Flexible univariate count models based on renewal processes. The models may include covariates and can be specified with familiar formula syntax as in glm() and package 'flexsurv'. The methodology is described in a forthcoming paper in the Journal of Statistical Software (included as vignette 'Countr_guide').
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.
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'.
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
headers 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.
introduced file .Rbuildignore in the root directory of the package.
shortened the name of subdirectory
Euler-van ...' to remove the complaint fromR 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).
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
pkg renamed from BivCount to Countr
alphagen2 changed to alphagen
oldCpp file removed
gamma-heterogeneity functions added to the origanal and fast version
covariates-heterogeneity functions added to the origanal and fast version
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 cRcpp::compileAttributes and devtools::test() and so needed to ber 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.