Do milestone folder(s) exists as needed for current or preceding GGIR part(s). If not, it creates them.
Are folders empty, if yes then give error telling the user what part(s) need to be run first.
This is useful when running part X when part X - 1 has not been run yet, which always produced cryptic error messages.
We already had some of this functionality but ad-hoc in some of the parts. In this PR I am moving all this to a central function to ensure we systematically do this for parts 1 to 5. I am skipping this for part 6, because part 6 is a bit different as it depends on threshold combination specific input folders.
Checklist before merging:
[ ] Existing tests still work (check by running the test suite, e.g. from RStudio).
[x] Added tests (if you added functionality) or fixed existing test (if you fixed a bug).
[x] Clean code has been attempted, e.g. intuitive object names and no code redundancy.
[ ] Documentation updated:
[x] Function documentation
[ ] Chapter vignettes for GitHub IO
[ ] Vignettes for CRAN
[x] Corresponding issue tagged in PR message. If no issue exist, please create an issue and tag it.
[x] Updated release notes in inst/NEWS.Rd with a user-readable summary. Please, include references to relevant issues or PR discussions.
[ ] Added your name to the contributors lists in the DESCRIPTION file, if you think you made a significant contribution.
[ ] GGIR parameters were added/removed. If yes, please also complete checklist below.
If NEW GGIR parameter(s) were added then these NEW parameter(s) are:
[ ] documented in man/GGIR.Rd
[ ] included with a default in R/load_params.R
[ ] included with value class check in R/check_params.R
[ ] included in table of vignettes/GGIRParameters.Rmd with references to the GGIR parts the parameter is used in.
[ ] mentioned in NEWS.Rd as NEW parameter
If GGIR parameter(s) were deprecated these parameter(s) are:
[ ] documented as deprecated in man/GGIR.Rd
[ ] removed from R/load_params.R
[ ] removed from R/check_params.R
[ ] removed from table in vignettes/GGIRParameters.Rmd
[ ] mentioned as deprecated parameter in NEWS.Rd
[ ] added to the list in R/extract_params.R with deprecated parameters such that these do not produce warnings when found in old config.csv files.
Fixes #1144
Function checks:
This is useful when running part X when part X - 1 has not been run yet, which always produced cryptic error messages.
We already had some of this functionality but ad-hoc in some of the parts. In this PR I am moving all this to a central function to ensure we systematically do this for parts 1 to 5. I am skipping this for part 6, because part 6 is a bit different as it depends on threshold combination specific input folders.
Checklist before merging:
inst/NEWS.Rd
with a user-readable summary. Please, include references to relevant issues or PR discussions.DESCRIPTION
file, if you think you made a significant contribution.If NEW GGIR parameter(s) were added then these NEW parameter(s) are:
man/GGIR.Rd
R/load_params.R
R/check_params.R
vignettes/GGIRParameters.Rmd
with references to the GGIR parts the parameter is used in.If GGIR parameter(s) were deprecated these parameter(s) are:
man/GGIR.Rd
R/load_params.R
R/check_params.R
vignettes/GGIRParameters.Rmd
R/extract_params.R
with deprecated parameters such that these do not produce warnings when found in old config.csv files.