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Convert tibble snapshots to data.frames, convert unneeded snapshot tests
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edelarua committed Apr 6, 2023
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126 changes: 39 additions & 87 deletions tests/testthat/_snaps/abnormal_by_worst_grade_worsen.md
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# A tibble: 20 x 8
# Groups: USUBJID, PARAMCD [15]
USUBJID PARAMCD VALUES MIN MAX WGRLOFL WGRHIFL GRADDR
<chr> <chr> <dbl> <dbl> <dbl> <chr> <chr> <chr>
1 4 ABC 0.0478 0.0478 187. "Y" "" Low
2 3 OPQ 0.314 0.314 144. "Y" "" Low
3 4 OPQ 0.455 0.455 193. "Y" "" Low
4 2 ABC 0.790 0.790 181. "Y" "" Low
5 2 OPQ 7.49 7.49 195. "Y" "" Low
6 5 OPQ 22.7 22.7 187. "Y" "" Low
7 1 OPQ 23.5 23.5 196. "Y" "" Low
8 1 ABC 26.9 26.9 187. "Y" "" Low
9 3 ABC 37.9 37.9 197. "Y" "" Low
10 5 ABC 46.7 46.7 193. "Y" "" Low
11 3 OPQ 144. 0.314 144. "" "Y" High
12 3 XYZ 155. 17.1 155. "" "Y" High
13 2 XYZ 157. 7.79 157. "" "Y" High
14 4 XYZ 167. 0.276 167. "" "Y" High
15 5 OPQ 187. 22.7 187. "" "Y" High
16 5 XYZ 189. 16.1 189. "" "Y" High
17 4 OPQ 193. 0.455 193. "" "Y" High
18 2 OPQ 195. 7.49 195. "" "Y" High
19 1 OPQ 196. 23.5 196. "" "Y" High
20 1 XYZ 198. 16.5 198. "" "Y" High
USUBJID PARAMCD VALUES MIN MAX WGRLOFL WGRHIFL GRADDR
1 4 ABC 0.04777932 0.04777932 186.6068 Y Low
2 3 OPQ 0.31411084 0.31411084 143.8712 Y Low
3 4 OPQ 0.45459322 0.45459322 192.5216 Y Low
4 2 ABC 0.78966776 0.78966776 181.3203 Y Low
5 2 OPQ 7.48620657 7.48620657 194.7080 Y Low
6 5 OPQ 22.74372182 22.74372182 187.4772 Y Low
7 1 OPQ 23.49747233 23.49747233 195.6453 Y Low
8 1 ABC 26.93331945 26.93331945 187.4151 Y Low
9 3 ABC 37.89478708 37.89478708 196.5634 Y Low
10 5 ABC 46.70470511 46.70470511 192.5141 Y Low
11 3 OPQ 143.87116753 0.31411084 143.8712 Y High
12 3 XYZ 155.16467253 17.12241299 155.1647 Y High
13 2 XYZ 156.93855514 7.78729822 156.9386 Y High
14 4 XYZ 167.36031189 0.27616872 167.3603 Y High
15 5 OPQ 187.47716993 22.74372182 187.4772 Y High
16 5 XYZ 188.94406511 16.05289332 188.9441 Y High
17 4 OPQ 192.52160275 0.45459322 192.5216 Y High
18 2 OPQ 194.70798275 7.48620657 194.7080 Y High
19 1 OPQ 195.64528568 23.49747233 195.6453 Y High
20 1 XYZ 197.77834578 16.48751162 197.7783 Y High

