (47.2%) | |",
"| |Age | | | | | 0.918 |",
"| |- Mean (SD) | 41.000 (6.493) | 40.091 (4.571) | 40.364 (5.573) | 40.528 (5.537) | |",
"| |- Range | 29.000 - 53.000 | 33.000 - 48.000 | 30.000 - 49.000 | 29.000 - 53.000 | |",
"|B |Sex | | | | | 0.949 |",
"| |- Female | 8 (50.0%) | 10 (52.6%) | 9 (47.4%) | 27 (50.0%) | |",
"| |- Male | 8 (50.0%) | 9 (47.4%) | 10 (52.6%) | 27 (50.0%) | |",
"| |Age | | | | | 0.960 |",
"| |- Mean (SD) | 39.188 (6.047) | 39.368 (3.515) | 38.895 (5.646) | 39.148 (5.041) | |",
"| |- Range | 30.000 - 49.000 | 32.000 - 47.000 | 30.000 - 52.000 | 30.000 - 52.000 | |",
"" ,
"" ,
"|trt |ethan | Ethan (N=42) | Heinzen (N=45) | Total (N=87) | p value |" ,
"|:---|:------------|:---------------:|:---------------:|:---------------:|:-------:|" ,
"|A |Sex | | | | 0.112 |" ,
"| |- Female | 7 (41.2%) | 11 (68.8%) | 18 (54.5%) | |" ,
"| |- Male | 10 (58.8%) | 5 (31.2%) | 15 (45.5%) | |" ,
"| |Age | | | | 0.004 |" ,
"| |- Mean (SD) | 37.647 (5.689) | 42.938 (3.924) | 40.212 (5.533) | |" ,
"| |- Range | 29.000 - 53.000 | 36.000 - 49.000 | 29.000 - 53.000 | |" ,
"|B |Sex | | | | 0.413 |" ,
"| |- Female | 11 (44.0%) | 16 (55.2%) | 27 (50.0%) | |" ,
"| |- Male | 14 (56.0%) | 13 (44.8%) | 27 (50.0%) | |" ,
"| |Age | | | | 0.477 |" ,
"| |- Mean (SD) | 39.680 (4.785) | 38.690 (5.292) | 39.148 (5.041) | |" ,
"| |- Range | 30.000 - 48.000 | 30.000 - 52.000 | 30.000 - 52.000 | |"
)
)
})
###########################################################################################################
#### Reported bugs for tableby
###########################################################################################################
test_that("02/23/2018: wrapping long labels (#59)", {
labs <- list(
Group = "This is a really long label for the Group variable",
time = "Another really long label. Can you believe how long this is",
dt = "ThisLabelHasNoSpacesSoLetsSeeHowItBehaves",
trt = NULL
)
expect_identical(
capture.kable(print(summary(tableby(Sex ~ Group + time + dt, strata = trt, data = set_labels(mdat, labs)), text = TRUE), width = 30)),
c("|trt | | Female (N=46) | Male (N=44) | Total (N=90) | p value |",
"|:---|:------------------------------|:-----------------------:|:-----------------------:|:-----------------------:|:-------:|",
"|A |This is a really long label | | | | 0.670 |",
"| |for the Group variable | | | | |",
"| |- High | 7 (36.8%) | 7 (41.2%) | 14 (38.9%) | |",
"| |- Low | 7 (36.8%) | 4 (23.5%) | 11 (30.6%) | |",
"| |- Med | 5 (26.3%) | 6 (35.3%) | 11 (30.6%) | |",
"| |Another really long label. | | | | 0.831 |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |- Mean (SD) | 3.895 (1.560) | 3.765 (2.047) | 3.833 (1.781) | |",
"| |- Range | 1.000 - 6.000 | 0.000 - 7.000 | 0.000 - 7.000 | |",
"| |ThisLabelHasNoSpacesSoLetsSeeH | | | | 0.669 |",
"| |owItBehaves | | | | |",
"| |- Median | 1949-11-01 | 1950-02-06 | 1949-12-19 | |",
"| |- Range | 1939-04-01 - 1959-09-06 | 1939-04-03 - 1968-05-14 | 1939-04-01 - 1968-05-14 | |",
"|B |This is a really long label | | | | 0.949 |",
"| |for the Group variable | | | | |",
"| |- High | 8 (29.6%) | 8 (29.6%) | 16 (29.6%) | |",
"| |- Low | 10 (37.0%) | 9 (33.3%) | 19 (35.2%) | |",
"| |- Med | 9 (33.3%) | 10 (37.0%) | 19 (35.2%) | |",
"| |Another really long label. | | | | 0.118 |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |- Mean (SD) | 3.407 (2.153) | 4.333 (2.130) | 3.870 (2.172) | |",
