update `aet05` and `aet05_all` #678

duanx9 · 2023-10-19T03:21:46Z

Close #665

Update aet05 filter: only include "*AETTE", "*CQTTE", and "*SMQTTE".
Update the main function (aet05 and aet05_all) to let the dataset name be exposed to users.
Update syn_data.
Update unit tests.
Update Chevron catalog.
Turn off partial match and catch typos.
Update data.R.

R/aet05.R

Signed-off-by: Liming <[email protected]>

github-actions · 2023-10-24T00:05:35Z

🧪 Test coverage: 96.87%

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  ---------------------------------------------------------------------
R/ael01_nollt.R                 21       1  95.24%   72
R/aet01_aesi.R                 148       1  99.32%   211
R/aet01.R                       98       1  98.98%   168
R/aet02.R                       44       0  100.00%
R/aet03.R                       76       0  100.00%
R/aet04.R                       88       0  100.00%
R/aet05_all.R                   11       0  100.00%
R/aet05.R                       44       1  97.73%   114
R/aet10.R                       42       0  100.00%
R/assertions.R                  99       6  93.94%   88-93
R/cfbt01.R                     107       0  100.00%
R/checks.R                      14       0  100.00%
R/chevron_tlg-S4class.R         24       0  100.00%
R/chevron_tlg-S4methods.R      144       1  99.31%   67
R/cmt01a.R                      52       0  100.00%
R/coxt01.R                      49       1  97.96%   129
R/dmt01.R                       36       0  100.00%
R/dst01.R                       94       0  100.00%
R/dtht01.R                     102       6  94.12%   50, 54-58
R/egt02.R                       35       0  100.00%
R/egt03.R                       80       1  98.75%   153
R/egt05_qtcat.R                 78       0  100.00%
R/ext01.R                       59       1  98.31%   50
R/fstg01.R                      44       0  100.00%
R/fstg02.R                      49       0  100.00%
R/kmg01.R                       29       0  100.00%
R/lbt04.R                       90       0  100.00%
R/lbt05.R                       66       5  92.42%   123-128
R/lbt06.R                       70       3  95.71%   141-144
R/lbt07.R                       93       0  100.00%
R/lbt14.R                       64       0  100.00%
R/lbt15.R                       20       0  100.00%
R/mht01.R                       54       0  100.00%
R/mng01.R                       82       9  89.02%   82, 86-90, 110-111, 153
R/pdt01.R                       60       0  100.00%
R/pdt02.R                       68       0  100.00%
R/rmpt01.R                      59      11  81.36%   87-96, 131
R/rmpt06.R                     134       3  97.76%   209-212
R/rspt01.R                      73       3  95.89%   155-158
R/rtables_utils.R              325      23  92.92%   51, 68, 119, 243, 264, 409-416, 483, 498-500, 502, 571-577, 587, 608
R/standard_rules.R              13       0  100.00%
R/ttet01.R                     122       3  97.54%   203-206
R/utils.R                      156      21  86.54%   141, 156, 175-177, 294-297, 301-304, 331, 335, 347, 349, 361, 378-380
R/vst02.R                       45       1  97.78%   108
TOTAL                         3261     102  96.87%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/aet01_aesi.R                  -2       0  -0.01%
R/aet01.R                       +4       0  +0.04%
R/aet02.R                       -6       0  +100.00%
R/aet03.R                       -1       0  +100.00%
R/aet04.R                       -1       0  +100.00%
R/aet05.R                       +4       0  +0.23%
R/aet10.R                       -1       0  +100.00%
R/chevron_tlg-S4class.R         +6       0  +100.00%
R/chevron_tlg-S4methods.R       +8      -3  +2.25%
R/cmt01a.R                      -6      -6  +10.34%
R/coxt01.R                      +1       0  +0.04%
R/dmt01.R                       +7       0  +100.00%
R/dst01.R                       -1       0  +100.00%
R/dtht01.R                      -1       0  -0.06%
R/egt02.R                       -2       0  +100.00%
R/egt03.R                       +3       0  +0.05%
R/egt05_qtcat.R                 -1       0  +100.00%
R/ext01.R                       -1       0  -0.03%
R/fstg01.R                      -6       0  +100.00%
R/fstg02.R                      -6       0  +100.00%
R/lbt04.R                       -1       0  +100.00%
R/lbt05.R                       -1       0  -0.11%
R/lbt06.R                       -2       0  -0.12%
R/lbt07.R                       -1       0  +100.00%
R/lbt14.R                       -2       0  +100.00%
R/mht01.R                      -17       0  +100.00%
R/mng01.R                      -14      +8  -9.93%
R/pdt02.R                       -1       0  +100.00%
R/rmpt01.R                      -6       0  -1.72%
R/rmpt06.R                    +134      +3  +97.76%
R/rtables_utils.R              +25      +4  -0.74%
R/standard_rules.R              +2       0  +100.00%
R/ttet01.R                      +5       0  +0.11%
R/utils.R                      +72     +21  -13.46%
R/vst02.R                       -1       0  -0.05%
TOTAL                         +190     +27  -0.69%

Results for commit: f334b72

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-10-24T00:07:40Z

Unit Tests Summary

    1 files   53 suites 6m 13s ⏱️
239 tests 171 ✔️   68 💤 0 ❌
482 runs 318 ✔️ 164 💤 0 ❌

Results for commit f334b72.

