Final updated to remove errors and warnings for cran upload

DESCRIPTION

@@ -19,12 +19,12 @@ Description: Dominance analysis is a method that allows to compare the
              respectively.
 Authors@R: c(
   person("Claudio", "Bustos Navarrete", 
-         email = "[email protected]", role = c("aut", "cre"),
+         email = "[email protected]", role = c("aut", "cre", "cph"),
          comment = c(ORCID = "0000-0003-3478-9858")),
   person("Filipa", "Coutinho Soares", 
          email = "[email protected]", role = c("aut"),
          comment = c(ORCID = "0000-0002-7579-2538")))
-Version: 2.1.0
+Version: 2.0.0
 Depends:
     R (>= 4.0.0)
 License: GPL-2

NAMESPACE

@@ -3,6 +3,8 @@
 S3method(dominanceMatrix,data.frame)
 S3method(dominanceMatrix,dominanceAnalysis)
 S3method(dominanceMatrix,matrix)
+S3method(formula,lmWithCov)
+S3method(formula,mlmWithCov)
 S3method(plot,dominanceAnalysis)
 S3method(print,daAverageContribution)
 S3method(print,daContributionByLevel)

R/lmWithCov.r

@@ -38,7 +38,9 @@ lmWithCov<-function(f,x) {
 	class(out)<-"lmWithCov"
 	out
 }
-# @internal
-formula.lmWithCov<-function(x) {
+
+#' @keywords internal
+#' @export
+formula.lmWithCov<-function(x, ...) {
 	x$formula
 }

R/mlmWithCov.r

@@ -54,7 +54,8 @@ mlmWithCov<-function(f,x) {
 	class(out)<-"mlmWithCov"
 	out
 }
-# @internal
-formula.mlmWithCov<-function(x) {
+#' @keywords internal
+#' @export
+formula.mlmWithCov<-function(x, ...) {
 	x$formula
 }

README.Rmd

@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 ```
 # dominanceanalysis
 
-[![codecov](https://codecov.io/gh/clbustos/dominanceAnalysis/branch/master/graph/badge.svg)](https://codecov.io/gh/clbustos/dominanceAnalysis)
+[![codecov](https://codecov.io/gh/clbustos/dominanceAnalysis/branch/master/graph/badge.svg)](https://app.codecov.io/gh/clbustos/dominanceAnalysis)
 [![Stable version](http://www.r-pkg.org/badges/version-last-release/dominanceanalysis)](https://cran.r-project.org/package=dominanceanalysis)
 [![downloads](http://cranlogs.r-pkg.org/badges/grand-total/dominanceanalysis)](https://cran.r-project.org/package=dominanceanalysis)
 

README.md

@@ -3,7 +3,7 @@
 
 # dominanceanalysis
 
-[![codecov](https://codecov.io/gh/clbustos/dominanceAnalysis/branch/master/graph/badge.svg)](https://codecov.io/gh/clbustos/dominanceAnalysis)
+[![codecov](https://codecov.io/gh/clbustos/dominanceAnalysis/branch/master/graph/badge.svg)](https://app.codecov.io/gh/clbustos/dominanceAnalysis)
 [![Stable
 version](http://www.r-pkg.org/badges/version-last-release/dominanceanalysis)](https://cran.r-project.org/package=dominanceanalysis)
 [![downloads](http://cranlogs.r-pkg.org/badges/grand-total/dominanceanalysis)](https://cran.r-project.org/package=dominanceanalysis)

