v3.5.8

.Rbuildignore

@@ -13,3 +13,4 @@ README_devel.md
 ^sav[0-9]*[.]Rhistory
 ^\.github$
 ^codecov\.yml$
+.rsync_exclude

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Countr
 Type: Package
 Title: Flexible Univariate Count Models Based on Renewal Processes
-Version: 3.5.6.9000
+Version: 3.5.8
 Authors@R: c( person(given = "Tarak", family = "Kharrat",
                      role = c("aut"), 
                      email = "tarak@realanalytics.co.uk"),
@@ -13,6 +13,10 @@ Description: Flexible univariate count models based on renewal processes. The
     syntax as in glm() and package 'flexsurv'.  The methodology is described by
     Kharrat et all (2019) <doi:10.18637/jss.v090.i13> (included as vignette
     'Countr_guide' in the package).
+    If the suggested package 'pscl' is not available from CRAN, it can be
+    installed with 'remotes::install_github("cran/pscl")'. It is no longer used
+    by the functions in this package but is needed for some of the extended
+    examples.
 License: GPL (>= 2)
 URL: https://geobosh.github.io/Countr/ (doc), https://github.com/GeoBosh/Countr (devel)
 BugReports: https://github.com/GeoBosh/Countr/issues
@@ -35,17 +39,17 @@ Imports:
     RColorBrewer,
     dplyr,
     standardize,
-    pscl,
     lmtest,
     xtable
 LinkingTo: Rcpp, RcppArmadillo
 Suggests:
     testthat,
-    knitr
+    knitr,
+    pscl
 RdMacros: Rdpack
 VignetteBuilder: knitr
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 NeedsCompilation: yes
 Collate: 
     'Countr-package.R'
@@ -58,6 +62,7 @@ Collate:
     'dWeibull.R'
     'dWeibullgamma.R'
     'data.R'
+    'probpredict.R'
     'renewal_IV.R'
     'renewal_tools.R'
     'renewal_cstr.R'

NAMESPACE

@@ -17,6 +17,7 @@ S3method(nobs,renewal)
 S3method(predict,renewal)
 S3method(print,renewal)
 S3method(print,summary.renewal)
+S3method(prob_predict,glm)
 S3method(renewalCoef,default)
 S3method(renewalCoef,glm)
 S3method(renewalCoef,renewalCoefList)
@@ -49,6 +50,7 @@ export(evWeibullCount)
 export(evWeibullgammaCount)
 export(frequency_plot)
 export(getParNames)
+export(prob_predict)
 export(renewal)
 export(renewal.control)
 export(renewal.convPars)
@@ -64,7 +66,6 @@ export(surv)
 import(Formula)
 import(Matrix)
 import(Rcpp)
-import(dplyr)
 import(flexsurv)
 import(optimx)
 importFrom(MASS,ginv)
@@ -76,13 +77,15 @@ importFrom(VGAM,logit)
 importFrom(VGAM,probit)
 importFrom(boot,boot)
 importFrom(car,Boot)
+importFrom(dplyr,contains)
+importFrom(dplyr,groups)
+importFrom(dplyr,left_join)
 importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(lattice,barchart)
 importFrom(lmtest,lrtest)
 importFrom(numDeriv,hessian)
 importFrom(numDeriv,jacobian)
-importFrom(pscl,predprob)
 importFrom(standardize,standardize)
 importFrom(stats,AIC)
 importFrom(stats,as.formula)
@@ -92,6 +95,7 @@ importFrom(stats,confint.default)
 importFrom(stats,density)
 importFrom(stats,dnbinom)
 importFrom(stats,dpois)
+importFrom(stats,family)
 importFrom(stats,formula)
 importFrom(stats,getCall)
 importFrom(stats,glm.fit)

NEWS.md

@@ -1,4 +1,22 @@
-# Countr 3.5.6 (CRAN)
+# Countr 3.5.8
+
+- This is an emergency release to keep the package on CRAN in case the scheduled
+  archival of package 'pscl' happens.
+
+# Countr 3.5.7
+
+- 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 3.5.6
 
 - several documentation files had duplicated descriptions of some arguments.
 
@@ -10,21 +28,21 @@
 - switched from travisci to github actions.
 
 
-# Countr 3.5.5 (CRAN)
+# Countr 3.5.5
 
 - changed maintainer.
 
 - fixed a doi reference in DESCRIPTION to be in proper format.
 
 
-# Countr 3.5.4 (CRAN)
+# Countr 3.5.4
 
 - fixed wrong links in inst/doc/index.html.
 
 
-# Countr 3.5.3
+# Countr 3.5.3 (not on CRAN)
 
-- consolidation after the refactoring of the reposotory.
+- consolidation after the refactoring of the repository.
 
 - created pkgdown website.
 
@@ -36,7 +54,7 @@
   JSS paper.
 
 
-# Countr 3.5.2 (CRAN)
+# Countr 3.5.2
 
 - small adjustments before submission.
 
@@ -45,105 +63,105 @@
 - updated the main vignette with the accepted version of the JSS paper.
 
 
-# Countr 3.5.0
+# 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
+# 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
+# Countr 3.4.2 (not on CRAN)
 - fixed the url's in the references for the vignettes in REFERENCES.bib.
 
-# Countr 3.4.1 (2017-11-20)
+# Countr 3.4.1 (CRAN 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
+# 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
+# Countr 3.3.0 (not on CRAN)
 - first changes on bitbucket.
 