# h_adlb_worsen stacks data correctly

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# A tibble: 8 x 9
USUBJID ARMCD AVISIT PARAMCD ATOXGR BTOXGR WGRLOFL WGRHIFL GRADDR
<chr> <fct> <fct> <chr> <fct> <fct> <chr> <chr> <chr>
1 AB12345-CHN-1-id-53 ARM B WEEK ~ IGA 0 0 "" "Y" High
2 AB12345-CHN-3-id-128 ARM B WEEK ~ IGA 4 0 "" "Y" High
3 AB12345-CHN-1-id-53 ARM B WEEK ~ ALT 4 0 "" "Y" High
4 AB12345-CHN-3-id-128 ARM B WEEK ~ ALT 1 0 "" "Y" High
5 AB12345-CHN-1-id-53 ARM B WEEK ~ CRP 0 1 "Y" "Y" Low
6 AB12345-CHN-3-id-128 ARM B WEEK ~ CRP 0 0 "Y" "" Low
7 AB12345-CHN-1-id-53 ARM B WEEK ~ ALT -4 0 "Y" "" Low
8 AB12345-CHN-3-id-128 ARM B WEEK ~ ALT -4 0 "Y" "" Low
USUBJID ARMCD AVISIT PARAMCD ATOXGR BTOXGR WGRLOFL
1 AB12345-CHN-1-id-53 ARM B WEEK 1 DAY 8 IGA 0 0
2 AB12345-CHN-3-id-128 ARM B WEEK 5 DAY 36 IGA 4 0
3 AB12345-CHN-1-id-53 ARM B WEEK 3 DAY 22 ALT 4 0
4 AB12345-CHN-3-id-128 ARM B WEEK 4 DAY 29 ALT 1 0
5 AB12345-CHN-1-id-53 ARM B WEEK 3 DAY 22 CRP 0 1 Y
6 AB12345-CHN-3-id-128 ARM B WEEK 1 DAY 8 CRP 0 0 Y
7 AB12345-CHN-1-id-53 ARM B WEEK 5 DAY 36 ALT -4 0 Y
8 AB12345-CHN-3-id-128 ARM B WEEK 5 DAY 36 ALT -4 0 Y
WGRHIFL GRADDR
1 Y High
2 Y High
3 Y High
4 Y High
5 Y Low
6 Low
7 Low
8 Low

# h_worsen_counter counts data (low) correctly

Expand Down Expand Up @@ -221,55 +225,3 @@
4 7/69 (10.1%) 6/72 (8.3%) 4/55 (7.3%)
Any 30/69 (43.5%) 26/72 (36.1%) 19/55 (34.5%)

# h_adlb_worsen all high

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# A tibble: 600 x 51
STUDYID COUNTRY SITEID SUBJID AGE SEX ARMCD ARM ACTAR~1 ACTARM RACE
<chr> <fct> <chr> <chr> <dbl> <fct> <fct> <fct> <fct> <fct> <fct>
1 AB12345 BRA BRA-1 id-105 37.8 F ARM A A: Drug~ ARM A A: Dr~ ASIAN
2 AB12345 BRA BRA-1 id-105 37.8 F ARM A A: Drug~ ARM A A: Dr~ ASIAN
3 AB12345 BRA BRA-1 id-105 37.8 F ARM A A: Drug~ ARM A A: Dr~ ASIAN
4 AB12345 BRA BRA-1 id-171 29.8 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
5 AB12345 BRA BRA-1 id-171 29.8 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
6 AB12345 BRA BRA-1 id-171 29.8 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
7 AB12345 BRA BRA-1 id-177 38.9 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
8 AB12345 BRA BRA-1 id-177 38.9 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
9 AB12345 BRA BRA-1 id-177 38.9 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
10 AB12345 BRA BRA-1 id-23 41.3 F ARM A A: Drug~ ARM A A: Dr~ AMER~
# ... with 590 more rows, 40 more variables: TRTSDTM <dttm>, TRTEDTM <dttm>,
# EOSDY <dbl>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>,
# REGION1 <fct>, SAFFL <fct>, USUBJID <chr>, PARAM <fct>, AVISIT <fct>,
# AVAL <dbl>, LBCAT <fct>, PARAMCD <chr>, AVALU <fct>, AVISITN <dbl>,
# ABLFL2 <chr>, ABLFL <chr>, BASE <dbl>, BASETYPE <chr>, ANRIND <fct>,
# ANRLO <dbl>, ANRHI <dbl>, DTYPE <lgl>, ATOXGR <fct>, BTOXGR <fct>,
# ATOXDSCL <chr>, ATOXDSCH <chr>, ADTM <dttm>, ASPID <int>, LBSEQ <int>, ...

