Closes #1: Update `admiraltemplate` to `admiraldata` and copy from admiral.test

[kaz462]

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[kaz462]

Following updates in this PR:

1. Copied R/data.R, dev and data folders from admiral.test to admiraldata

   git clone https://github.com/pharmaverse/admiral.test.git --branch devel --single-branch ./admiral.test --depth 1
   cp -R ./admiral.test/data  ./admiraldata
   cp -R ./admiral.test/dev  ./admiraldata
   cp ./admiral.test/R/data.R  ./admiraldata/R
   rm -rf admiral.test

2. Updated the following and removed some template files & tests folder

   6. Update/Remove the following files to use your extension name:
      • DESCRIPTION File - Name, Authors
      • admiraltemplate.Rproj
      • testthat.R
      • News.md
      • .Rbuildignore
      • .gitignore
      • .lycheeignore
      • _pkgdown.yml

3. devtools::document() + resolve workflow issues

[kaz462]

@kaz462 is it worth not copying the data in the {admiral.test} data folder and just regenerating it with the files that you copy over? Just to make sure that what you copied over genuinely makes the dataset that you expect?

I got some errors when I try to rerun the programs from admiral.test/dev. @manciniedoardo Should we merge this PR first, and create a separate issue for rerunning datasets (some programs need updates), so that we can work on other issues in parallel? - issue created

e.g., errors from dev/pp.R-

> data("pc")
Warning message:
In data("pc") : data set ‘pc’ not found
> 
> # Calculate subjects with all missing;
> blq_usubjid <- pc %>%
+   ungroup() %>%
+   group_by(STUDYID, DOMAIN, USUBJID) %>%
+   summarise(PPORRES = max(PCSTRESN, na.rm = TRUE))
> 
> # Remove from PC, subjects with all blq (placebos);
> remove_usubjid <- blq_usubjid %>% filter(PPORRES == 0)
> 
> pc1 <- anti_join(pc, remove_usubjid, by = c("STUDYID", "DOMAIN", "USUBJID"))
Error in `anti_join()`:
! Join columns in `y` must be present in the data.
✖ Problem with `STUDYID`, `DOMAIN`, and `USUBJID`.
Run `rlang::last_trace()` to see where the error occurred.

[kaz462]

@pharmaverse/admiraldata If you are assigned to admiraldata issues, please wait until this PR is merged