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ignore missmatch in grid argument #734

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Apr 2, 2024
Merged

ignore missmatch in grid argument #734

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84 changes: 47 additions & 37 deletions tests/testthat/test-kmg01.R
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Original file line number Diff line number Diff line change
@@ -1,57 +1,67 @@
# kmg01 functions ----

test_that("kmg01 works as expected", {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
pre_data <- expect_silent(kmg01_pre(filter_data, dataset = "adtte"))
raw_res <- expect_silent(kmg01_main(pre_data, dataset = "adtte"))
expect_true(ggplot2::is.ggplot(raw_res))
withr::with_options(opts_partial_match_old, {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
pre_data <- expect_silent(kmg01_pre(filter_data, dataset = "adtte"))
raw_res <- expect_silent(kmg01_main(pre_data, dataset = "adtte"))
expect_true(ggplot2::is.ggplot(raw_res))
})
})

# kmg01 ----

test_that("kmg01 works as expected with custom color set", {
col <- c(
"A: Drug X" = "black",
"B: Placebo" = "blue",
"C: Combination" = "gray"
)

filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data, dataset = "adtte", col = col))
expect_true(ggplot2::is.ggplot(res))
res <- expect_silent(run(kmg01, filter_data, dataset = "adtte", col = unname(col)))
expect_true(ggplot2::is.ggplot(res))
withr::with_options(opts_partial_match_old, {
col <- c(
"A: Drug X" = "black",
"B: Placebo" = "blue",
"C: Combination" = "gray"
)

filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data, dataset = "adtte", col = col))
expect_true(ggplot2::is.ggplot(res))
res <- expect_silent(run(kmg01, filter_data, dataset = "adtte", col = unname(col)))
expect_true(ggplot2::is.ggplot(res))
})
})

test_that("kmg01 works if change pvalue, ties and conf level", {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data,
dataset = "adtte",
pval_method = "log-rank",
ties = "efron",
conf_level = 0.99
))
expect_true(ggplot2::is.ggplot(res))
withr::with_options(opts_partial_match_old, {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data,
dataset = "adtte",
pval_method = "log-rank",
ties = "efron",
conf_level = 0.99
))
expect_true(ggplot2::is.ggplot(res))
})
})


test_that("kmg01 works if change annotation position", {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data,
dataset = "adtte", annot_surv_med = FALSE, annot_coxph = TRUE,
control_annot_coxph = control_coxph_annot(x = 0.78, y = 0.9)
))
expect_true(ggplot2::is.ggplot(res))
withr::with_options(opts_partial_match_old, {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data,
dataset = "adtte", annot_surv_med = FALSE, annot_coxph = TRUE,
control_annot_coxph = control_coxph_annot(x = 0.78, y = 0.9)
))
expect_true(ggplot2::is.ggplot(res))
})
})


test_that("kmg01 works for stratified analysis", {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data,
dataset = "adtte", annot_surv_med = FALSE,
position_coxph = c(0.4, 0.5),
position_surv_med = c(1, 0.7),
strata = c("STRATA1", "STRATA2")
))
expect_true(ggplot2::is.ggplot(res))
withr::with_options(opts_partial_match_old, {
filter_data <- dunlin::log_filter(syn_data, PARAMCD == "OS", "adtte")
res <- expect_silent(run(kmg01, filter_data,
dataset = "adtte", annot_surv_med = FALSE,
control_annot_coxph = tern::control_coxph_annot(x = 0.4, y = 0.5),
control_annot_surv_med = tern::control_surv_med_annot(x = 0.99, y = 0.7),
strata = c("STRATA1", "STRATA2")
))
expect_true(ggplot2::is.ggplot(res))
})
})
202 changes: 111 additions & 91 deletions tests/testthat/test-mng01.R
View file
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Original file line number Diff line number Diff line change
@@ -1,116 +1,136 @@
# mng01 functions ---

test_that("mng01 works as expected with default argument values", {
pre_data <- mng01_pre(syn_data, dataset = "adlb")
res <- mng01_main(pre_data, dataset = "adlb")
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("mng01 with default value", res[[1]])
withr::with_options(opts_partial_match_old, {
pre_data <- mng01_pre(syn_data, dataset = "adlb")
res <- mng01_main(pre_data, dataset = "adlb")
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("mng01 with default value", res[[1]])
})
})

test_that("mng01 works as expected with custom argument values", {
col <- c(
"B: Placebo" = "black",
"A: Drug X" = "blue",
"C: Combination" = "gray"
)

pre_data <- mng01_pre(syn_data, dataset = "adlb")
res <- mng01_main(
pre_data,
dataset = "adlb",
ggtheme = ggplot2::theme(axis.text.x = ggplot2::element_text(colour = "red", angle = 30, hjust = 1)),
line_col = col
)
expect_list(res, len = 3, types = "ggplot")