cran-comments.md

@@ -1,33 +1,34 @@
-## New version: 2.0.0
-
-This is a new version, that provides an important change on API and provides bug fixes. The changes from 1.3.0 are:
-- All submodels on fit functions are calculated using update(), so all settings on original model are used on dominance analysis. If R can't find the original dataset for update, just provide the dataset using the  *newdata* paramater on dominanceanalysis() method.
-- Little modification on dominanceMatrix
-- Added complete_flipped_axis parameter for plot() function. Added examples of flipped axis for plots
-- Tests for bootstrap analysis (betareg, lmm, glm). 
-- Added Nakagawa's indexes for linear mixed models. See README for examples.
-- On beta regression test, on test we check that using different estimator generates differents results
-- Bug fix: On R-devel, correct number of controls are provided for esoph dataset, breaking a test based on that example.
-- Bug fix: sort.matrix replaced to .sort.matrix to avoid sorting a standard matrix when devtools are used. 
-- Fixed documentation error on plot.dominanceAnalysis: default plot is for general dominance, no complete.
+## New version: 2.1.0
+
+This is a minor release, to provide a version of dominanceAnalysis that complies
+with current requirements of CRAN.
 
 ## Test environments
-* local Ubuntu 18.04 install, R 3.6.3
-* virtualized Ubuntu 18.04 install, R Under development (unstable) (2020-12-08 r79596) -- "Unsuffered Consequences"
-* Windows, R-devel, R Under development (unstable) (2020-12-09 r79601) (winbuilder)
-* Windows, R-release, R 4.0.3 (2020-10-10) (winbuilder)
-* Windows, R-old-release, R version 3.6.3 (2020-02-29) (winbuilder)
-* Ubuntu Linux 16.04 LTS, R-release, GCC (rhub)
-* Fedora Linux, R-devel, clang, gfortran (rhub)
+* local Ubuntu 22.04 install, R 4.3.2
+* remote macOS (r-release-macosx-arm64|4.3.0|macosx|macOS 13.3.1 (22E261)|Mac mini|Apple M1||en_US.UTF-8|macOS 11.3|clang-1403.0.22.14.1|GNU Fortran (GCC) 12.2.0 )
+* remote R-hub Windows Server 2022, R-devel, 64 bit
+* remote R-hub Fedora Linux, R-devel, clang, gfortran
+* remote winbuilder R devel (2024-01-31) x86_64-w64-mingw32
+* remote winbuilder R release R 4.3.2 (2023-10-31 ucrt)
 
 ## R CMD check results
-There were no ERRORs, WARNINGs or NOTEs on Ubuntu 18.04 local and virtualized, for R 3.6.3 and R devel.
+There were no ERRORs, WARNINGs or NOTEs on Ubuntu 22.04 local, for R 4.3.2 and for remote macOS 11.3, for R 4.3.0
+
+There is a common 1 WARNING in remote winbuilder R devel, remote winbuilder R release ,R-hub Windows Server 2022, R-devel, and remote R-hub Fedora Linux, R-devel, clang, gfortran: 
+
+  Possibly misspelled words in DESCRIPTION:
+    Azen (12:14, 16:14, 17:14, 18:25)
+    Budescu (11:14, 12:26, 16:26)
+    Luo (18:14)
+    Traxel (17:26)
+
+This WARNING addresses alleged misspellings of four authors' names in the DESCRIPTION; however, this is a bogus issue as the names are indeed correctly spelled.
 
-There are two notes on Ubuntu Linux 16.04 (rhub), Fedora Linux, R-devel (rhub), and 3 Windows version on winbuilder:
+There were no ERRORs or NOTEs for remote winbuilder R devel and remote winbuilder R release.
 
-* Possibly mis-spelled words in DESCRIPTION -> There are names of 4 authors of papers related to dominance, included on WORDLIST.
-* CRAN repository db overrides: X-CRAN-Comment: Archived on 2020-12-10 as check problems were not corrected in time -> This version fix the problem with test broken by new version of esoph data.
+There were 1 WARNING (already explained) and one NOTE on remote R-hub Fedora Linux, R-devel, clang, gfortran. The NOTE relate to examples with CPU (user + system) or elapsed time > 5s.
 
+There was 1 WARNING (already explained) and 3 NOTES for R-hub Windows Server 2022, R-devel. The NOTES relate to (1) the unavailability of the V8 package for the HTML manual version, (2) an extra directory in the check directory, and (3) an additional 'lastMiKTeXException' file. These NOTES are not directly related to the package's features but are specific to issues on the remote platform
 
 ## Downstream dependencies
 There are currently no downstream dependencies for this package