NEWS
fido 1.1.1 (2024-06-05)
- Fixing a minor bug in the configure script
fido 1.1.0 (2024-05-30)
- Updating the basset model to allow for additive Gaussian processes.
- Updating the random seed generation.
- Removed maltipoo as an export. There were a few small changes to names of internal maltipoo functions (e.g., "verify.maltipoo" became "verify_maltipoo").
- Updating the configure script to a compile but that occured when OpenMP is present but R is not configured to use it.
- Fixed a few small bugs (predicting with one sample; wrong constant; etc.).
fido 1.0.4 (2023-03-24)
- changing default optimizer (lbfgs rather than adam), adam is more sensitive to random seed
- adding new r2 methods for calculating Bayesian R2 for pibble and basset models
- predict.bassetfit now accepts a newdata=NULL argument to predict on training set
bug fixes
- fixing a few discrepancies with base R commands (print, summary, etc).
fido 1.0.3 (2022-08-23)
bug fixes
- Updating documentation under the newest version of R (4.2.1)
fido 1.0.2 (2022-07-06)
bug fixes
- Removing a timing test because it is irrelevant and can fail under certain set-ups.
fido 1.0.1 (2022-05-17)
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.
fido 1.0.0 (2022-02-16)
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.
fido 0.1.14
- 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)
fido 0.1.13
- 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
fido 0.1.12
- orthus added for jointly fitting multinomial and gaussian data (e.g., 16S microbiome and metabolomics data)
fido 0.1.11
- 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
fido 0.1.10
- 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.