Nothing
context("significance tests")
if(isTRUE(getOption("covr"))) {
data(mtcars)
mtcars = apply_labels(mtcars,
mpg = "Miles/(US) gallon",
cyl = "Number of cylinders",
disp = "Displacement (cu.in.)",
hp = "Gross horsepower",
drat = "Rear axle ratio",
wt = "Weight (lb/1000)",
qsec = "1/4 mile time",
vs = "Engine",
vs = c("V-engine" = 0,
"Straight engine" = 1),
am = "Transmission",
am = c("Automatic" = 0,
"Manual"=1),
gear = "Number of forward gears",
carb = "Number of carburetors"
)
tbl = t(table(mtcars$am, mtcars$vs))
expect_equal(compare_proportions(12/18, 7/14, 18, 14),
prop.test(tbl, correct = FALSE)$p.value)
tbl[2,1] = 0
expect_equal(compare_proportions(12/18, 0/7, 18, 7),
suppressWarnings(prop.test(tbl, correct = FALSE))$p.value)
t_test_pval = t.test(mpg ~ am, data = mtcars)$p.value
res = with(mtcars,
compare_means(
mean(mpg[am==0]), mean(mpg[am==1]),
sd(mpg[am==0]), sd(mpg[am==1]),
length(mpg[am==0]), length(mpg[am==1])
))
expect_equal(res, t_test_pval)
res = with(mtcars,
compare_means(
c(mean(mpg[am==0]), mean(mpg[am==0])), c(mean(mpg[am==1]), mean(mpg[am==1])),
c(sd(mpg[am==0]), sd(mpg[am==0])), c(sd(mpg[am==1]), sd(mpg[am==1])),
c(length(mpg[am==0]), length(mpg[am==0])), c(length(mpg[am==1]), length(mpg[am==1]))
))
expect_equal(res, c(t_test_pval, t_test_pval))
t_test_pval = t.test(mpg ~ am, data = mtcars, var.equal = TRUE)$p.value
res = with(mtcars,
compare_means(
c(mean(mpg[am==0]), mean(mpg[am==0])), c(mean(mpg[am==1]), mean(mpg[am==1])),
c(sd(mpg[am==0]), sd(mpg[am==0])), c(sd(mpg[am==1]), sd(mpg[am==1])),
c(length(mpg[am==0]), length(mpg[am==0])), c(length(mpg[am==1]), length(mpg[am==1])),
var_equal = TRUE
))
expect_equal(res, c(t_test_pval, t_test_pval))
context("significance_cpct")
mtcars_table = cro_cpct(list(mtcars$cyl, mtcars$gear),
list(total(), mtcars$vs, mtcars$am))
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none"),
"rds/signif_cpct1.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, inequality_sign = TRUE, keep = "none"),
"rds/signif_cpct1_greater_sign.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none", subtable_marks = "less"),
"rds/signif_cpct1_less.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, inequality_sign = TRUE,
keep = "none", subtable_marks = "less"),
"rds/signif_cpct1_less_sign.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none", subtable_marks = "both"),
"rds/signif_cpct1_both.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, inequality_sign = FALSE,
keep = "none", subtable_marks = "both"),
"rds/signif_cpct1_both_no_signs.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none", na_as_zero = TRUE),
"rds/signif_cpct2.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
keep = "none",
sig_labels = paste0("(",letters, ")")),
"rds/signif_cpct3.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
keep = "none",
sig_labels = NULL),
"rds/signif_cpct4.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none",
compare_type = c("subtable", "first_column")),
"rds/signif_cpct5.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none",
compare_type = c("subtable", "adjusted_first_column")),
"rds/signif_cpct6.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none",
compare_type = c("subtable", "adjusted_first_column"),
na_as_zero = TRUE
),
"rds/signif_cpct7.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none"
, compare_type = c("previous_column")),
"rds/signif_cpct8.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "none",
compare_type = c("previous_column"),
na_as_zero = TRUE),
"rds/signif_cpct9.rds", update = FALSE)
#####################
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "bases"),
"rds/signif_cpct10.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table),
"rds/signif_cpct11.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table),
"rds/signif_cpct11.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, delta_cpct = 50),
"rds/signif_cpct11_delta.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table, keep = "percent"),
