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687 fix from formatters na str@main #690

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merged 12 commits into from
Aug 26, 2022
Merged

687 fix from formatters na str@main #690

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d5c6264
adapting to the new standard
Melkiades Aug 25, 2022
7fd9e8f
add NEWS
Melkiades Aug 25, 2022
a793138
Merge 7fd9e8f14ca2b63a9a2f3e02491ec6700238be17 into a4ad5e8a9db67042b…
Melkiades Aug 25, 2022
87a2aad
[skip actions] Restyle files
github-actions[bot] Aug 25, 2022
5d52d88
phantom changes for rebooting checks
Melkiades Aug 25, 2022
ca85e53
Fixing typo in stats::ancova (possible update of stats)
Melkiades Aug 26, 2022
65013aa
fixing class statement for expected (possible update of stats)
Melkiades Aug 26, 2022
a1e75ed
news update
Melkiades Aug 26, 2022
e18e6ac
merging
Melkiades Aug 26, 2022
d7c5b79
Merge e18e6ac3d602f5e0d809294be202263c3d36eb5b into a4ad5e8a9db67042b…
Melkiades Aug 26, 2022
f064ceb
[skip actions] Restyle files
github-actions[bot] Aug 26, 2022
32aaff6
phantom changes
Melkiades Aug 26, 2022
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1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -37,6 +37,7 @@
* Renamed `test-assertthat.R` to `test-utils_checkmate.R`.

### Bug Fixes
* Fixed tests to respect the new standard print for `NA`.
* Fixed error in tests coming from changes in `formatters::var_labels()`.
* Identified bug in `prop_diff` functions. Coding of responses have been corrected (TRUE is a success).
* Fixed error coming from comparing factors vector to characters vector.
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4 changes: 2 additions & 2 deletions tests/testthat/test-response_subgroups.R
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Expand Up @@ -366,10 +366,10 @@ testthat::test_that("tabulate_rsp_subgroups functions as expected when 0 obs in
"n", "100", "", "50", "23", "19", "7", "1", "B: Placebo", "Response (%)",
"71.0%", "", "66.0%", "65.2%", "78.9%", "100.0%", "100.0%", "A: Drug X",
"n", "100", "", "56", "26", "15", "3", "0", "A: Drug X", "Response (%)",
"90.0%", "", "87.5%", "92.3%", "100.0%", "66.7%", "NA%", " ", "Odds Ratio",
"90.0%", "", "87.5%", "92.3%", "100.0%", "66.7%", "NA", " ", "Odds Ratio",
"3.68", "", "3.61", "6.40", ">999.99", "<0.01", "NA", " ", "95% CI",
"(1.68, 8.04)", "", "(1.35, 9.65)", "(1.19, 34.29)", "(0.00, >999.99)",
"(0.00, >999.99)", "(NA, NA)", " ", "p-value (Chi-Squared Test)",
"(0.00, >999.99)", "NA", " ", "p-value (Chi-Squared Test)",
"0.0007", "", "0.0083", "0.0189", "0.0585", "0.1074", "NA"
),
.Dim = c(9L, 9L)
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16 changes: 8 additions & 8 deletions tests/testthat/test-summarize_variables.R
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Expand Up @@ -407,12 +407,12 @@ testthat::test_that("create_afun_summary creates an `afun` that works", {
"", "2", "2 (100%)", "0", "0", "", "", "2", "6", "5.0 - 8.0", "(-12.56, 25.56)",
"", "2", "2 (100%)", "0", "0", "", "", "2", "6", "4.0 - 7.0", "(-13.56, 24.56)",
"", "2", "2 (100%)", "0", "0", "B", "", "", "1", "3", "3.0 - 3.0",
"(NA, NA)", "", "2", "0", "2 (100%)", "0", "", "", "1", "2",
"2.0 - 2.0", "(NA, NA)", "", "2", "0", "2 (100%)", "0", "", "", "1",
"1", "1.0 - 1.0", "(NA, NA)", "", "2", "0", "2 (100%)", "0", "C",
"", "", "0", "NA", "NA - NA", "(NA, NA)", "", "2", "0", "0",
"2 (100%)", "", "", "0", "NA", "NA - NA", "(NA, NA)", "", "2",
"0", "0", "2 (100%)", "", "", "0", "NA", "NA - NA", "(NA, NA)",
"NA", "", "2", "0", "2 (100%)", "0", "", "", "1", "2",
"2.0 - 2.0", "NA", "", "2", "0", "2 (100%)", "0", "", "", "1",
"1", "1.0 - 1.0", "NA", "", "2", "0", "2 (100%)", "0", "C",
"", "", "0", "NA", "NA", "NA", "", "2", "0", "0",
"2 (100%)", "", "", "0", "NA", "NA", "NA", "", "2",
"0", "0", "2 (100%)", "", "", "0", "NA", "NA", "NA",
"", "2", "0", "0", "2 (100%)"
),
.Dim = c(34L, 4L)
Expand Down Expand Up @@ -470,7 +470,7 @@ testthat::test_that("`summarize_vars` works with healthy input, alternative `na.