# h_adlb_worsen all low

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# A tibble: 600 x 51
STUDYID COUNTRY SITEID SUBJID AGE SEX ARMCD ARM ACTAR~1 ACTARM RACE
<chr> <fct> <chr> <chr> <dbl> <fct> <fct> <fct> <fct> <fct> <fct>
1 AB12345 BRA BRA-1 id-105 37.8 F ARM A A: Drug~ ARM A A: Dr~ ASIAN
2 AB12345 BRA BRA-1 id-105 37.8 F ARM A A: Drug~ ARM A A: Dr~ ASIAN
3 AB12345 BRA BRA-1 id-105 37.8 F ARM A A: Drug~ ARM A A: Dr~ ASIAN
4 AB12345 BRA BRA-1 id-171 29.8 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
5 AB12345 BRA BRA-1 id-171 29.8 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
6 AB12345 BRA BRA-1 id-171 29.8 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
7 AB12345 BRA BRA-1 id-177 38.9 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
8 AB12345 BRA BRA-1 id-177 38.9 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
9 AB12345 BRA BRA-1 id-177 38.9 F ARM B B: Plac~ ARM B B: Pl~ ASIAN
10 AB12345 BRA BRA-1 id-23 41.3 F ARM A A: Drug~ ARM A A: Dr~ AMER~
# ... with 590 more rows, 40 more variables: TRTSDTM <dttm>, TRTEDTM <dttm>,
# EOSDY <dbl>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>,
# REGION1 <fct>, SAFFL <fct>, USUBJID <chr>, PARAM <fct>, AVISIT <fct>,
# AVAL <dbl>, LBCAT <fct>, PARAMCD <chr>, AVALU <fct>, AVISITN <dbl>,
# ABLFL2 <chr>, ABLFL <chr>, BASE <dbl>, BASETYPE <chr>, ANRIND <fct>,
# ANRLO <dbl>, ANRHI <dbl>, DTYPE <lgl>, ATOXGR <fct>, BTOXGR <fct>,
# ATOXDSCL <chr>, ATOXDSCH <chr>, ADTM <dttm>, ASPID <int>, LBSEQ <int>, ...

113 changes: 39 additions & 74 deletions tests/testthat/_snaps/h_map_for_count_abnormal.md
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# A tibble: 6 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL

# h_map_for_count_abnormal returns the correct map for range method with healthy single input

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Output
# A tibble: 6 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL

# h_map_for_count_abnormal returns the correct map for default method with unused LOW LOW/HIGH HIGH input

Code
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Output
# A tibble: 6 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL

---

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Output
# A tibble: 7 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT LOW
3 ALT LOW LOW
4 ALT NORMAL
5 CPR HIGH
6 CPR LOW
7 CPR NORMAL
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL

# h_map_for_count_abnormal returns the correct map for range method with unused LOW LOW/HIGH HIGH input

Code
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Output
# A tibble: 10 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT HIGH HIGH
3 ALT LOW
4 ALT LOW LOW
5 ALT NORMAL
6 CPR HIGH
7 CPR HIGH HIGH
8 CPR LOW
9 CPR LOW LOW
10 CPR NORMAL
PARAM ANRIND
1 ALT HIGH
2 ALT HIGH HIGH
3 ALT LOW
4 ALT LOW LOW
5 ALT NORMAL
6 CPR HIGH
7 CPR HIGH HIGH
8 CPR LOW
9 CPR LOW LOW
10 CPR NORMAL

---

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Output
# A tibble: 6 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL
1 ALT HIGH
2 ALT LOW
3 ALT NORMAL
4 CPR HIGH
5 CPR LOW
6 CPR NORMAL

---

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Output
# A tibble: 4 x 2
# Groups: PARAM [2]
PARAM ANRIND
<chr> <chr>
1 ALT HIGH
2 ALT NORMAL
3 CPR LOW
4 CPR NORMAL
1 ALT HIGH
2 ALT NORMAL
3 CPR LOW
4 CPR NORMAL

29 changes: 18 additions & 11 deletions tests/testthat/_snaps/h_stack_by_baskets.md
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Expand Up @@ -3,17 +3,24 @@
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# A tibble: 8 x 6
STUDYID USUBJID ASTDTM AEDECOD AESEQ SMQ
<fct> <fct> <dttm> <fct> <int> <fct>
1 AB12345 AB12345-BRA-11-id-8 2021-12-05 02:02:07 dcd D.2.1.5.3 2 D.2.1.5~
2 AB12345 AB12345-BRA-12-id-120 2020-02-05 01:42:29 dcd D.2.1.5.3 2 D.2.1.5~
3 AB12345 AB12345-BRA-1-id-171 2022-11-29 12:18:31 dcd C.1.1.1.3 2 C.1.1.1~
4 AB12345 AB12345-BRA-1-id-23 2020-07-10 07:32:49 dcd B.2.2.3.1 3 C.1.1.1~
5 AB12345 AB12345-BRA-1-id-59 2021-10-10 23:54:46 dcd C.1.1.1.3 4 C.1.1.1~
6 AB12345 AB12345-BRA-1-id-9 2021-06-01 14:39:09 dcd C.1.1.1.3 1 C.1.1.1~
7 AB12345 AB12345-BRA-11-id-8 2021-12-21 02:02:07 dcd C.1.1.1.3 3 C.1.1.1~
8 AB12345 AB12345-BRA-12-id-120 2020-10-01 01:42:29 dcd C.1.1.1.3 3 C.1.1.1~
STUDYID USUBJID ASTDTM AEDECOD AESEQ
1 AB12345 AB12345-BRA-11-id-8 2021-12-05 02:02:07 dcd D.2.1.5.3 2
2 AB12345 AB12345-BRA-12-id-120 2020-02-05 01:42:29 dcd D.2.1.5.3 2
3 AB12345 AB12345-BRA-1-id-171 2022-11-29 12:18:31 dcd C.1.1.1.3 2
4 AB12345 AB12345-BRA-1-id-23 2020-07-10 07:32:49 dcd B.2.2.3.1 3
5 AB12345 AB12345-BRA-1-id-59 2021-10-10 23:54:46 dcd C.1.1.1.3 4
6 AB12345 AB12345-BRA-1-id-9 2021-06-01 14:39:09 dcd C.1.1.1.3 1
7 AB12345 AB12345-BRA-11-id-8 2021-12-21 02:02:07 dcd C.1.1.1.3 3
8 AB12345 AB12345-BRA-12-id-120 2020-10-01 01:42:29 dcd C.1.1.1.3 3
SMQ
1 D.2.1.5.3/A.1.1.1.1 aesi
2 D.2.1.5.3/A.1.1.1.1 aesi
3 C.1.1.1.3/B.2.2.3.1 aesi(BROAD)
4 C.1.1.1.3/B.2.2.3.1 aesi(BROAD)
5 C.1.1.1.3/B.2.2.3.1 aesi(BROAD)
6 C.1.1.1.3/B.2.2.3.1 aesi(BROAD)
7 C.1.1.1.3/B.2.2.3.1 aesi(BROAD)
8 C.1.1.1.3/B.2.2.3.1 aesi(BROAD)

