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Removal of internal df_explicit_na #1023

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merged 10 commits into from
Aug 14, 2023
+18 −15
Merged

Removal of internal df_explicit_na #1023

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c6159ea
fix
Melkiades Aug 4, 2023
b38ae92
Merge c6159ea58133378e21ecc44b17a498cc7cfc9768 into 88ab66736c3c23ca0…
Melkiades Aug 4, 2023
37216ff
[skip actions] Restyle files
github-actions[bot] Aug 4, 2023
abe9b17
Update NEWS.md
Melkiades Aug 4, 2023
25505b2
Merge branch 'main' into 1019_remove_internal_expl_na@main
Melkiades Aug 4, 2023
a887bc5
Update NEWS.md
Melkiades Aug 7, 2023
1ecacf3
Merge branch 'main' into 1019_remove_internal_expl_na@main
Melkiades Aug 10, 2023
4399e8d
Merge branch 'main' into 1019_remove_internal_expl_na@main
Melkiades Aug 11, 2023
266c74b
Merge branch 'main' into 1019_remove_internal_expl_na@main
shajoezhu Aug 14, 2023
0d3bd4a
update docs with warning
Melkiades Aug 14, 2023
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1 change: 1 addition & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
### Miscellaneous
* Fix swapped descriptions for the `.N_row` and `.N_col` parameters.
* Fix bug in `analyze_vars_in_cols` when categorical data was used.
* Removal of internal calls to `df_explicit_na`. Changes in `NA` values should happen externally to `tern` functions, depending on users' needs.

# tern 0.8.5

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1 change: 0 additions & 1 deletion R/h_adsl_adlb_merge_using_worst_flag.R
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Expand Up @@ -137,7 +137,6 @@ h_adsl_adlb_merge_using_worst_flag <- function(adsl, # nolint
adlb_out$ATOXGR <- as.factor(adlb_out$ATOXGR)
adlb_out$BTOXGR <- as.factor(adlb_out$BTOXGR)

adlb_out <- df_explicit_na(adlb_out)
formatters::var_labels(adlb_out) <- adlb_var_labels

adlb_out
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3 changes: 0 additions & 3 deletions R/h_stack_by_baskets.R
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Expand Up @@ -62,9 +62,6 @@ h_stack_by_baskets <- function(df,
keys = c("STUDYID", "USUBJID", "ASTDTM", "AEDECOD", "AESEQ"),
aag_summary = NULL,
na_level = "<Missing>") {
# Use of df_explicit_na() in case the user has not previously used
df <- df_explicit_na(df, na_level = na_level)

smq_nam <- baskets[startsWith(baskets, "SMQ")]
# SC corresponding to NAM
smq_sc <- gsub(pattern = "NAM", replacement = "SC", x = smq_nam, fixed = TRUE)
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15 changes: 8 additions & 7 deletions tests/testthat/test-h_adsl_adlb_merge_using_worst_flag.R
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Expand Up @@ -4,9 +4,10 @@ testthat::test_that("h_adsl_adlb_merge_using_worst_flag generates missing for pa
adlb_f <- tern_ex_adlb %>%
dplyr::filter(USUBJID %in% c("AB12345-CHN-3-id-128"))

result <- h_adsl_adlb_merge_using_worst_flag(adsl_f, adlb_f, worst_flag = c("WGRHIFL" = "Y"))

res <- testthat::expect_silent(result)
testthat::expect_silent(
result <- h_adsl_adlb_merge_using_worst_flag(adsl_f, adlb_f, worst_flag = c("WGRHIFL" = "Y"))
)
res <- df_explicit_na(result)
testthat::expect_snapshot(res)
})

Expand All @@ -20,7 +21,7 @@ testthat::test_that("h_adsl_adlb_merge_using_worst_flag generates missing for pa

result <- h_adsl_adlb_merge_using_worst_flag(adsl_f, adlb_f, worst_flag = c("WGRHIFL" = "Y"))

res <- testthat::expect_silent(result)
res <- df_explicit_na(result)
testthat::expect_snapshot(res)
})

Expand All @@ -34,7 +35,7 @@ testthat::test_that("h_adsl_adlb_merge_using_worst_flag generates missing for pa

result <- h_adsl_adlb_merge_using_worst_flag(adsl_f, adlb_f, worst_flag = c("WGRHIFL" = "Y"))

res <- testthat::expect_silent(result)
res <- df_explicit_na(result)
testthat::expect_snapshot(res)
})

Expand All @@ -50,7 +51,7 @@ testthat::test_that(

result <- h_adsl_adlb_merge_using_worst_flag(adsl_f, adlb_f, worst_flag = c("WGRHIFL" = "Y"))

res <- testthat::expect_silent(result)
res <- df_explicit_na(result)
testthat::expect_snapshot(res)
}
)
Expand All @@ -63,6 +64,6 @@ testthat::test_that("h_adsl_adlb_merge_using_worst_flag generates missing and by

result <- h_adsl_adlb_merge_using_worst_flag(adsl_f, adlb_f, worst_flag = c("WGRHIVFL" = "Y"), by_visit = TRUE)

res <- testthat::expect_silent(result)
res <- df_explicit_na(result)
testthat::expect_snapshot(res)
})
1 change: 1 addition & 0 deletions tests/testthat/test-h_stack_by_baskets.R
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@@ -1,5 +1,6 @@
# Local data pre-processing
adae_local <- tern_ex_adae[1:20, ] %>% df_explicit_na()
adae_local[1, ] <- NA

testthat::test_that("h_stack_by_baskets returns the correct dataframe", {
result <- h_stack_by_baskets(df = adae_local) %>% data.frame()
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