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Changelog

Source: NEWS.md

singleRcapture 0.2.1.2

CRAN release: 2024-07-18

  • 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 lok-likelihood function (by default) or if deriv argument is set to 1 or 2 respectively either a gradient or hessian of lok-likelihood function.

singleRcapture 0.2.1.1

CRAN release: 2023-10-23

  • Bugfix for tests failing with noLongDouble

singleRcapture 0.2.1

CRAN release: 2023-10-14

  • 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

CRAN release: 2023-06-11

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