Merging latest updated in fdaPDE/fdaPDE

.Rbuildignore

@@ -1 +1,8 @@
-^LICENSE
+^LICENSE.md
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^tests$
+[.]so$
+[.]o$
+^fdaPDE.Rcheck$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,65 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      RGL_USE_NULL: true
+      DISPLAY: 99.0
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: installing rgl support on Linux 
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libgl1-mesa-dev libglu1-mesa-dev
+        shell: bash
+
+      - name: install rgl support on macOS     
+        if: runner.os == 'macOS' 
+        run: |
+            brew install xquartz
+        shell: bash
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.gitignore

@@ -0,0 +1,13 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.o
+*.so
+*.dll
+*.html
+fdaPDE.Rproj
+fdaPDE.Rcheck/
+tests/data/SR-PDE
+tests/data/DE-PDE
+tests/data/tSR-PDE

DESCRIPTION

@@ -1,9 +1,11 @@
 Package: fdaPDE
-Version: 1.1-15
-Date: 2023-07-28
-Title: Functional Data Analysis and Partial Differential Equations (PDE); Statistical Analysis of Functional and Spatial Data, Based on Regression with PDE Regularization
+Version: 1.1-17
+Date: 2023-11-01
+Title: Physics-Informed Spatial and Functional Data Analysis
 Authors@R: c(person("Eleonora", "Arnone", role = c("aut", "cre"),
 		     email = "[email protected]"),
+		 person("Aldo", "Clemente", role = "aut",
+		     email = " [email protected]"),
 	     person("Laura M.", "Sangalli", role = c("aut"),
 		     email = "[email protected]"),
 	     person("Eardi", "Lila", role = c("aut"),
@@ -15,7 +17,6 @@ Authors@R: c(person("Eleonora", "Arnone", role = c("aut", "cre"),
 		    person("Giovanni", "Ardenghi", role = "ctb"),
 		    person("Blerta", "Begu", role = "ctb"),
 		    person("Michele", "Cavazzutti", role = "ctb"),
-		    person("Aldo", "Clemente", role = "ctb"),
 		    person("Alessandra", "Colli", role = "ctb"),
 		    person("Alberto", "Colombo", role = "ctb"),
 		    person("Luca", "Colombo", role = "ctb"),
@@ -33,7 +34,9 @@ Authors@R: c(person("Eleonora", "Arnone", role = c("aut", "cre"),
 		    person("Andrea", "Poiatti", role = "ctb"),
 		    person("Gian Matteo", "Rinaldi", role = "ctb"),
 	            person("Stefano", "Spaziani", role = "ctb"),
-		    person("Andrea", "Vicini", role = "ctb")
+		    person("Andrea", "Vicini", role = "ctb"),
+		    person("David C.", "Sterratt", role=c("cph"), 
+		            comment = "Author of included Triangle source files")
 		    )
 Maintainer: Eleonora Arnone <[email protected]>
 Depends: 
@@ -44,11 +47,11 @@ LinkingTo:
 	RcppEigen, Rcpp
 Suggests: 
     MASS,
-    testthat
-Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization. See Sangalli, L. M. (2021). Spatial Regression With Partial Differential Equation Regularisation. International Statistical Review, 89(3), 505-531. for an overview. The release 1.1-15 requires R (>= 4.2.0) to be installed on windows machines.
-License: CC BY-NC-SA 4.0
-Copyright: See the individual source files for copyrights information
+    testthat (>= 3.0.0)
+Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization. See Sangalli, L. M. (2021) <doi:10.1111/insr.12444> "Spatial Regression With Partial Differential Equation Regularisation" for an overview. The release 1.1-9 requires R (>= 4.2.0) to be installed on windows machines.
+License: GPL-3
 NeedsCompilation: yes
 SystemRequirements: GNU make
 RoxygenNote: 7.2.3
 Encoding: UTF-8
+Config/testthat/edition: 3

LICENSE.note

@@ -1,7 +1,4 @@
 This file summarizes ownerships and copyrights. Where possible further copyright and license information on the external code used for this project, can be found in individual files.
 
-- Triangle is "freely available, copyrighted by the author and may not be sold or included in commercial products without a license." (http://www.cs.cmu.edu/~quake/triangle.html). The Triangle source files are src/triangle.c and src/triangle.h .
+- Triangle is "freely available, copyrighted by the author and may not be sold or included in commercial products without a license." (http://www.cs.cmu.edu/~quake/triangle.html). The Triangle source files are src/C_Libraries/triangle.c and src/C_Libraries/triangle.h .
 
-- All other files are released under license CC BY-NC-SA 4.0
-
-The entire package is released under a Creative Common Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0), respecting all the individual licenses of the files. See http://creativecommons.org/licenses/by-nc-sa/4.0/ for details about this license.

R/InferenceDataObject.R

@@ -118,11 +118,11 @@ inferenceDataObject<-setClass("inferenceDataObject", slots = list(test = "intege
 #'n_cov = NULL,
 #'locations = NULL,
 #'locations_indices = NULL,
-#'locations_by_nodes = F,
+#'locations_by_nodes = FALSE,
 #'coeff = NULL, 
 #'beta0 = NULL, 
 #'f0 = NULL,
-#'f_var = F,
+#'f_var = FALSE,
 #'level = 0.95,
 #'n_flip = 1000)
 #' @export
@@ -138,11 +138,11 @@ inferenceDataObjectBuilder<-function(test = NULL,
                                 n_cov = NULL,
                                 locations = NULL,
                                 locations_indices = NULL,
-                                locations_by_nodes = F,
+                                locations_by_nodes = FALSE,
                                 coeff = NULL, 
                                 beta0 = NULL,
                                 f0 = NULL,
-                                f_var = F,
+                                f_var = FALSE,
                                 level = 0.95,
                                 n_flip = 1000)
 {

