Added standalone ratioReg() support for weighted ratio
regression, optional one-inflation model selection, bootstrap intervals,
and diagnostic plots.
Added the oichao() family, a modified Chao estimator
based on counts 2 and 3 for improved robustness to one-inflation.
Updated rare-count-family simulation support so
oichao() works correctly through the public
simulate() methods.
Updated README and package documentation to describe the new
oichao() model.
ratioReg(): fixed subset so that bare
expressions like subset = grp == "a" evaluate inside
data as documented.
ratioReg(): fixed bootstrap with
model = "M0" or model = "M1", which previously
errored because the primary population estimate was not yet attached
when resampling started.
Expanded test coverage for oichao() (mu, variance,
density, deviance residuals, analytic population variance) and for
ratioReg() (validation paths, maxCount,
subset, alternative estimators,
extractAIC/nobs, custom
ratioFormula, fixed-model bootstrap).
Split family tests into dedicated test_fam_* files and
added focused family files for chao() and
oichao() to make CI failures identify the affected model
directly.
Cyprian Jurkowski contributed the first implementations
of oichao() and ratioReg().
singleRcapture 1.0.1
fixed checks of the variables
singleRcapture 1.0.0
Fixed mixed up ztoi* and oizt*
families
Fixed documentation for the estimatePopsize()
function
A CITATION file added with reference to the JSS
paper
singleRcapture 0.2.3
BugFix for anova and other not working methods
Tests for not working methods added
Small changes to the documentation
singleRcapture 0.2.2
Fixing documentation typos and errors
plot now has a default value of qq
Vignette added based on the paper submitted to the JSS
singleRcapture 0.2.1.2
Bugfix for interaction terms in formula not being considered
Small changes in summary for marginal count distributions
Small fixes for standard errors in predicted means
Code coverage raised to nearly 90%
The logLik.singleRStaticCountData method now has a
type argument that, if set to "function" makes
the function return the minus log-likelihood function (by default) or if
deriv argument is set to 1 or 2
respectively either a gradient or hessian of log-likelihood
function.
singleRcapture 0.2.1.1
Bugfix for tests failing with noLongDouble
singleRcapture 0.2.1
Fixed bugs in IRLS fitting when providing
weights argument when calling
estimatePopsize
The weightsAsCounts option in controlModel
now works properly, dfbeta and dfpopsize
decrease weight of selected row in a model matrix instead of deleting it
when this is set to TRUE
simulate method now works for both family object (like
ztpoisson()) and for objects returned by
estimatePopsize
Introduced singleRStaticCountData sub class for
singleRclass and made estimatePopsize a method
so that a new package singleRcaptureExtra (under
development) can make all necessary calculations for pop size estimation
when providing object fitted by countreg::zerotrunc or
VGAM::vglm/VGAM::vgam
Some bugfixes for multicore bootstrap
Code was re-factored to make further development/maintenance for the
package much easier
Update will be uploaded to CRAN
semiparametric bootstrap now has a much faster sampling
algorithm (that does the same job)
Unit tests: * Reduced computational burden of unit tests * Multicore
tests will only be performed after
TEST_SINGLERCAPTURE_MULTICORE_DEVELOPER is set to
"true" via Sys.setenv and
_R_CHECK_LIMIT_CORES_ to false
singleRcapture 0.2.0.1
Added offset argument to
estimatePopsize
Added options for parallel computing in bootstrap and
in dfbeta
Added deviance for all negative binomial based models. (NOTE: They
are very slow for now and I believe it may change after I verify one
theoretical results that will lead to significant speed increase for
these computations)
Overhaul of starting points (new methods and added linear predictors
start in IRLS)
Vastly improved redoPopSize which now handles bootstrap
on a fitted model non standard covariance matrixes newdata
argument user supplied coef etc.
Added predict.singleR method which offers standard
error for both link, response as well as
mean predictions
No unexpected warnings should occur now in main function when using
the package correctly
All control arguments are now verified before being passed
Fitting is now more reliable
Added information about stats::optim error codes
Added warnings for functions computing deviance
bugfixes:
fixed bugs occurring when using mathematical functions as part of
formulas i.e. when setting formula to something like:
y ~ log(x) + I(x ^ t) + I(t ^ 2)
singleRcapture 0.1.4
features
Added ztoinegbin, oiztnegbin and
ztHurdlenegbin models
Added an optional arguments to all family-functions to specify a
link function for distribution parameters
Updated and standardized documentation
Added more warnings
Added some more methods for singleR class in some
commonly used glm functions, in particular
texreg::screenreg should work well now
changes
Changed some default arguments
Added option to save logs from IRLS fitting
bugfixes
Fixed some issues with intercept only models
Fixed some slight miscalculations in information matrixes for one
inflated models making fitting them much more reliable
github repository
More and better Rcmd tests
singleRcapture 0.1.3.2 – NTTS
features:
Added function that implements population size estimates for
stratas
More warnings in fitting
More options in control functions
Corrected/implemented deviance residuals for more models
changes:
Now the whole package uses camelCase
Performance upgrades
Corrected some miss calculated moments
Change exported data so that factors are actually factors not just
characters
Removed unused dependency
github repository
Added automated R-cmd check
singleRcapture 0.1.3.1
features:
Basically all of documentation was redone and now features most of
important theory on SSCR methods and some information on (v)glms
Added checks on positivity of working weights matrixes to stabilise
"IRLS" algorithm
Added most of sandwich capabilities to the package, in particular:
S3 method for vcovHC was implemented
vcovCL should work on singleR class
objects should work with "HC0" and "HC1"type argument values
Basic version of function redoPopEstimation for
updating the population size estimation after post-hoc procedures was
implemented
popSizeEst function for extracting population size
estimation results was implemented
Minor improvements to memory usage were made and computation was
speed up a little
Changed names of mle and robust fitting methods to optim and IRLS
respectively
Some bugfixes
More warnings messages in estimate_popsize.fit
singleRcapture 0.1.3
features:
Multiple new models
IRLS generalised for distributions with multiple
parameters
bugfixes
QOL improvements
extended bootstrap and most other methods for new models
singleRcapture 0.1.2
features:
control parameters for model
control parameters for regression in bootstrap sampling
leave one out diagnostics for popsize and regression parameters
(dfbetas were corrected)
fixes for Goodness of fit tests in zero one truncated models
computational improvements in IRLS
other small bugfixes
singleRcapture 0.1.1
bug fixes and some of the promised features for 0.2.0 in particular
More tiny tests
Some fixes for marginal frequencies
Deviance implemented
dfbetas and levarage matrix
Parametric bootstraps work correctly for the most part there is just
some polishing left to do