"rds/signif_cpct12.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("subtable", "first_column")),
"rds/signif_cpct13.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("subtable", "adjusted_first_column")),
"rds/signif_cpct14.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("subtable", "adjusted_first_column"),
na_as_zero = TRUE
),
"rds/signif_cpct15.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("previous_column")),
"rds/signif_cpct16.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
delta_cpct = 65,
compare_type = c("previous_column")),
"rds/signif_cpct16_delta.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
delta_cpct = 65,
na_as_zero = TRUE,
compare_type = c("previous_column")),
"rds/signif_cpct16_delta2.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("previous_column"),
na_as_zero = TRUE),
"rds/signif_cpct17.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("previous_column"),
na_as_zero = TRUE,
min_base = 14),
"rds/signif_cpct18.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
na_as_zero = TRUE,
sig_level = 0.9),
"rds/signif_cpct19.rds", update = FALSE)
#####################
mtcars_table2 = cro_cpct(list(mtcars$vs, mtcars$am),
list(total(), mtcars$cyl))
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
bonferroni = FALSE,
na_as_zero = FALSE,
sig_level = 0.004),
"rds/signif_cpct20.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
sig_level = 0.1),
"rds/signif_cpct20greater.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
subtable_marks = "less",
sig_level = 0.1),
"rds/signif_cpct20less.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
subtable_marks = "both",
sig_level = 0.1),
"rds/signif_cpct20both.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
bonferroni = TRUE,
na_as_zero = FALSE,
sig_level = 0.004),
"rds/signif_cpct20boneferrony.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
bonferroni = FALSE,
na_as_zero = FALSE,
sig_level = 0.002),
"rds/signif_cpct20_2.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
bonferroni = TRUE,
na_as_zero = FALSE,
sig_level = 0.002),
"rds/signif_cpct20boneferrony_2.rds", update = FALSE)
#####################
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("subtable", "first_column"),
digits = 2),
"rds/signif_cpct21.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table,
compare_type = c("subtable", "first_column"),
delta_cpct = 30,
digits = 2),
"rds/signif_cpct21_delta.rds", update = FALSE)
expect_error(
significance_cpct(mtcars_table,
compare_type = c("first_column",
"previous_column",
"subtable"),
total_marker = "@"))
mtcars_table2 = mtcars_table
mtcars_table2[[1]] = gsub("#", "@", mtcars_table2[[1]])
expect_equal_to_reference(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
total_marker = "@"),
"rds/signif_cpct22.rds", update = FALSE)
expect_error(
significance_cpct(mtcars_table2,
compare_type = c("first_column",
"previous_column",
"subtable"),
total_marker = "@",
total_row = 2))
mtcars_table3 = cro_cpct(list(mtcars$cyl, mtcars$gear),
list(total(), mtcars$vs, mtcars$am),
weight = 1/100,
total_row_position = "above",
total_statistic = c("w_cases", "u_cases")
)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("first_column",
"previous_column",
"subtable")),
"rds/signif_cpct23.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("first_column",
"previous_column",
"subtable"),
total_row = 2),
"rds/signif_cpct24.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("first_column",
"previous_column",
"subtable"),
total_row = "#Total cases"),
"rds/signif_cpct24.rds", update = FALSE)
mtcars_table3 = cro_cpct(list(mtcars$cyl, mtcars$gear),
list(total(), mtcars$vs, mtcars$am),
total_row_position = "above"
)
expect_equal_to_reference(
significance_cpct(mtcars_table3, keep = "none"),
"rds/signif_cpct1a.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3, keep = "none", sig_labels = "a"),
"rds/signif_cpct25.rds", update = FALSE)
mtcars_table3 = cro_cpct(list(mtcars$cyl, mtcars$gear),
unvr(list(total(), mtcars$vs, mtcars$am)),
total_row_position = "above"
