bug fixes
- Updating documentation under the newest version of R (4.2.1)
bug fixes
- Removing a timing test because it is irrelevant and can fail under certain set-ups.
bug fixes
- Changing phyloseq from imports to depends, was causing issues installing from CRAN.
- Fixing bug in configure.ac that was causing openmp parallelization to not work on some machines.
More changes to make the final push for CRAN! Changes include:
- Updating the description file to match CRAN’s standards
- Removing the dependency to driver
- Linking the one remote package (MicrobeDS) to a separate CRAN-like Github repo using the “drat” package. This is to match CRAN’s policy against no use of “Remotes”.
- Precomputing the longer running vignettes, cutting R CMD check times in half. The original vignettes can be found in the vignettes folder with a “.orig” extension for reproducibility.
- More changes to prepare for version 0.2 (and CRAN soon), including:
- Lots of cleaning of small warnings and notes
- Fixing erorrs with the base plot function
- Cleaning up some manual entries
- Fixing the errors posted on Github (to_ilr among others)
- tons of tiny changes to prepare for version 0.2 (and ultimately CRAN) featured changes include:
- plot and coef methods for *fit objects now abide by CRAN generic naming scheme - may cause some problems if prior code had positional arguments to these functions
- now being tested using travis integration (vignettes not tested there due to time constraints)
- merged Kim’s fixes to maltipoo code (will almost certainly change maltipoo results; there had been a bug in prior versions)
- Internally stored mallard and mallard_family data now import as
mallard and mallard_family rather than both importing as ps. Solved a R CMD CHECK warning.
- Lots of tiny updates to documentation
- orthus added for jointly fitting multinomial and gaussian data (e.g., 16S microbiome and metabolomics data)
- Kim fixed windows installation problems (Thanks Kim!)
- Fixed bug in predict that was effecting ppc
- Fixed error when pars!=NULL in summary
- lambda_to_iqlr now had default behavior when focus.cov=NULL
- Fixed issue with Xi=NULL in pibblefit when trying to transform
- small changes to make pibble wrapper around c++ functions faster
- basset added for fitting non-linear regression using fido
- numerous changes to make installation easier
- Added a
NEWS.md file to track changes to the package.