"| |- Range | 0.000 - 7.000 | 0.000 - 7.000 | 0.000 - 7.000 | |",
"| |ThisLabelHasNoSpacesSoLetsSeeH | | | | 0.102 |",
"| |owItBehaves | | | | |",
"| |- Median | 1948-05-31 | 1951-03-31 | 1949-09-09 | |",
"| |- Range | 1935-08-15 - 1957-08-15 | 1937-02-08 - 1958-07-30 | 1935-08-15 - 1958-07-30 | |"
)
)
})
test_that("strata with includeNA()", {
expect_identical(
capture.kable(summary(tableby(list(sex, arm) ~ age, data = mockstudy, strata = includeNA(mdquality.s, "NA")),
text = TRUE, labelTranslations = c('includeNA(mdquality.s, "NA")' = "QOL"))),
c("|QOL | | Male (N=916) | Female (N=583) | Total (N=1499) | p value |" ,
"|:---|:------------|:---------------:|:---------------:|:---------------:|:-------:|" ,
"|0 |Age in Years | | | | 0.648 |" ,
"| |- Mean (SD) | 59.714 (12.246) | 60.702 (10.634) | 60.089 (11.627) | |" ,
"| |- Range | 29.000 - 82.000 | 35.000 - 81.000 | 29.000 - 82.000 | |" ,
"|1 |Age in Years | | | | 0.013 |" ,
"| |- Mean (SD) | 60.445 (11.447) | 58.693 (11.611) | 59.763 (11.537) | |" ,
"| |- Range | 19.000 - 88.000 | 26.000 - 88.000 | 19.000 - 88.000 | |" ,
"|NA |Age in Years | | | | 0.933 |" ,
"| |- Mean (SD) | 60.876 (10.589) | 61.000 (12.557) | 60.925 (11.379) | |" ,
"| |- Range | 36.000 - 85.000 | 22.000 - 81.000 | 22.000 - 85.000 | |" ,
"" ,
"" ,
"|QOL | | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value |",
"|:---|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|:-------:|",
"|0 |Age in Years | | | | | 0.238 |",
"| |- Mean (SD) | 58.317 (11.869) | 62.154 (11.037) | 58.968 (12.098) | 60.089 (11.627) | |",
"| |- Range | 30.000 - 79.000 | 41.000 - 82.000 | 29.000 - 76.000 | 29.000 - 82.000 | |",
"|1 |Age in Years | | | | | 0.891 |",
"| |- Mean (SD) | 59.560 (11.279) | 59.944 (11.663) | 59.698 (11.647) | 59.763 (11.537) | |",
"| |- Range | 28.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |",
"|NA |Age in Years | | | | | 0.949 |",
"| |- Mean (SD) | 61.364 (11.522) | 60.788 (11.725) | 60.854 (10.009) | 60.925 (11.379) | |",
"| |- Range | 27.000 - 81.000 | 22.000 - 85.000 | 40.000 - 81.000 | 22.000 - 85.000 | |"
)
)
})
####################################################
test_that("01/31/2019: modpval.tableby (#174, #175)", {
tmp <- tableby(sex ~ age + arm, data = mockstudy, strata = fu.stat, test = FALSE)
expect_true(!any(c("test", "p.value") %in% names(as.data.frame(tmp))))
tmp <- modpval.tableby(tmp, data.frame(y = "sex", strata = c("1", "2"), x = c("age", "arm"), p = c(1, 0.5)), use.pname = TRUE)
expect_identical(
capture.kable(summary(tmp, pfootnote = TRUE, text = TRUE)),
c("|fu.stat | | Male (N=916) | Female (N=583) | Total (N=1499) | p |",
"|:-------|:-------------|:---------------:|:---------------:|:---------------:|:---------:|",
"|1 |Age in Years | | | | 1.000 (1) |",
"| |- Mean (SD) | 58.253 (12.048) | 61.018 (10.649) | 59.336 (11.561) | |",
"| |- Range | 32.000 - 85.000 | 35.000 - 80.000 | 32.000 - 85.000 | |",
"| |Treatment Arm | | | | |",
"| |- A: IFL | 14 (16.1%) | 4 (7.1%) | 18 (12.6%) | |",
"| |- F: FOLFOX | 56 (64.4%) | 43 (76.8%) | 99 (69.2%) | |",
"| |- G: IROX | 17 (19.5%) | 9 (16.1%) | 26 (18.2%) | |",
"|2 |Age in Years | | | | |",
"| |- Mean (SD) | 60.686 (11.278) | 59.059 (11.824) | 60.054 (11.516) | |",
"| |- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |",
"| |Treatment Arm | | | | 0.500 (1) |",
"| |- A: IFL | 263 (31.7%) | 147 (27.9%) | 410 (30.2%) | |",
"| |- F: FOLFOX | 355 (42.8%) | 237 (45.0%) | 592 (43.7%) | |",