)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("previous_column", "subtable"),
sig_labels = "a"),
"rds/signif_cpct26.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("previous_column", "subtable"),
sig_labels = NULL),
"rds/signif_cpct26a.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("previous_column", "subtable")),
"rds/signif_cpct27.rds", update = FALSE)
mtcars_table3 = cro_cpct(list(mtcars$cyl),
unvr(list(total(), mtcars$vs, mtcars$am)),
total_row_position = "above"
)
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("previous_column", "subtable")),
"rds/signif_cpct28.rds", update = FALSE)
colnames(mtcars_table3) = rep("", NCOL(mtcars_table3))
expect_equal_to_reference(
significance_cpct(mtcars_table3,
compare_type = c("previous_column", "subtable")),
"rds/signif_cpct29.rds", update = FALSE)
expect_error(
significance_cpct(mtcars_table3,
compare_type = c("first_column", "adjusted_first_column"))
)
mtcars_table3 = cro_cpct(list(mtcars$cyl),
(list(total(), mtcars$vs, mtcars$am)),
total_row_position = "above"
)
expect_equal_to_reference(
significance_cpct(mtcars_table3[ ,1],
compare_type = c("first_column", "subtable")),
"rds/signif_cpct30.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3[ ,1:2],
compare_type = c("first_column", "subtable")),
"rds/signif_cpct31.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3[ ,1:3],
compare_type = c("first_column", "subtable")),
"rds/signif_cpct32.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table3[ ,c(1:2,4,5)],
compare_type = c("first_column", "subtable")),
"rds/signif_cpct33.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table[ ,1]),
"rds/signif_cpct34.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table[ ,1],
subtable_marks = "both"
),
"rds/signif_cpct34.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table[ ,1],
compare_type = c("previous", "first", "subtable"),
subtable_marks = "both"
),
"rds/signif_cpct34.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table[ ,1],
keep = "bases"),
"rds/signif_cpct34.rds", update = FALSE)
expect_equal_to_reference(
significance_cpct(mtcars_table[ ,1],
keep = "none"),
"rds/signif_cpct35.rds", update = FALSE)
if(sessionInfo()$R.version$arch!="i386"){
expect_identical(
significance_cpct(cro_cpct(NA)),
structure(list(row_labels = c("NA", "NA|#Total cases"), `#Total` = c("",
"")), row.names = c(NA, -2L), class = c("etable", "data.frame"
)))
}
mtcars_table4 = cross_cpct(mtcars, list(cyl, gear),
list(total(), vs, am, vs %nest% am))
expect_equal_to_reference(
significance_cpct(mtcars_table4, compare_type = c("first_column", "subtable")),
"rds/signif_cpct37.rds", update = FALSE)
colnames(mtcars_table4) = gsub("ss", "s\ns", colnames(mtcars_table4), perl = TRUE)
colnames(mtcars_table4) = gsub("aight", "ai\rght", colnames(mtcars_table4), perl = TRUE)
expect_equal_to_reference(
significance_cpct(mtcars_table4, compare_type = c("first_column", "subtable")),
"rds/signif_cpct37b.rds", update = FALSE)
mtcars_table5 = cro_cpct(list(mtcars$cyl, mtcars$gear),
unvr(list(total(), mtcars$vs, mtcars$am)))
expect_equal_to_reference(
significance_cpct(mtcars_table5), "rds/signif_cpct38.rds", update = FALSE)
context("significance_cpct issue #100")
expss_digits(0)
target = c(65.5, 34.5)*10
odd_df = data.frame(
a = c(rep(1:2, times = target), rep(2:1, times = target), rep(1, sum(target)), rep(1:2, times = c(1, sum(target)-1)), 1),
b = rep(1:5, times = c(sum(target), sum(target), sum(target), sum(target), 1))
)
expss_round_half_to_even(TRUE)
res = as.data.frame(cross_cpct(odd_df, a, b) %>% significance_cpct(digits = 0, min_base = 0))
expect_equal(trimws(res[2,2]), "34")
expect_equal(trimws(res[1,4]), "100 A B D")
expect_equal(trimws(res[1,6]), "100 D")
expss_round_half_to_even(FALSE)
res = as.data.frame(cross_cpct(odd_df, a, b) %>% significance_cpct(digits = 0, min_base = 0, as_spss = TRUE))
expect_equal(trimws(res[2,2]), "35")
expect_equal(trimws(res[1,4]), "100")
expect_equal(trimws(res[1,6]), "100")
expss_round_half_to_even(TRUE)
}
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