Changelog

Source: NEWS.md

Countr 3.5.82024-01-14

• This is an emergency release to keep the package on CRAN in case the scheduled archival of package ‘pscl’ happens.

Countr 3.5.72023-11-28

• a missing ‘@’ symbol had caused roxygen to generate items for ‘inheritParams’ in the arguments section of a couple of Rd files.

• fixed new warnings from the C++ compiler like ’ RcppExports.cpp:528:18: warning: format string is not a string literal (potentially insecure) [-Wformat-security]’.

• now import selectively from ‘dplyr’. Also, see the ‘todo’ note in ‘Countr-package.R’.

Countr 3.5.62022-11-12

• several documentation files had duplicated descriptions of some arguments.

• changed several instances of class(...) = "..." to use inherits.

• changed http://www.football-data.co.uk/englandm.php to https://www.football-data.co.uk to fix a NOTE from R check.

• switched from travisci to github actions.

Countr 3.5.52021-03-03

• changed maintainer.

• fixed a doi reference in DESCRIPTION to be in proper format.

Countr 3.5.42019-08-21

• fixed wrong links in inst/doc/index.html.

Countr 3.5.3 (not on CRAN)

• consolidation after the refactoring of the repository.

• created pkgdown website.

• dealt with ‘xtimes’ problem on Windows (issue#1: the data frame returned by optimx_2018-7.10 on Windows has a column xtime not xtimes).

• a number of updates in connection of the forthcoming release of the JSS paper.

Countr 3.5.22018-10-04

• small adjustments before submission.

• renamed ‘Countr.R’ to ‘Countr-package.R’.

• updated the main vignette with the accepted version of the JSS paper.

Countr 3.5.0 (not on CRAN)

• now covariates for ancilliary parameters for the renewal regression model can be specified as part of argument ‘formula’. This uses the extended formulas provided by package Formula. The syntax with argument anc remains available.

Countr 3.4.3 (not on CRAN)

• dealt with warnigs from the compiler about unused variables (and a few others).
• When there is no precomputed bootstrap sample in the object, se.coef.renewal() now prints a slightly more informative message without raising a warning.

Countr 3.4.2 (not on CRAN)

• fixed the url’s in the references for the vignettes in REFERENCES.bib.

Countr 3.4.1 (CRAN 2017-11-20)2017-11-20

• bugs fixed in convolution methods.
• option added to rescale covariates (standardise, standardise_scale).
• new vignettes added + many examples with different datasets fitted.
• Bibtex entries for citation of the vignettes added to REFERENCES.bib.
• numerous small improvements throughout the package.

Countr 3.3.1 (not on CRAN)

• new type = "prob" for residuals - changes in residuals.renewal, .objectiveFunction and renewal(). Comments and asome examples are temporarily put in the documentation of renewal().
• new argument ‘log’ for .objectiveFunction(). It is now passed on to probability computing functions to specify whether logged values are required when summa = FALSE.

Countr 3.3.0 (not on CRAN)

• first changes on bitbucket.

Countr 3.2.8 (CRAN 2016-12-20)2016-12-20

• the call in the printout of renewal objects (and summary()) could be very wide (annoying in Sweave output), now print.renewal() and print.summary.renewal() obey ‘width’ when possible (see helper function .deparseCall()).
• bugs corrected in print.summary.renewal() when failure to compute variance or residuals.

Countr 3.2.7 (CRAN 2016-10-06)2016-10-06

• fixed some bugs in printing methods.
• added a jss_paper vignette.

Countr 3.2.6 (CRAN 2016-09-14)2016-09-14

Countr 3.2.4 (not on CRAN)

• merged changes done separately by T. and G. to Version 3.2.2.
• fixed some bugs introduced in 3.2.3.

Countr 3.2.3 (not on CRAN)

• all count functions vectorized in c++.
• likelihood functions improved.

Countr 3.2.2 (not on CRAN)

• minor bug fixed in .checkInitialValues in the anc parameters.
• all bivariate functionalities removed.
• fertility dataset now exported with data().

Countr 3.2.1 (not on CRAN)

• minor bugs fixed in .objectiveFunction and predict with std.error.
• last location “/…” vectorial parameters returned.
• sign in the Frank Copula package changed to be more consistent with the intuitive results: theta <0 -> negative dependence.

Countr 3.2.0 (CRAN 2016-03-23)2016-03-23

• consolidated the documentation.
• first CRAN version.

Countr 3.1.x (not on CRAN)

• clean-up for CRAN submission.

Countr 3.0.0 (not on CRAN)

• renewal constructor + formula + methods.
• dePril convolution added.
• changed the way built in distributions are called.

Countr 2.0.3 (not on CRAN)

• inclusion of covariates using formula.
• Burr (weibull-gamma) distribution added.
• delayed first arrival included.

Countr 2.0.1 (not on CRAN)

• dePril convolution option added.

Countr 2.0.0 (not on CRAN)

• header files added taking advantage of Rcpp attributes.
• conv_utils.cpp added (contains the convolution general methods).
• weibull, gamma, gengamma counting processes added.
• option to add user based inter-arrival times distribution using routines getProbs_directConv, getProbs_minConv; see tests for examples.

Countr 1.1.9 (not on CRAN)

• incorporated the convolution computations from Tarak’s paper.

Countr 1.1.8 (not on CRAN)

• introduced file .Rbuildignore in the root directory of the package.
• shortened the name of subdirectory ‘Euler-van …’ to remove the complaint from ‘R CMD build’ about long paths. Also, to remove the warning by ‘R CMD check’ about ‘not fully portable file names’, replaced space with undescore in the directory name and the pdf file in it.
• in file ‘DESCRIPTION’ - moved Rcpp from DEPENDS to IMPORTS:.
• completed the roxigen argument descriptions (in the sense that ‘R CMD check’ doesn’t complain).

Countr 1.1.7 (not on CRAN)

• gam_weiH and gam_weiA renamed ccX and ccY.
• vectorial version dWeibullInterArrivalCountInd and dWeibullInterArrivalCountFrankCopula improved.
• vectorial version with gamma heterogeinity added: Note that you only pass X %*% beta and not the exponential.
• tests added based on Examples from McShane(2008) paper.
• tests added for bivariate vectorial functions.
• cRes object removed from “R/” to free some space.

Countr 1.1.5 (not on CRAN)

• pkg renamed from BivCount to Countr.
• alphagen2 changed to alphagen.
• oldCpp file removed.
• gamma-heterogeneity functions added to the original and fast version.
• covariates-heterogeneity functions added to the original and fast version.

Countr 1.1.0 (not on CRAN)

• renamed alphagen to alphagenOrig.

• the signatures of the cpp functions now have namespace prefixes for namespaces other than Rcpp. In this way RcppExports.cpp does not need using namespace arma which is not included by Rcpp::compileAttributes and devtools::test() and so needed to be added manually after these calls.

  I actually used search and replace to replace occurences in the body of the functions in our cpp files, but since we can put the ‘using namespace’ directives in them, only the signatures of exported functions are important for the abovde purpose.

• replaced std::cout with calls to Rprintf() in C++ code, since direct printing from C++ inside R can cause problems (and is caught by R CMD check). Also removed <iostream.