fido 1.1.0

• 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

• 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

bug fixes

• Updating documentation under the newest version of R (4.2.1)

fido 1.0.2

bug fixes

• Removing a timing test because it is irrelevant and can fail under certain set-ups.

fido 1.0.1

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

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.