try to harmonize the templates (#496)

following #476, I tried to make the templates a bit clearer. something
added

1. for aet01_aesi and aet01 template, remove the check functions in pre.
all these derivations are executed without check! as users are
responsible for these derivations and they are clear. more checks added
in `main` functions
    1. check the arm variable are identical in levels (in adsl and adae)
    2. check variables to analyze exists (especially those new derived)
3. remove `deco`. titles/footnotes should be handled in citril using
lopo
1. remove aet01_2. this can be handled through arguments of aet01
1. for aet02 template, variants are removed. can be achieved through
argument `row_split_var`
2. add many utility functions (currently put in aet02.R but should go
into utility.R)
    3. valid_row_path. this checks if a row_path is valid for a table
4. valid_sort_at_path. this conduct the sort based on `row_path` if it
is valid. (sort_at_path gives error on incorrect row_path provided, and
aet02_1 previously will run into issues if prune_0 = FALSE on empty
data)
5. get_sort_path. this function will create "*" between variables, e.g,
`get_sort_path(c("A","B"))` will give "A" "*" "B", this is required by
`sort_at_path`
6. tlg_sort_by_var. this functions will sort using "A" and "B", instead
of "A" "*" "B". Also will check if the table contains the path. if does
not contain the path, the sorting will be ignored.

I think some of the funcitonality should go into tern/rtables. But for
now let's use them.

Please review this update in general and I will finalize this PR if no
objections. Then everyone can collaborate to harmonize all templates.

@Teninq @BFalquet @duanx9 @crazycatandy @barnett11

---------

Signed-off-by: b_falquet <[email protected]>
Co-authored-by: benoit <[email protected]>
Co-authored-by: b_falquet <[email protected]>

.Rbuildignore

@@ -3,11 +3,14 @@
 ^\.pre-commit-config\.yaml$
 ^data-raw
 ^temp$
-^.github$
-^staged_dependencies.yaml$
-_pkgdown.yaml
+^\.github$
+^staged_dependencies\.yaml$
+_pkgdown\.yaml
 docs
-^.lintr
-^.gitlab-ci.yml
-CODE_OF_CONDUCT.md
-SECURITY.md
+^\.lintr
+^\.gitlab-ci\.yml
+CODE_OF_CONDUCT\.md
+SECURITY\.md
+^doc$
+^Meta$
+^\.vscode$

.gitignore

@@ -10,3 +10,6 @@ temp
 .Renviron
 .Rprofile
 .vscode
+doc/
+Meta/
+*pdf

DESCRIPTION

@@ -30,11 +30,14 @@ Imports:
     magrittr,
     methods,
     nestcolor (>= 0.1.1),
+    purrr,
+    stringr,
     rlang,
     rlistings (>= 0.2.1),
     rtables (>= 0.6.0),
     tern (>= 0.8.1),
-    tibble
+    tibble,
+    utils
 Suggests:
     knitr,
     rmarkdown,
@@ -92,7 +95,10 @@ Collate:
     'package.R'
     'pdt01.R'
     'pdt02.R'
+    'reexports.R'
     'rmpt01.R'
     'rspt01.R'
+    'rtables_utils.R'
+    'standard_rules.R'
     'vst01.R'
     'vst02.R'