expected <- structure(
c(
"", "n", "Mean (SD)", "Median", "Min - Max", "all obs",
"6", "NA (NA)", "NA", "NA - NA"
"6", "NA", "NA", "NA"
),
.Dim = c(5L, 2L)
)
Expand Down Expand Up @@ -632,7 +632,7 @@ testthat::test_that("`summarize_vars` works with empty named numeric variables",
result_matrix <- to_string_matrix(result)
expected_matrix <- structure(
c(
"", "n", "Mean (SD)", "Median", "Min - Max", "a", "0", "NA (NA)", "NA", "NA - NA",
"", "n", "Mean (SD)", "Median", "Min - Max", "a", "0", "NA", "NA", "NA",
"b", "2", "3.5 (0.7)", "3.5", "3.0 - 4.0", "c", "2", "5.5 (0.7)", "5.5", "5.0 - 6.0"
),
.Dim = c(5:4)
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2 changes: 1 addition & 1 deletion tests/testthat/test-survival_duration_subgroups.R
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Expand Up @@ -426,7 +426,7 @@ testthat::test_that("tabulate_survival_subgroups functions as expected when one
"1260.5", "", "1274.8", "1327.8", "774.7", "849.3", "NA", "NA",
" ", "Hazard Ratio", "0.72", "", "0.75", "0.63", "0.69", "1.01",
"NA", "NA", " ", "95% Wald CI", "(0.53, 0.98)", "", "(0.48, 1.17)",
"(0.32, 1.25)", "(0.35, 1.35)", "(0.28, 3.61)", "(NA, NA)", "(NA, NA)",
"(0.32, 1.25)", "(0.35, 1.35)", "(0.28, 3.61)", "NA", "NA",
" ", "p-value (log-rank)", "0.0334", "", "0.2012", "0.1832",
"0.2745", "0.9839", "NA", "NA"
),
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6 changes: 3 additions & 3 deletions tests/testthat/test-table_egt01.R
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Expand Up @@ -42,7 +42,7 @@ testthat::test_that("EGT01 default variant is produced correctly", {
"69.3", "22.3 - 116.5", "", "134", "66.4 (19.7)", "65.4", "23.9 - 110.4",
"", "134", "46.2 (12.2)", "47.3", "8.5 - 85.6", "", "134", "91.7 (13.9)",
"90.0", "54.0 - 131.7", "A: Drug X", "Absolute Change from Baseline",
"", "0", "NA (NA)", "NA", "NA - NA", "", "134", "-1.3 (26.0)",
"", "0", "NA", "NA", "NA", "", "134", "-1.3 (26.0)",
"-2.2", "-51.0 - 89.2", "", "134", "-1.1 (26.3)", "-1.1", "-85.0 - 67.5",
"", "134", "-3.2 (28.7)", "-2.2", "-81.2 - 72.6", "", "134",
"-1.4 (26.6)", "-4.5", "-58.1 - 77.3", "", "134", "-5.0 (27.1)",
Expand All @@ -55,7 +55,7 @@ testthat::test_that("EGT01 default variant is produced correctly", {
"", "134", "71.3 (18.9)", "70.9", "25.9 - 125.7", "", "134",
"47.1 (14.1)", "47.3", "9.2 - 83.0", "", "134", "93.5 (14.4)",
"91.0", "63.6 - 130.4", "B: Placebo", "Absolute Change from Baseline",
"", "0", "NA (NA)", "NA", "NA - NA", "", "134", "-0.4 (29.7)",
"", "0", "NA", "NA", "NA", "", "134", "-0.4 (29.7)",
"-0.5", "-68.2 - 88.4", "", "134", "1.3 (31.4)", "-0.3", "-73.1 - 81.4",
"", "134", "-0.9 (30.1)", "1.2", "-73.0 - 103.3", "", "134", "1.8 (30.3)",
"-0.9", "-64.3 - 85.3", "", "134", "1.4 (27.1)", "0.6", "-71.2 - 67.4",
Expand All @@ -67,7 +67,7 @@ testthat::test_that("EGT01 default variant is produced correctly", {
"71.0 (20.6)", "70.5", "10.4 - 117.3", "", "132", "71.3 (18.6)",
"73.3", "23.9 - 117.2", "", "132", "47.4 (12.6)", "48.2", "10.4 - 80.4",
"", "132", "92.6 (12.1)", "93.4", "65.7 - 120.5", "C: Combination",
"Absolute Change from Baseline", "", "0", "NA (NA)", "NA", "NA - NA",
"Absolute Change from Baseline", "", "0", "NA", "NA", "NA",
"", "132", "-0.7 (27.8)", "-0.8", "-68.2 - 67.2", "", "132",
"-0.1 (28.6)", "-1.5", "-67.7 - 66.3", "", "132", "1.5 (27.3)",
"0.1", "-64.5 - 72.5", "", "132", "1.7 (29.6)", "3.8", "-65.9 - 105.7",
