Merge branch 'CRAN-3.1.0-release'

Author: billy34

.Rbuildignore

@@ -11,3 +11,4 @@
 ^vignettes$
 ^cran-comments\.md$
 ^pkgdown$
+^CRAN-SUBMISSION$

.gitignore

@@ -5,3 +5,4 @@ inst/doc
 .Rapp.history
 local
 docs
+CRAN-SUBMISSION

DESCRIPTION

@@ -4,26 +4,71 @@ Title: Supervised Component Generalized Linear Regression
 Description: 
     An extension of the Fisher Scoring Algorithm to combine PLS regression with GLM 
     estimation in the multivariate context. Covariates can also be grouped in themes.
-Version: 3.0.9000
-Date: 2024-02-24
-Authors@R: c(
-    person("Guillaume","Cornu",,"gcornu@cirad.fr", role=c("aut","cre"), comment=c(ORCID="0000-0002-7523-5176")),
-    person("Frederic","Mortier",,"fmortier@cirad.fr",role="aut", comment=c(ORCID="0000-0001-5473-709X")),
-    person("Catherine","Trottier",,"catherine.trottier@univ-montp3.fr",role="aut"),
-    person("Xavier","Bry",,"xavier.bry@univ-montp2.fr",role="aut"),
-    person("Jocelyn","Chauvet",,,role="aut", comment=c(ORCID="0000-0002-4466-6483")),
-    person("Sylvie","Gourlet-Fleury",,"sylvie.gourlet-fleury@cirad.fr",role="dtc",comment=c(ORCID="0000-0002-1136-4307",CoForChange="<http://coforchange.cirad.fr/>")),
-    person("Claude","Garcia",,"claude.garcia@cirad.fr",role="dtc",comment=c(ORCID="0000-0002-7351-0226",CoForTips="<https://www.cofortips.org/>"))  
-  )
+Version: 3.1.0
+Date: 2025-03-24
+Authors@R:
+    c(person(
+      given = "Guillaume",
+      family = "Cornu",
+      email = "gcornu@cirad.fr", 
+      role = c("aut","cre"), 
+      comment = c(ORCID = "0000-0002-7523-5176")),
+    person(
+      given = "Frederic",
+      family = "Mortier",
+      email = "fmortier@cirad.fr",
+      role = "aut", 
+      comment = c(ORCID = "0000-0001-5473-709X")),
+    person(
+      given = "Catherine",
+      family = "Trottier",
+      email = "catherine.trottier@univ-montp3.fr",
+      role = "aut"),
+    person(
+      given = "Xavier",
+      family = "Bry",
+      email = "xavier.bry@univ-montp2.fr",
+      role = "aut"),
+    person(
+      given = "Jocelyn",
+      family = "Chauvet",
+      role = "aut", 
+      comment = c(ORCID="0000-0002-4466-6483")),
+    person(
+      given = "Sylvie",
+      family = "Gourlet-Fleury",
+      email = "sylvie.gourlet-fleury@cirad.fr",
+      role = "dtc",
+      comment = c(ORCID = "0000-0002-1136-4307", "Projet CoForChange <https://coforchange.cirad.fr>")),
+    person(
+      given = "Claude",
+      family = "Garcia",
+      email = "claude.garcia@cirad.fr",
+      role = "dtc",
+      comment = c(ORCID = "0000-0002-7351-0226", "Projet CoForTips <https://www.cofortips.org>")),
+    person(
+      "GAMBAS", 
+      role = "fnd",
+      comment = "<https://gambas.cirad.fr>")
+    )
 License: CeCILL-2 | GPL-2
 URL: https://scnext.github.io/SCGLR/, https://github.com/scnext/SCGLR, https://cran.r-project.org/package=SCGLR
 BugReports: https://github.com/SCnext/SCGLR/issues
 Depends:
     R (>= 3.0.0)
 Imports:
-    Matrix,Formula,graphics,ggplot2 (>= 3.0.0),grid,pROC (>= 1.9),ade4,rlang,pls
+    Matrix,
+    Formula,
+    graphics,
+    ggplot2 (>= 3.0.0),
+    grid,pROC (>= 1.9),
+    ade4,
+    rlang,
+    pls
 Suggests:
-    future,future.apply,progressr
+    future,
+    future.apply,
+    progressr
 LazyData: yes
 RoxygenNote: 7.3.2
 Encoding: UTF-8

NEWS.md

@@ -1,4 +1,17 @@
-# version 3.0.9000 (dev)
+# version 3.1
+
+## New features
+- preliminary integration of code from `SCnext/mixedSCGLR` written by Jocelyn Chauvet (issue #11)
+- moved parallelization to `future` framework. Need `future.apply` package (issue #16)
+- added progress to `scglrCrossVal` and `scglrThemeBackward` functions using `progressr` package (issue #17)
+
+## Deprecations
+- parameter `nfolds` of `scglrCrossVal` as been renamed to `folds` and now accepts also vectors.
+For now a warning is issued and provided value is used but update your code as it will likely be removed
+in a future version.
+- parameter `mc.cores` of `scglrCrossVal` is now deprecated as of the move to `future` framework for parallelization.
+
+## bug fixes and improvements
 - fix bug happening when providing a single Y variable to `sglrTheme` (issue #1)
 - allow to provide folds for cross validation defined by user (issue #2)
 - individual beta and gamma for themes were not properly computed (issue #5) 
@@ -12,17 +25,6 @@
 - move from `plsdepot::plsreg2` to `pls::plsr` to initialize mixed model components (issue #22)
 - fix rstudio bug displaying error message when printing a MultivariateFormula (in fact a Formula) (issue #23).
 
