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.