"| |- G: IROX | 211 (25.5%) | 143 (27.1%) | 354 (26.1%) | |",
"1. Modified by user"
)
)
})
test_that("05/20/2019: non-alphabetical strata with missing values (#215)", {
dat <- data.frame(
strat = factor(rep(1:2, each = 5), levels = 2:1),
a = c("a", "a", "a", "b", NA, "b", "a", "b", "a", "b")
)
expect_identical(
capture.kable(summary(tableby(~ a, data = dat, strata = strat))),
c("|strat | | Overall (N=10) |",
"|:-----|:------------------------|:--------------:|",
"|2 |**a** | |",
"| | a | 2 (40.0%) |",
"| | b | 3 (60.0%) |",
"|1 |**a** | |",
"| | N-Miss | 1 |",
"| | a | 3 (75.0%) |",
"| | b | 1 (25.0%) |"
)
)
})
test_that("06/11/2019: retaining control.list with merge() (#221)", {
tab1 <- tableby(sex ~ age, data = mockstudy)
tab2 <- tableby(sex ~ anova(ps, digits = 0), data = mockstudy)
# this also doesn't work... I'm planning to fix this
expect_identical(
capture.kable(summary(merge(tab1, tab2))),
capture.kable(summary(merge(tab2, tab1)[2:1]))
)
expect_identical(
capture.kable(summary(merge(tab1, tab2), text = TRUE)),
c("| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|",
"|:------------|:---------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | 0.048|",
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |",
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |",
"|ps | | | | 0.345|",
"|- N-Miss | 162 | 104 | 266 | |",
"|- Mean (SD) | 1 (1) | 1 (1) | 1 (1) | |",
"|- Range | 0 - 2 | 0 - 2 | 0 - 2 | |"
)
)
})
test_that("Multiple labels work (#310)", {
tb <- tableby(list(sex, arm) ~ age, data = mockstudy)
expect_identical(
capture.kable(summary(tb, title = "Just one", text=TRUE)),
c("Table: Just one" ,
"" ,
"| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|" ,
"|:------------|:---------------:|:---------------:|:---------------:|-------:|" ,
"|Age in Years | | | | 0.048|" ,
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |" ,
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |" ,
"" ,
"" ,
"| | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value|",
"|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | | 0.614|",
"|- Mean (SD) | 59.673 (11.365) | 60.301 (11.632) | 59.763 (11.499) | 59.985 (11.519) | |",
"|- Range | 27.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |"
)
)
expect_identical(
capture.kable(summary(tb, title = c("Just one", "both"), text=TRUE)),
c("Table: Just one" ,
"" ,
"| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|" ,
"|:------------|:---------------:|:---------------:|:---------------:|-------:|" ,
"|Age in Years | | | | 0.048|" ,
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |" ,
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |" ,
"" ,
"" ,
"Table: both" ,
"" ,
"| | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value|",
"|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | | 0.614|",
"|- Mean (SD) | 59.673 (11.365) | 60.301 (11.632) | 59.763 (11.499) | 59.985 (11.519) | |",
"|- Range | 27.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |"
)
)
expect_identical(
capture.kable(summary(tb, title = list(NULL, "both"), text=TRUE)),
c("| | Male (N=916) | Female (N=583) | Total (N=1499) | p value|" ,
"|:------------|:---------------:|:---------------:|:---------------:|-------:|" ,
"|Age in Years | | | | 0.048|" ,
"|- Mean (SD) | 60.455 (11.369) | 59.247 (11.722) | 59.985 (11.519) | |" ,
"|- Range | 19.000 - 88.000 | 22.000 - 88.000 | 19.000 - 88.000 | |" ,
"" ,
"" ,
"Table: both" ,
"" ,