-## New features
-- preliminary integration of code from `SCnext/mixedSCGLR` written by Jocelyn Chauvet (issue #11)
-- moved parallelization to `future` framework. Need `future.apply` package (issue #16)
-- added progress to `scglrCrossVal` and `scglrThemeBackward` functions using `progressr` package (issue #17)
-
-## Deprecations
-- parameter `nfolds` of `scglrCrossVal` as been renamed to `folds` and now accepts also vectors.
-For now a warning is issued and provided value is used but update your code as it will be removed
-in a next version.
-- parameter `mc.cores` of `scglrCrossVal` is now deprecated as of the move to `future` framework for parallelization.
-
 # version 3.0
 This major version introduces a new feature allowing to group covariates in so called **themes**.
 

R/data.r

@@ -11,7 +11,7 @@
 #'  used to describe the physical factors as well as vegetation characteristics. 
 #'  14 physical factors were used pertaining the description of topography, geology and rainfall 
 #'  of each plot. Vegetation is characterized through 16-days enhanced vegetation index (EVI) data.
-#' @references S. Gourlet-Fleury et al. (2009--2014) CoForChange project: \url{http://coforchange.cirad.fr/}
+#' @references S. Gourlet-Fleury et al. (2009--2014) CoForChange project: \url{https://coforchange.cirad.fr/}
 #' @references C. Garcia et al. (2013--2015) CoForTips project: \url{https://www.cofortips.org/}
 #' @format
 #' \tabular{ll}{

R/dataGen.R

@@ -11,7 +11,7 @@
 #'  used to describe the physical factors as well as vegetation characteristics.
 #'  On each plot, 34 physical factors were used pertaining the description of topography, geology, rainfall... 
 #'  Vegetation is characterized through 16-days enhanced vegetation index (EVI) data.
-#' @references S. Gourlet-Fleury et al. (2009--2014) CoForChange project: \url{http://coforchange.cirad.fr/}
+#' @references S. Gourlet-Fleury et al. (2009--2014) CoForChange project: \url{https://coforchange.cirad.fr/}
 #' @references C. Garcia et al. (2013--2015) CoForTips project: \url{https://www.cofortips.org/}
 #' @format
 #' \tabular{ll}{

R/genus2.R

@@ -11,7 +11,7 @@
 #'  used to describe the physical factors as well as vegetation characteristics.
 #'  23 physical factors were used pertaining the description of topography, geology and rainfall
 #'  of each plot. Vegetation is characterized through 16-days enhanced vegetation index (EVI) data.
-#' @references S. Gourlet-Fleury et al. (2009--2014) CoForChange project: \url{http://coforchange.cirad.fr/}
+#' @references S. Gourlet-Fleury et al. (2009--2014) CoForChange project: \url{https://coforchange.cirad.fr/}
 #' @references C. Garcia et al. (2013--2015) CoForTips project: \url{https://www.cofortips.org/}
 #' @format
 #' \tabular{ll}{

R/methods.r

@@ -7,6 +7,7 @@
 #'@param maxiter integer for maximum number of iterations of \code{SR} function
 #'@param epsilon positive convergence threshold
 #'@param bailout integer argument
+#'@returns an object of class \code{method.SCGLR}
 methodSR <- function(phi="vpi", l=1, s=1/2, maxiter=1000, epsilon=1e-6, bailout=10) {
 
   # check arguments

R/scglrCrossVal.r

@@ -194,15 +194,15 @@ scglrCrossVal <-  function(formula,data,family,K=1,folds=10,type="mspe",size=NUL
       xnew <- cbind(1,AX[valid,,drop=FALSE])
       beta.coefs <- sapply(gamma.fit, coef)
     }
-    
+
     predict <- multivariatePredictGlm(Xnew=xnew,family,
       beta.coefs,offset[valid,,drop=FALSE])
 
     if(type=="auc"){
       cvNull[1:ny] <- auc(roc(y[valid,,drop=FALSE],predict, quiet=TRUE))
     } else if(type%in%c("likelihood","aic","bic","aicc","mspe")){
       cvNull[1:ny] <- infoCriterion(ynew=y[valid,,drop=FALSE],predict,family,
-        type=type,size=size[valid,,drop=FALSE],npar=nrow(gamma.coefs))
+        type=type,size=size[valid,,drop=FALSE],npar=nrow(beta.coefs))
     }
 
     try_result <- try({

README.Rmd

@@ -10,7 +10,7 @@ bibliography: assets/SCGLR.bib
 ---
 <!-- File generated from README.Rmd. Changes must be done from there -->
 
-# SCGLR <img src="man/figures/SCGLR_small.jpg" align="right">
+# SCGLR <img src="man/figures/SCGLR_small.jpg" align="right" alt="SCGLR logo">
 
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/SCGLR)](https://cran.r-project.org/package=SCGLR)