♻️ This comment has been updated with latest results.

clarkliming

data.R also need to be updated

clarkliming · 2023-10-24T00:34:49Z

Turn off partial match and catch typos.

could you also follow https://github.com/insightsengineering/coredev-tasks/issues/478 to turn off partial matching (I mean, no only in your side; this is not reflect in your code)

clarkliming

looks good, thank you

mistake

clarkliming · 2023-10-30T01:48:07Z

R/aet05.R

-    filter(grepl("AETTE", .data$PARAMCD)) %>%
+aet05_pre <- function(adam_db, dataset = "adsaftte", ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(grepl("(AE|CQ|SMQ)TTE", .data$PARAMCD)) %>%
    mutate(
      n_events = as.integer(.data$CNSR == 0)


if possible let's use upper case for all variables

clarkliming · 2023-10-30T01:50:52Z

R/aet05_all.R

    filter(.data$PARAMCD == "AEREPTTE") %>%
    select(all_of(c("USUBJID", "AVAL")))

-  adam_db$adaette <- adam_db$adaette %>%
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
    filter(grepl("TOT", .data$PARAMCD)) %>%
    mutate(
      n_events = as.integer(.data$AVAL)


mutate(, AVAL = NULL) if you don't need aval

or select(n_events = AVAL, USUBJID)

clarkliming · 2023-11-01T08:19:10Z

R/aet05.R

@@ -43,11 +51,11 @@ aet05_main <- function(adam_db,
    lbl_overall = lbl_overall,
    param_label = "PARAM",
    vars = "AVAL",
-    n_events = "n_events",
+    N_EVENTS = "N_EVENTS",


argument name should not be upper-case

Signed-off-by: Liming <[email protected]>

clarkliming

looks good thank you!

Signed-off-by: Liming <[email protected]>

update aet05 filter and main expose dataset name (#665)

1443fde

duanx9 self-assigned this Oct 19, 2023

duanx9 requested a review from clarkliming as a code owner October 19, 2023 03:21

duanx9 added 3 commits October 20, 2023 02:26

update syn_data and chevron catalog (#665)

067e3b7

[skip ci] turn off partial macth and catch typos (#665)

7859b5e

[skip ci] update aet05 filter (#665)

6962263

clarkliming reviewed Oct 20, 2023

View reviewed changes

R/aet05.R Show resolved Hide resolved

clarkliming added blocked chevron and removed blocked labels Oct 20, 2023

Merge branch 'main' into 665_update_aet05@main

d60b16d

Signed-off-by: Liming <[email protected]>

clarkliming reviewed Oct 24, 2023

View reviewed changes

duanx9 added 2 commits October 26, 2023 05:14

merge main branch into 665_update_aet05@main

ce6b82a

update (#665)

00e3336

clarkliming previously approved these changes Oct 26, 2023

View reviewed changes

turn off partial match options (#665)

773166e

clarkliming reviewed Oct 30, 2023

View reviewed changes

minor vars names uppercase convention (#665)

30a4e70

clarkliming reviewed Nov 1, 2023

View reviewed changes

duanx9 and others added 6 commits November 1, 2023 08:41

minor vars names uppercase convention (#665)

2308cac

partial match check pass (#665)

d3ffb40

Merge branch 'main' into 665_update_aet05@main

95b9848

update news.md (#665)

bf55565

update news.md (#665)

cd0cdc3

Update NEWS.md

f1e9dc2

Signed-off-by: Liming <[email protected]>

clarkliming approved these changes Nov 6, 2023

View reviewed changes

Update NEWS.md

f334b72

Signed-off-by: Liming <[email protected]>

clarkliming merged commit cc736c8 into main Nov 10, 2023
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clarkliming deleted the 665_update_aet05@main branch November 10, 2023 04:20

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update `aet05` and `aet05_all` #678

update `aet05` and `aet05_all` #678

duanx9 commented Oct 19, 2023 •

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update aet05 and aet05_all #678

update aet05 and aet05_all #678

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duanx9 commented Oct 19, 2023 • edited Loading

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Unit Tests Summary

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update `aet05` and `aet05_all` #678

update `aet05` and `aet05_all` #678

duanx9 commented Oct 19, 2023 •

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github-actions bot commented Oct 24, 2023 •

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