Nothing
skip_on_cran()
skip_if_not(broom.helpers::.assert_package("survey", pkg_search = "gtsummary", boolean = TRUE))
strial <- trial %>%
survey::svydesign(data = ., ids = ~1, weights = ~1)
d <- survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)
test_that("add_p creates output without error/warning", {
expect_snapshot(
tbl_svysummary(strial, by = grade) %>% add_p() %>% as.data.frame()
)
expect_snapshot(
strial %>%
tbl_svysummary(by = trt) %>%
add_p() %>%
as.data.frame()
)
expect_warning(
strial %>%
tbl_svysummary(by = trt) %>%
add_p(),
NA
)
expect_message(
strial %>%
tbl_svysummary(by = trt) %>%
add_p(),
NA
)
expect_warning(
tbl_svysummary(d, by = Survived) %>% add_p(),
NA
)
expect_message(
tbl_svysummary(d, by = Survived) %>% add_p(),
NA
)
})
test_that("add_p creates output without error/warning with continuous2", {
expect_snapshot(
tbl_svysummary(strial, by = grade, type = all_continuous() ~ "continuous2") %>%
add_p() %>%
as.data.frame()
)
expect_snapshot(
strial %>%
tbl_svysummary(by = trt, type = all_continuous() ~ "continuous2") %>%
add_p() %>%
as.data.frame()
)
expect_warning(
strial %>%
tbl_svysummary(by = trt, type = all_continuous() ~ "continuous2") %>%
add_p(),
NA
)
expect_message(
strial %>%
tbl_svysummary(by = trt, type = all_continuous() ~ "continuous2") %>%
add_p(),
NA
)
expect_warning(
tbl_svysummary(d, by = Survived, type = all_continuous() ~ "continuous2") %>% add_p(),
NA
)
expect_message(
tbl_svysummary(d, by = Survived, type = all_continuous() ~ "continuous2") %>% add_p(),
NA
)
})
test_that("add_p creates errors with bad args", {
expect_error(
tbl_svysummary(strial, by = trt) %>%
add_p(pvalue_fun = mtcars),
NULL
)
expect_error(
tbl_svysummary(strial, by = grade, include = -response) %>%
add_p(test = "chisq"),
NULL
)
expect_error(
tbl_svysummary(strial, by = grade, include = -response) %>%
add_p(test = list(all_continuous() ~ "ttttessstttt")),
NULL
)
})
test_that("add_p works well", {
skip_if_not(broom.helpers::.assert_package("flextable", pkg_search = "gtsummary", boolean = TRUE))
expect_error(
tbl1 <-
tbl_svysummary(strial, by = response) %>%
add_p(test = list(
age ~ "svy.t.test",
marker ~ "svy.wilcox.test",
trt ~ "svy.chisq.test",
stage ~ "svy.adj.chisq.test",
death ~ "svy.wald.test"
)),
NA
)
expect_snapshot(tbl1 %>% as.data.frame())
expect_equal(
dplyr::filter(tbl1$meta_data, variable == "age")$p.value,
survey::svyttest(age ~ response, strial)$p.value %>% rlang::set_names(NULL)
)
expect_equal(
dplyr::filter(tbl1$meta_data, variable == "marker")$p.value,
survey::svyranktest(marker ~ response, strial, test = "wilcoxon")$p.value %>% rlang::set_names(NULL)
)
expect_equal(
dplyr::filter(tbl1$meta_data, variable == "trt")$p.value,
survey::svychisq(~ trt + response, strial, statistic = "F")$p.value %>% rlang::set_names(NULL),
tolerance = 10^-4 # see issue https://github.com/ddsjoberg/gtsummary/issues/702
)
expect_equal(
dplyr::filter(tbl1$meta_data, variable == "stage")$p.value,
survey::svychisq(~ stage + response, strial, statistic = "Chisq")$p.value %>% rlang::set_names(NULL)
)
# TO DO: fix test
expect_equal(
dplyr::filter(tbl1$meta_data, variable == "death")$p.value,
survey::svychisq(~ death + response, strial, statistic = "Wald")$p.value %>% rlang::set_names(NULL) %>% .[[1]],
tolerance = 10^-2 # see issue https://github.com/ddsjoberg/gtsummary/issues/702
)
expect_error(
tbl2 <-
tbl_svysummary(strial, by = response) %>%
add_p(test = list(
age ~ "svy.vanderwaerden.test",
ttdeath ~ "svy.kruskal.test",
marker ~ "svy.median.test",
trt ~ "svy.adj.wald.test",
stage ~ "svy.lincom.test",
death ~ "svy.saddlepoint.test"
)),
NA
)
expect_snapshot(tbl2 %>% as.data.frame())
expect_error(as_flex_table(tbl2), NA)
expect_equal(
dplyr::filter(tbl2$meta_data, variable == "age")$p.value,
survey::svyranktest(age ~ response, strial, test = "vanderWaerden")$p.value %>% rlang::set_names(NULL)
)
expect_equal(
dplyr::filter(tbl2$meta_data, variable == "ttdeath")$p.value,
survey::svyranktest(ttdeath ~ response, strial, test = "KruskalWallis")$p.value %>% rlang::set_names(NULL)
)
expect_equal(
dplyr::filter(tbl2$meta_data, variable == "marker")$p.value,
survey::svyranktest(marker ~ response, strial, test = "median")$p.value %>% rlang::set_names(NULL)
)
expect_equal(
dplyr::filter(tbl2$meta_data, variable == "trt")$p.value,
survey::svychisq(~ trt + response, strial, statistic = "adjWald")$p.value %>% as.numeric(),
tolerance = 10^-4 # see issue https://github.com/ddsjoberg/gtsummary/issues/702
)
expect_equal(
dplyr::filter(tbl2$meta_data, variable == "stage")$p.value,
survey::svychisq(~ stage + response, strial, statistic = "lincom")$p.value %>% as.numeric(),
tolerance = 10^-2 # see issue https://github.com/ddsjoberg/gtsummary/issues/702
)
# TO DO: fix test
expect_equal(
dplyr::filter(tbl2$meta_data, variable == "death")$p.value,
survey::svychisq(~ death + response, strial, statistic = "saddlepoint")$p.value %>% as.numeric(),
tolerance = 10^-2 # see issue https://github.com/ddsjoberg/gtsummary/issues/702
)
})
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