spAbundance 0.2.1
- Fixed a
C++ memory issue in
predict.spAbund() that could result in crashes under
certain situations.
spAbundance 0.2.0
- Updated
svcAbund() to now work with Poisson and
negative binomial families. Note that the function now defaults to use
family = 'Poisson', which differs from the previous
implementation when only family = 'Gaussian' was supported.
This switch was done to maintain consistency with other spAbundance
model-fitting functions.
- Added functionality for independent priors on the species-specific
effects to allow species-effects to be treated as fixed effects as
opposed to random effects from a common community-level distribution for
the following model types:
msNMix().
- Added in a check at the top of all model fitting functions to return
an error when the number of posterior samples saved based on the MCMC
criteria (
n.batch, batch.length,
n.samples, n.burn, n.thin,
n.chains) are specified in a way that leads to a
non-integer value. In such situations, models would previously run and
return without an error, but sometimes the last posterior sample in any
given chain could have widely inaccurate values, or values that
prevented subsequent functions from working. Thanks to Wendy Leuenberger
for bringing this to my attention.
- Fixed some typos in the documentation.
- Updated C++ code to adhere to the new lack of re-mapping of
functions in Rinternals.h and R_ext/Error.h when building packages on
CRAN.
- Fixed a typo in the generation of initial values for latent
unstructured random effects in all model functions. The typo had no
major ramifications, if anything it just led to slower convergence, as
it resulted in very large (or very small) initial values for the latent
random effects that are not really viable on the log scale.
- Moved GitHub development page to the “biodiverse” group. The GitHub
link for the development repository is now https://github.com/biodiverse/spAbundance.
spAbundance 0.1.3
- Added in the
independent.betas tag into the
priors list for certain multi-species model types to allow
for specifying an independent prior on the species-specific effects as
opposed to treating species-specific effects as random effects. This can
be useful under certain circumstances when the distribution of effects
across species may not be adequately represented by a Gaussian
distribution. This tag is available for the following functions:
lfMsAbund (Gaussian only), sfMsAbund (Gaussian
only), and svcMsAbund.
- Fixed a bug in zero-inflated Gaussian latent factor abundance models
(
lfMsAbund).
- Fixed a bug in
waicAbund() that prevented it from
working with svcMsAbund models.
- Fixed minor issues in C++ to pass CRAN additional checks.
spAbundance 0.1.1
- Updated the
neonDWP data set after NEON announced an
error in some of the bird point count data (more information here.
Also updated the associated vignette that uses these data.
- Updated the
msAbund() function to make it compatible
with spOccupancy::updateMCMC(), which allows for picking up
a model run where it left off instead of having to restart the MCMC from
scratch. I am planning to allow this functionality for all model fitting
functions in spAbundance in a future version.
- Updated all model fitting functions to fix a potential error that
could arise in the calculation of Rhat that could lead to the function
failing under certain circumstances. This was particularly the case in
multi-species models with large amounts of rare species.
spAbundance 0.1.0
- This is the first release of
spAbundance