bad_col <- c(
"B: Placebo" = "black",
"A: Drug X" = "blue"
)

expect_error(
mng01_main(pre_data, dataset = "adlb", line_col = bad_col),
"Missing color matching for C: Combination",
fixed = TRUE
)

skip_on_ci()
vdiffr::expect_doppelganger("mng01 with custom theme", res[[1]], )
withr::with_options(opts_partial_match_old, {
col <- c(
"B: Placebo" = "black",
"A: Drug X" = "blue",
"C: Combination" = "gray"
)

pre_data <- mng01_pre(syn_data, dataset = "adlb")

res <- mng01_main(
pre_data,
dataset = "adlb",
ggtheme = ggplot2::theme(axis.text.x = ggplot2::element_text(colour = "red", angle = 30, hjust = 1)),
line_col = col
)

expect_list(res, len = 3, types = "ggplot")

bad_col <- c(
"B: Placebo" = "black",
"A: Drug X" = "blue"
)

expect_error(
mng01_main(pre_data, dataset = "adlb", line_col = bad_col),
"Missing color matching for C: Combination",
fixed = TRUE
)

skip_on_ci()
vdiffr::expect_doppelganger("mng01 with custom theme", res[[1]])
})
})


# mng01 ----

test_that("mng01 works as expected with custom color set", {
col <- c(
"B: Placebo" = "black",
"A: Drug X" = "blue",
"C: Combination" = "gray"
)

proc_data <- syn_data
res <- run(mng01, proc_data, dataset = "adlb", line_col = col)
expect_list(res, len = 3, types = "ggplot")

res2 <- run(mng01, proc_data, dataset = "adlb", line_col = unname(col))
expect_list(res2, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with custom color set", res[[1]])
vdiffr::expect_doppelganger("run mng01 with custom unnamed color set", res2[[1]])
withr::with_options(opts_partial_match_old, {
col <- c(
"B: Placebo" = "black",
"A: Drug X" = "blue",
"C: Combination" = "gray"
)
proc_data <- syn_data

res <- run(mng01, proc_data, dataset = "adlb", line_col = col)
expect_list(res, len = 3, types = "ggplot")

res2 <- run(mng01, proc_data, dataset = "adlb", line_col = unname(col))
expect_list(res2, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with custom color set", res[[1]])
vdiffr::expect_doppelganger("run mng01 with custom unnamed color set", res2[[1]])
})
})

test_that("mng01 works with table = NULL", {
proc_data <- syn_data
res <- run(mng01, proc_data, dataset = "adlb", table = NULL)
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 without table", res[[1]])
withr::with_options(opts_partial_match_old, {
proc_data <- syn_data
res <- run(mng01, proc_data, dataset = "adlb", table = NULL)
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 without table", res[[1]])
})
})

test_that("mng01 works with combination of x variables", {
proc_data <- syn_data
res <- run(
mng01,
proc_data,
dataset = "adlb",
x_var = c("AVISIT", "AVISITN")
)
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with combination of x variables", res[[1]])
withr::with_options(opts_partial_match_old, {
proc_data <- syn_data
res <- run(
mng01,
proc_data,
dataset = "adlb",
x_var = c("AVISIT", "AVISITN")
)

expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with combination of x variables", res[[1]])
})
})

test_that("mng01 works with numeric x variable", {
proc_data <- syn_data
proc_data$adlb$AVISITN[1:20] <- 10
proc_data$adlb$AVISITN[21:40] <- -3
res <- run(
mng01,
proc_data,
dataset = "adlb",
x_var = c("AVISITN")
)
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with numeric x variables", res[[1]])
withr::with_options(opts_partial_match_old, {
proc_data <- syn_data
proc_data$adlb$AVISITN[1:20] <- 10
proc_data$adlb$AVISITN[21:40] <- -3

res <- run(
mng01,
proc_data,
dataset = "adlb",
x_var = c("AVISITN")
)

expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with numeric x variables", res[[1]])
})
})

test_that("mng01 works with numeric jitter", {
proc_data <- syn_data
res <- run(
mng01,
proc_data,
dataset = "adlb",
jitter = 0.7
)
expect_list(res, len = 3, types = "ggplot")

skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with jitter", res[[1]])
withr::with_options(opts_partial_match_old, {
proc_data <- syn_data

res <- run(
mng01,
proc_data,
dataset = "adlb",
jitter = 0.7
)

expect_list(res, len = 3, types = "ggplot")
skip_on_ci()
vdiffr::expect_doppelganger("run mng01 with jitter", res[[1]])
})
})
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