"| | A: IFL (N=428) | F: FOLFOX (N=691) | G: IROX (N=380) | Total (N=1499) | p value|",
"|:------------|:---------------:|:-----------------:|:---------------:|:---------------:|-------:|",
"|Age in Years | | | | | 0.614|",
"|- Mean (SD) | 59.673 (11.365) | 60.301 (11.632) | 59.763 (11.499) | 59.985 (11.519) | |",
"|- Range | 27.000 - 88.000 | 19.000 - 88.000 | 26.000 - 85.000 | 19.000 - 88.000 | |"
)
)
})
test_that("total.pos = 'before' (#320)", {
expect_identical(
capture.kable(summary(tableby(sex ~ age, data = mockstudy, strata = arm, total.pos = "before"), text = TRUE)),
c("|Treatment Arm | | Total (N=1499) | Male (N=916) | Female (N=583) | p value |",
"|:-------------|:------------|:---------------:|:---------------:|:---------------:|:-------:|",
"|A: IFL |Age in Years | | | | 0.572 |",
"| |- Mean (SD) | 59.673 (11.365) | 59.903 (11.347) | 59.252 (11.422) | |",
"| |- Range | 27.000 - 88.000 | 28.000 - 83.000 | 27.000 - 88.000 | |",
"|F: FOLFOX |Age in Years | | | | 0.286 |",
"| |- Mean (SD) | 60.301 (11.632) | 60.691 (11.598) | 59.729 (11.679) | |",
"| |- Range | 19.000 - 88.000 | 19.000 - 88.000 | 22.000 - 83.000 | |",
"|G: IROX |Age in Years | | | | 0.051 |",
"| |- Mean (SD) | 59.763 (11.499) | 60.702 (10.999) | 58.355 (12.113) | |",
"| |- Range | 26.000 - 85.000 | 29.000 - 85.000 | 26.000 - 82.000 | |"
)
)
})
test_that("cat.droplevels (#318)", {
d <- data.frame(
z = rep(LETTERS[1:3], each = 10),
x = rep(c("a", "b", "b"), each = 10),
y = rep(LETTERS[1:3], times = 10),
stringsAsFactors = FALSE
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = FALSE), text = TRUE)),
c("|z | | A (N=10) | B (N=10) | C (N=10) | Total (N=30) | p value |",
"|:--|:----|:----------:|:----------:|:----------:|:------------:|:-------:|",
"|A |x | | | | | |",
"| |- a | 4 (100.0%) | 3 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"| |- b | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |",
"|B |x | | | | | |",
"| |- a | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |",
"| |- b | 3 (100.0%) | 4 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"|C |x | | | | | |",
"| |- a | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | |",
"| |- b | 3 (100.0%) | 3 (100.0%) | 4 (100.0%) | 10 (100.0%) | |"
)
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE), text = TRUE)),
c("|z | | A (N=10) | B (N=10) | C (N=10) | Total (N=30) | p value |",
"|:--|:----|:----------:|:----------:|:----------:|:------------:|:-------:|",
"|A |x | | | | | |",
"| |- a | 4 (100.0%) | 3 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"|B |x | | | | | |",
"| |- b | 3 (100.0%) | 4 (100.0%) | 3 (100.0%) | 10 (100.0%) | |",
"|C |x | | | | | |",
"| |- b | 3 (100.0%) | 3 (100.0%) | 4 (100.0%) | 10 (100.0%) | |"
)
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE), text = TRUE)),
capture.kable(summary(tableby(y ~ chisq(x, cat.droplevels = TRUE), data = d, strata = z), text = TRUE))
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE, test.always = TRUE), text = TRUE)),
capture.kable(summary(tableby(y ~ chisq(x, cat.droplevels = TRUE), data = d, strata = z, test.always = TRUE), text = TRUE))
)
expect_identical(
capture.kable(summary(tableby(y ~ x, data = d, strata = z, cat.droplevels = TRUE, test.always = TRUE), text = TRUE)),
capture.kable(summary(tableby(y ~ x, data = d, strata = z, test.always = TRUE), text = TRUE))[c(1:4, 6, 8:9, 11)]
)
})
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