-# Countr 3.2.8  (2016-12-20)
+# Countr 3.2.8  (CRAN 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  (2016-10-06)
+# Countr 3.2.7  (CRAN 2016-10-06)
 - fixed some bugs in printing methods.
 - added a jss_paper vignette.
 
-# Countr 3.2.6 (2016-09-14)
+# Countr 3.2.6 (CRAN 2016-09-14)
 
-# Countr 3.2.4
+# 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
+# Countr 3.2.3 (not on CRAN)
 - all count functions vectorized in c++.
 - likelihood functions improved.
 
-# Countr 3.2.2
+# 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
+# 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 (2016-03-23)
+# Countr 3.2.0 (CRAN 2016-03-23)
 - consolidated the documentation.
-- to be first CRAN version.
+- first CRAN version.
 
-# Countr 3.1.x
+# Countr 3.1.x (not on CRAN)
 - clean-up for CRAN submission.
 
-# Countr 3.0.0
+# 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
+# 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
+# Countr 2.0.1 (not on CRAN)
 - dePril convolution option added.
 
-# Countr 2.0.0
+# 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
+# Countr 1.1.9 (not on CRAN)
 - incorporated the convolution computations from Tarak's paper.
 
-# Countr 1.1.8
+# 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
@@ -153,7 +171,7 @@
 - completed the roxigen argument descriptions (in the sense that 'R CMD check'
   doesn't complain).
 
-# Countr 1.1.7
+# Countr 1.1.7 (not on CRAN)
 - `gam_weiH` and `gam_weiA` renamed `ccX` and `ccY`.
 - vectorial version `dWeibullInterArrivalCountInd` and
   `dWeibullInterArrivalCountFrankCopula` improved.
@@ -163,14 +181,14 @@
 - tests added for bivariate vectorial functions.
 - `cRes` object removed from "R/" to free some space.
 
-# Countr 1.1.5
+# 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
+# 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

R/Countr-package.R

@@ -12,30 +12,36 @@
 #'
 #' @useDynLib Countr
 #'
-#' @import Matrix Rcpp Formula flexsurv dplyr
+#' @import Matrix Rcpp Formula flexsurv
+#' 
 #' @importFrom stats nobs AIC  coef  confint  confint.default
 #' @importFrom stats formula as.formula getCall  glm.fit  logLik  model.frame
 #' @importFrom stats model.matrix  model.response  model.weights
 #' @importFrom stats na.pass  pnorm  poisson  printCoefmat  quantile
 #' @importFrom stats dnbinom dpois lm pchisq
 #' @importFrom stats residuals update.formula  vcov
 #' @importFrom stats density predict qqline qqnorm terms.formula
+#' 
 #' @importFrom graphics par plot
+#' @importFrom utils capture.output
+#'
+#' @importFrom standardize standardize
+#' @importFrom dplyr left_join contains groups
 #' @importFrom RColorBrewer brewer.pal
+#' @importFrom Rdpack reprompt
+#'
 #' @importFrom lattice barchart
 #' @importFrom car Boot
-#' @importFrom Rdpack reprompt
-#' @importFrom utils capture.output
-#' @importFrom standardize standardize
 #' @importFrom lmtest lrtest
 #' @importFrom xtable xtable
 #'
+#' @importFrom stats family
+#' 
 #' @details
 #'
-#' The methodology is described in the forthcoming paper
-#' \insertCiteOnly{CountrJssArticle}{Countr}
-#' in the Journal of Statistical Software (included in the package as vignette
-#' \code{vignette('Countr_guide_paper', package = "Countr")}).
+#' The methodology is described by
+#' \insertCiteOnly{CountrJssArticle;textual}{Countr}.  The paper is included in
+#' the package as vignette \code{vignette('Countr_guide_paper', package = "Countr")}).
 #'
 #' The main function is \code{\link{renewalCount}}, see its documentation for
 #' examples.
@@ -46,16 +52,14 @@
 #'
 #' @references
 #'
-#' \insertRef{CountrJssArticle}{Countr}
-#' 
 #' \insertRef{baker2017event}{Countr}
 #'
 #' \insertRef{boshnakov2017bivariate}{Countr}
 #'
 #' \insertRef{cameron2013regression}{Countr}
 #'
-#' \insertRef{TarakEtAl2018jss}{Countr}
-#'
+#' \insertRef{CountrJssArticle}{Countr}
+#' 
 #' \insertRef{mcshane2008count}{Countr}
 #'
 #' \insertRef{winkelmann1995duration}{Countr}
@@ -67,3 +71,13 @@ utils::globalVariables(
     c("Counts", "Actual" # see compareToGLM()
       )
 )
+## (jan 2023) *TODO*: maybe "groups" should be added to utils::globalVariables
+## (and not imported from 'dplyr', see the call
+##     lattice::barchart(preds ~ count_range, data = df, groups = groups, ...
+## in frequency_plot().
+## Rcheck doesn't complain about undefined variable 'groups' since there is a
+## function groups() in 'dplyr'. However, at first sight at least, it seems that
+## in 'group = groups' the right-hand side is the name of the column in the data
+## frame as symbol. When checking, note that the above call invokes the formula
+## method of lattice::barchart and see also the panel function
+## lattice::panel.barchart()