Merge pull request #2 from oelhammouchi/develop

Tweak some more CRAN things and add requirement for Fortran 2003

DESCRIPTION

@@ -1,42 +1,44 @@
-Package: trngl
 Type: Package
+Package: trngl
 Title: Bootstrap Simulations for Claims Reserving Models
 Version: 0.1.0
-Date: 2023-02-08
-Authors@R: c(
+Authors@R: 
     person("Othman", "El Hammouchi", , "[email protected]", role = c("aut", "cph", "cre"))
-  )
-Description: Check the assumptions of popular actuarial reserving models against a given claims triangle using
-    efficient parallel bootstrap simulations. Various simulation configurations are supported for the Mack and ODP models. 
-    Facilities are provided for visualising the results and flagging suspicious observations.
+Description: Check the assumptions of popular actuarial reserving models
+    against a given claims triangle using efficient parallel bootstrap
+    simulations. Various simulation configurations are supported for the
+    Mack and overdispersed Poisson models.  Facilities are provided for visualising the
+    results and flagging suspicious observations.
 License: MIT + file LICENSE
-Depends: R (>= 3.5.0)
+Depends: 
+    R (>= 3.5.0)
 Imports: 
-    rTRNG (>= 4.23.1.2),
     ChainLadder (>= 0.2.18),
+    cli (>= 3.6.2),
     ggplot2 (>= 3.5.1),
     ggrepel (>= 0.9.5),
     reshape2 (>= 1.4.4),
     rlang (>= 1.1.3),
-    cli (>= 3.6.2)
-LinkingTo: 
-    Rcpp (>= 0.11.0),
-    RcppArmadillo (>= 0.12.8.2.1),
-    BH (>= 1.84.0.0), 
-    rTRNG (>= 4.23.1.2), 
-    RcppProgress (>= 0.4.2)
+    rTRNG (>= 4.23.1.2)
 Suggests: 
     covr,
     testthat (>= 3.0.0),
     withr (>= 3.0.0)
-LazyData: true
+LinkingTo: 
+    BH (>= 1.84.0.0),
+    Rcpp (>= 0.11.0),
+    RcppArmadillo (>= 0.12.8.2.1),
+    RcppProgress (>= 0.4.2),
+    rTRNG (>= 4.23.1.2)
+Config/testthat/edition: 3
+Config/testthat/parallel: true
 Encoding: UTF-8
-RoxygenNote: 7.2.3
-Roxygen: list(load = "source", old_usage = TRUE, markdown = TRUE)
+LazyData: true
 NeedsCompilation: yes
 Packaged: 2023-02-26 18:07:38 UTC; othman
-Config/testthat/edition: 3
-Config/testthat/parallel: true
+Roxygen: list(load = "source", old_usage = TRUE, markdown = TRUE)
+RoxygenNote: 7.2.3
+SystemRequirements: Fortran 2003
 Collate: 
     'RcppExports.R'
     'boot_res.R'

NAMESPACE

@@ -13,12 +13,6 @@ S3method(plot,single)
 S3method(print,mack)
 S3method(print,odp)
 S3method(print,trngl)
-export(.mackPairsBoot)
-export(.mackPairsSim)
-export(.mackParamBoot)
-export(.mackParamSim)
-export(.mackResidBoot)
-export(.mackResidSim)
 export(UKMotor)
 export(as.trngl)
 export(cum2incr)

R/RcppExports.R

@@ -32,32 +32,26 @@ getTrnglSeed <- function() {
     .Call('_trngl_getTrnglSeed', PACKAGE = 'trngl')
 }
 
-#' @export
 .mackParamBoot <- function(trngl, dist, cond, n_boot = 1e3L, n_sim = 1e3L, progress = TRUE) {
     .Call('_trngl_mackParamBoot', PACKAGE = 'trngl', trngl, dist, cond, n_boot, n_sim, progress)
 }
 
-#' @export
 .mackResidBoot <- function(trngl, resid_type, cond, n_boot = 1e3L, n_sim = 1e3L, progress = TRUE) {
     .Call('_trngl_mackResidBoot', PACKAGE = 'trngl', trngl, resid_type, cond, n_boot, n_sim, progress)
 }
 
-#' @export
 .mackPairsBoot <- function(trngl, n_boot = 1e3L, n_sim = 1e3L, progress = TRUE) {
     .Call('_trngl_mackPairsBoot', PACKAGE = 'trngl', trngl, n_boot, n_sim, progress)
 }
 
-#' @export
 .mackPairsSim <- function(trngl, sim_type, n_boot, n_sim, progress) {
     .Call('_trngl_mackPairsSim', PACKAGE = 'trngl', trngl, sim_type, n_boot, n_sim, progress)
 }
 