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4 changes: 2 additions & 2 deletions tests/testthat/test-table_lbt01.R
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Expand Up @@ -43,11 +43,11 @@ testthat::test_that("LBT01 default variant is produced correctly", {
"0.3 (5.8)", "0.5", "-16.0 - 16.3", "", "134", "0.6 (6.5)", "0.4",
"-17.0 - 18.8", "", "134", "0.6 (6.1)", "0.9", "-16.0 - 16.1", "B: Placebo",
"Analysis Value", "", "134", "20.2 (4.2)", "20.1", "8.1 - 34.6", "", "0",
"NA (NA)", "NA", "NA - NA", "", "134", "20.1 (4.3)", "20.0", "7.2 - 30.5",
"NA", "NA", "NA", "", "134", "20.1 (4.3)", "20.0", "7.2 - 30.5",
"", "134", "19.8 (3.9)", "19.9", "11.9 - 28.2", "", "134", "19.6 (4.3)",
"19.2", "11.5 - 32.0", "", "134", "19.9 (4.2)", "20.1", "10.3 - 29.1",
"B: Placebo", "Absolute Change from Baseline", "", "134", "0.0 (0.0)",
"0.0", "0.0 - 0.0", "", "0", "NA (NA)", "NA", "NA - NA", "", "134",
"0.0", "0.0 - 0.0", "", "0", "NA", "NA", "NA", "", "134",
"-0.0 (6.3)", "-0.4", "-18.4 - 14.4", "", "134", "-0.3 (5.6)", "-0.2",
"-18.5 - 15.0", "", "134", "-0.5 (6.3)", "-1.2", "-16.6 - 17.2", "", "134",
"-0.3 (6.3)", "0.7", "-19.0 - 12.6", "C: Combination", "Analysis Value",
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6 changes: 3 additions & 3 deletions tests/testthat/test-table_vst01.R
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Expand Up @@ -86,7 +86,7 @@ testthat::test_that("VST01 default variant is produced correctly", {
"", "134", "50.6 (7.5)", "49.4", "35.1 - 72.2", "", "134", "50.6 (7.5)",
"49.4", "35.1 - 72.2", "", "134", "41.6 (4.8)", "42.1", "29.1 - 54.2",
"", "134", "60.0 (4.9)", "59.7", "47.6 - 74.9", "A: Drug X", "Change from Baseline",
"(N=134)", "", "0", "NA (NA)", "NA", "NA - NA", "", "134", "0.0 (0.0)",
"(N=134)", "", "0", "NA", "NA", "NA", "", "134", "0.0 (0.0)",
"0.0", "0.0 - 0.0", "", "134", "1.7 (10.8)", "0.6", "-20.4 - 29.9",
"", "134", "2.2 (11.8)", "3.1", "-23.9 - 39.2", "", "134", "2.1 (10.9)",
"2.6", "-25.8 - 30.7", "", "134", "1.5 (10.9)", "1.2", "-30.9 - 24.8",
Expand All @@ -101,7 +101,7 @@ testthat::test_that("VST01 default variant is produced correctly", {
"47.7", "30.4 - 70.6", "", "134", "48.4 (8.0)", "47.7", "30.4 - 70.6",
"", "134", "40.3 (5.3)", "40.3", "24.5 - 55.4", "", "134", "58.5 (4.8)",
"58.3", "47.8 - 70.6", "B: Placebo", "Change from Baseline",
"(N=134)", "", "0", "NA (NA)", "NA", "NA - NA", "", "134", "0.0 (0.0)",
"(N=134)", "", "0", "NA", "NA", "NA", "", "134", "0.0 (0.0)",
"0.0", "0.0 - 0.0", "", "134", "-0.8 (10.9)", "-1.1", "-25.8 - 28.4",
"", "134", "-0.7 (12.4)", "-0.7", "-28.4 - 37.0", "", "134", "-1.3 (11.1)",
"-2.3", "-28.1 - 33.9", "", "134", "-0.8 (10.6)", "-0.8", "-33.2 - 35.9",
Expand All @@ -116,7 +116,7 @@ testthat::test_that("VST01 default variant is produced correctly", {
"49.2", "30.6 - 72.9", "", "132", "49.1 (7.6)", "49.2", "30.6 - 72.9",
"", "132", "40.5 (5.3)", "40.5", "24.8 - 54.9", "", "132", "58.6 (4.8)",
"59.0", "41.8 - 72.9", "C: Combination", "Change from Baseline",
"(N=132)", "", "0", "NA (NA)", "NA", "NA - NA", "", "132", "0.0 (0.0)",
"(N=132)", "", "0", "NA", "NA", "NA", "", "132", "0.0 (0.0)",
"0.0", "0.0 - 0.0", "", "132", "-2.3 (10.4)", "-2.2", "-22.1 - 22.4",
"", "132", "-1.1 (11.6)", "-2.3", "-29.2 - 30.7", "", "132",
"-1.2 (10.9)", "-0.6", "-29.7 - 27.0", "", "132", "-1.4 (11.0)",
Expand Down