R/mesh.R

@@ -186,7 +186,7 @@ create.mesh.2D <- function(nodes, nodesattributes = NA, segments = NA, holes = N
     flags = paste(flags,"o2",sep = '')
   }
   if(order < 1 || order >2){
-    print('Order must be 1 or 2')
+    stop('Order must be 1 or 2')
   }
 
   if(nrow(triangles) > 0){
@@ -491,7 +491,7 @@ create.mesh.2.5D<- function(nodes, triangles = NULL, order = 1, nodesattributes
                 edges=outCPP[[1]], edgesmarkers=outCPP[[2]], neighbors=outCPP[[4]], holes=holes, order=order)
   }
   else if(order==2 && ncol(triangles) == 3){
-    print("You set order=2 but passed a matrix of triangles with just 3 columns. The midpoints for each edge will be computed.")
+    message("You set order=2 but passed a matrix of triangles with just 3 columns. The midpoints for each edge will be computed.")
 
     outCPP <- .Call("CPP_SurfaceMeshOrder2", triangles, nodes, PACKAGE = "fdaPDE")
 
@@ -693,7 +693,7 @@ create.mesh.3D<- function(nodes, tetrahedrons, order = 1, nodesattributes = NULL
                 holes=holes, order=order)
   }
   else if(order==2 && ncol(tetrahedrons) == 4){
-    print("You set order=2 but passed a matrix of tetrahedrons with just 4 columns. The midpoints for each edge will be computed.")
+    message("You set order=2 but passed a matrix of tetrahedrons with just 4 columns. The midpoints for each edge will be computed.")
 
     outCPP <- .Call("CPP_VolumeMeshOrder2", tetrahedrons, nodes, PACKAGE = "fdaPDE")
 
@@ -900,7 +900,7 @@ create.mesh.1.5D <- function(nodes, edges = NULL, order = 1, nodesattributes = N
 
   }
   else if( order==2 && ncol(edges)==2){
-    print("You set order=2 but passed a matrix of edges with just 2 columns. The midpoints for each edge will be computed.")
+    message("You set order=2 but passed a matrix of edges with just 2 columns. The midpoints for each edge will be computed.")
     outCPP <- .Call("CPP_EdgeMeshOrder2", edges, nodes, PACKAGE = "fdaPDE")
     edges = cbind( edges , outCPP[[6]])
     nodes=rbind(nodes, outCPP[[5]])

R/plot.R

@@ -15,6 +15,7 @@
 #' @usage \method{plot}{FEM}(x, colormap = "heat.colors", num_refinements = NULL, ...)
 #' @export
 #' @seealso \code{\link{FEM}}, \code{\link{image.FEM}}
+#' @return No return value
 #' @examples
 #' library(fdaPDE)
 #' ## Upload the horseshoe2D data
@@ -84,6 +85,7 @@ if(is(x$FEMbasis$mesh, "mesh.2D")){
 #'                 add = FALSE, main = NULL, col = "red", ...)
 #' @export
 #' @seealso \code{\link{FEM.time}}, \code{\link{image.FEM.time}}
+#' @return No return value
 #' @examples
 #' library(fdaPDE)
 #' ## Upload the horseshoe2D data
@@ -297,6 +299,7 @@ plot.FEM.time = function(x, time_locations = NULL, locations = NULL,
 
 #' @usage \method{plot}{mesh.2D}(x, ...)
 #' @export
+#' @return No return value
 #' @examples
 #' library(fdaPDE)
 #'
@@ -329,6 +332,7 @@ plot.mesh.2D<-function(x, ...)
 #' @name plot.mesh.2.5D
 
 #' @usage \method{plot}{mesh.2.5D}(x, ...)
+#' @return No return value
 #' @examples
 #' library(fdaPDE)
 #'
@@ -368,8 +372,8 @@ plot.mesh.2.5D<-function(x,...){
 #' @description Plot a \code{mesh.3D} object, generated by \code{create.mesh.3D}.
 #' @export
 #' @name plot.mesh.3D
-
 #' @usage \method{plot}{mesh.3D}(x, ...)
+#' @return No return value
 #' @examples
 #' library(fdaPDE)
 #'
@@ -414,8 +418,8 @@ plot.mesh.3D<-function(x,...){
 #' @param ... Arguments representing graphical options to be passed to \link[graphics]{par}.
 #' @description Plot a mesh.1.5D object, generated by \code{create.mesh.1.5D} or \code{refine.mesh.1.5D}.
 #' @name plot.mesh.1.5D
-
 #' @usage \method{plot}{mesh.1.5D}(x, ...)
+#' @return No return value
 #' @export
 plot.mesh.1.5D<-function(x, ...)
 {
@@ -657,6 +661,7 @@ R_plot_graph = function(FEM, ...){
  #' @method image FEM
  #' @seealso \code{\link{FEM}} \code{\link{plot.FEM}}
  #' @export
+ #' @return No return value
  #' @examples
  #' library(fdaPDE)
  #' ## Upload the horseshoe2D data
@@ -704,6 +709,7 @@ R_plot_graph = function(FEM, ...){
  #' @usage \method{image}{FEM.time}(x,t,lambdaS=1,lambdaT=1,num_refinements=NULL,...)
  #' @method image FEM.time
  #' @seealso \code{\link{FEM.time}} \code{\link{image.FEM.time}}
+ #' @return No return value
  #' @export
  #' @examples
  #' library(fdaPDE)