singleRcapture (development version)

singleRcapture 1.0.0

• Fixed mixed up ztoi* and oizt* families
• Fixed documentation for the estimatePopsize() function
• Fixed vignette
• Fixed README.Rmd
• Logo added [thanks to Oliwia Awuku]
• 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)
• Code for weights in IRLS fitting was speed up
• Minor bugfixes

singleRcapture 0.2.0

The package is now at CRAN

• features and improvements:
  • Added final Hurdleztnegbin model
  • 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 cammelCase
  • 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

singleRcapture 0.1.0

• first version of the package released