# 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](https://www.instagram.com/abenakrzywo/)]
-   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](https://cran.r-project.org/package=singleRcapture)

-   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
