issue with pre functions

[clarkliming]

export checks and use :: in pre functions

part of #476

[BFalquet]

Looks good to me

[github-actions]

Unit Tests Summary

    1 files    33 suites   1m 35s ⏱️
178 tests 128 ✔️   50 💤 0 ❌
348 runs  234 ✔️ 114 💤 0 ❌

Results for commit 6d13c28.

♻️ This comment has been updated with latest results.

[github-actions]

🧪 $Test coverage: 97.14%$

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  --------------------------------------------------------------
R/ael01_nollt.R                 26       2  92.31%   82-91
R/aet01_aesi.R                 189       7  96.30%   51, 53-57, 285
R/aet01.R                      342       5  98.54%   41, 253, 328, 334, 562
R/aet02.R                      235       1  99.57%   493
R/aet03.R                       83       0  100.00%
R/aet04.R                      106       2  98.11%   169, 186
R/aet10.R                       50       1  98.00%   102
R/assertions.R                  71       5  92.96%   178-182
R/checks.R                      20       0  100.00%
R/chevron_tlg-S4class.R         21       0  100.00%
R/chevron_tlg-S4methods.R      136      12  91.18%   410-482
R/cmt01a.R                     186       0  100.00%
R/cmt02_pt.R                    49       0  100.00%
R/dmt01.R                       30       0  100.00%
R/dst01.R                      290       0  100.00%
R/dtht01.R                      98       0  100.00%
R/egt01.R                       45       0  100.00%
R/egt02.R                       56       0  100.00%
R/egt03.R                      132       3  97.73%   118, 164, 322
R/egt05_qtcat.R                 57       0  100.00%
R/ext01.R                       71       4  94.37%   230-231, 235-236
R/kmg01.R                       37       7  81.08%   58-66, 106
R/lbt01.R                       94       0  100.00%
R/lbt04.R                       49       0  100.00%
R/lbt05.R                       68       5  92.65%   148-153
R/lbt07.R                       90       1  98.89%   171
R/lbt14.R                      188      24  87.23%   54, 56, 108-109, 111-117, 144, 257, 259, 311-312, 314-320, 347
R/mht01.R                       69       2  97.10%   33-34
R/mng01.R                       95      12  87.37%   114, 118-121, 130-138, 180
R/pdt01.R                       57       0  100.00%
R/pdt02.R                       65       0  100.00%
R/utils.R                       73       0  100.00%
R/vst01.R                       47       0  100.00%
R/vst02.R                       92       2  97.83%   109, 240
TOTAL                         3317      95  97.14%

Diff against main

Filename          Stmts    Miss  Cover
--------------  -------  ------  -------
R/aet01_aesi.R       +4       0  +0.08%
TOTAL                +4       0  +0.00%

Results for commit: 19e2725d16d02bca953b402c0a49be7f637daa10

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

new update in code

[BFalquet]

Minor point inside (could be solved later). Thank you for the hard work

[BFalquet]

Not sure if missing should appear (I dont think so). What do you think @barnett11

[clarkliming]

this is a difficult issue. We can expect Missing grade in adae.atoxgr, (even in cleaned adam). We should not filter this out because we also need to count the number of events. But this should not be counted in the count_occurrences_by_grade.

[clarkliming]

ok. for ATOXGR, those records are still using NA (not convertet to a level) and then will be discarded.

[clarkliming]

another update: ADAE.ATOXGR is a string (character in R's language). in rtables we require ATOXGR to be factor. Then we need to convert it into factor.
so here while we apply reformating, we need to populate NA for empty strings. Very different logic here!

reformat(c('1','2','3','4','5',''), rule('1'='1','2'='2','3'='3','4'='4','5'='5'))

my suggestion is to keep this missing level for now (as this solves many issues) and open another issue to deal with this.

[clarkliming]

probably need to evaluate the reformat when it is partial match of the whole set, option 1, keep the rest, option 2, discard the rest levels (use NA to replace) (but this is really contradictory to what we are doing to conver NA to "Missing"!) The logic/design behind this need to be further evaluated.

[BFalquet]

issue opened here: #492

[BFalquet]

Good to merge from my side @clarkliming, issue has been opened for the reaming details

[clarkliming]

I further adapt the code to remove the missing levels. hope this time it works