# h_stack_by_baskets returns an empty dataframe with desired variables and labels when there are no adverse events falling within any of the baskets selected

Expand Down
10 changes: 4 additions & 6 deletions tests/testthat/_snaps/split_cols_by_groups.md
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Expand Up @@ -3,12 +3,10 @@
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# A tibble: 3 x 4
valname label levelcombo exargs
<chr> <chr> <list> <list>
1 AnyGrade Any Grade (%) <chr [5]> <list [0]>
2 Grade34 Grade 3-4 (%) <chr [2]> <list [0]>
3 Grade5 Grade 5 (%) <chr [1]> <list [0]>
valname label levelcombo exargs
1 AnyGrade Any Grade (%) 1, 2, 3, 4, 5 NULL
2 Grade34 Grade 3-4 (%) 3, 4 NULL
3 Grade5 Grade 5 (%) 5 NULL

# combine_groups combines character vectors

Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/test-abnormal_by_worst_grade_worsen.R
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Expand Up @@ -48,7 +48,7 @@ testthat::test_that("h_adlb_worsen stacks data correctly (simple case)", {
direction_var = "GRADDR"
)

result <- result[order(result$VALUES), ]
result <- result[order(result$VALUES), ] %>% data.frame()

p1 <- input_data %>% dplyr::filter(WGRLOFL == "Y" & GRADDR == "L")
p2 <- input_data %>% dplyr::filter(WGRHIFL == "Y" & GRADDR == "H")
Expand All @@ -74,7 +74,9 @@ testthat::test_that("h_adlb_worsen stacks data correctly", {
direction_var = "GRADDR"
)

result <- result %>% dplyr::select(USUBJID, ARMCD, AVISIT, PARAMCD, ATOXGR, BTOXGR, WGRLOFL, WGRHIFL, GRADDR)
result <- result %>%
dplyr::select(USUBJID, ARMCD, AVISIT, PARAMCD, ATOXGR, BTOXGR, WGRLOFL, WGRHIFL, GRADDR) %>%
data.frame()

res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
Expand Down Expand Up @@ -225,10 +227,9 @@ testthat::test_that("h_adlb_worsen all high", {
worst_flag_high = c("WGRHIFL" = "Y"),
direction_var = "GRADDR"
)
result <- result[order(result$USUBJID, result$AVISIT, result$PARAMCD), ]

res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
testthat::expect_true(all(result$WGRHIFL == "Y" & result$GRADDR == "High"))
testthat::expect_identical(nrow(result), 600L)
})

testthat::test_that("h_adlb_worsen all low", {
Expand All @@ -247,8 +248,7 @@ testthat::test_that("h_adlb_worsen all low", {
worst_flag_low = c("WGRLOFL" = "Y"),
direction_var = "GRADDR"
)
result <- result[order(result$USUBJID, result$AVISIT, result$PARAMCD), ]

res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
testthat::expect_true(all(result$WGRLOFL == "Y" & result$GRADDR == "Low"))
testthat::expect_identical(nrow(result), 600L)
})
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