-#' @export
 .mackParamSim <- function(trngl, sim_type, cond, dist, n_boot, n_sim, progress) {
     .Call('_trngl_mackParamSim', PACKAGE = 'trngl', trngl, sim_type, cond, dist, n_boot, n_sim, progress)
 }
 
-#' @export
 .mackResidSim <- function(trngl, sim_type, cond, resid_type, n_boot, n_sim, progress) {
     .Call('_trngl_mackResidSim', PACKAGE = 'trngl', trngl, sim_type, cond, resid_type, n_boot, n_sim, progress)
 }

configure

@@ -0,0 +1,42 @@
+#!/usr/bin/env sh
+
+cat <<EOF > test-f03.f90
+module mod_test
+  implicit none
+
+  type t_test
+    integer :: test_field
+
+  contains
+    procedure :: set_test_field
+  end type t_test
+
+contains
+  subroutine set_test_field(this, val)
+    class(t_test) :: this
+    integer :: val
+    this%test_field = val
+  end subroutine set_test_field
+end module mod_test
+
+program test
+  use mod_test
+  implicit none
+
+  type(t_test) :: test_var
+
+  call test_var%set_test_field(0)
+end program test
+EOF
+
+if ! "${R_HOME}"/bin/R CMD SHLIB test-f03.f90; then
+    echo "*********************************************************************************"
+    echo "Your Fortran compiler does not appear to support all features of the 2003"
+    echo "standard. Please install a compatible compiler, set this in your ~/.R/Makevars"
+    echo "and try again."
+    echo "*********************************************************************************"
+
+    exit 1
+fi
+
+rm -f test-f03.* mod_test.*

cran-comments.md

@@ -1,3 +1,16 @@
+## Resubmission
+
+* Spelled out "ODP" as "overdispersed Poisson".
+
+* Removed erroneous export of internal package functions.
+
+* Removed the "Date" field in DESCRIPTION.
+
+* Added Fortran 2003 to "SystemRequirements" as well as a configure script that
+  checks whether the compiler supports this standard.
+
+* Remove erroneously included "Rplots.pdf".
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note

inst/include/mask.h

@@ -6,6 +6,7 @@ class Mask {
     Mask(int n_row, int n_col) : n_row_(n_row), n_col_(n_col) {
         data_ = new bool[n_row * n_col];
 
+        // column major
         for (int i = 0; i < n_row; i++) {
             for (int j = 0; j < n_col; j++) {
                 if (j >= n_col - i) {
@@ -16,15 +17,17 @@ class Mask {
             }
         }
     };
+
     Mask(int n_dev) : Mask(n_dev, n_dev){};
     ~Mask() { delete[] data_; }
 
     bool* begin() { return data_; }
-    int n_row() { return n_row_; }
-    int n_col() { return n_col_; }
-    int size() { return n_row_ * n_col_; }
+    int n_row() const { return n_row_; }
+    int n_col() const { return n_col_; }
+    int size() const { return n_row_ * n_col_; }
 
     bool& operator()(int i, int j) { return data_[i + j * n_row_]; }
+    bool get(int i, int j) const { return data_[i + j * n_row_]; }
 
     class RowProxy {
        public:
@@ -70,10 +73,10 @@ class Mask {
         }
     }
 
-    friend std::ostream& operator<<(std::ostream& os, Mask& mask) {
+    friend std::ostream& operator<<(std::ostream& os, const Mask& mask) {
         for (int i = 0; i < mask.n_row(); i++) {
             for (int j = 0; j < mask.n_col(); j++) {
-                os << (mask(i, j) ? "T" : "F") << " ";
+                os << (mask.get(i, j) ? "T" : "F") << " ";
             }
             os << std::endl;
         }

src/mack.cpp

@@ -23,7 +23,6 @@ void mack_pairs_boot_cpp(int n_dev, double* triangle, int n_boot, int n_sim,
                          bool* mask, double* reserve, void* pgb);
 }
 
-//' @export
 // [[Rcpp::export(.mackParamBoot)]]
 Rcpp::List mackParamBoot(Rcpp::NumericMatrix trngl, Rcpp::String dist,
                          bool cond, int n_boot = 1e3, int n_sim = 1e3,
@@ -60,7 +59,6 @@ Rcpp::List mackParamBoot(Rcpp::NumericMatrix trngl, Rcpp::String dist,
     return res;
 };
 
-//' @export
 // [[Rcpp::export(.mackResidBoot)]]
 Rcpp::List mackResidBoot(Rcpp::NumericMatrix trngl, Rcpp::String resid_type,
                          bool cond, int n_boot = 1e3, int n_sim = 1e3,
@@ -96,7 +94,6 @@ Rcpp::List mackResidBoot(Rcpp::NumericMatrix trngl, Rcpp::String resid_type,
     return res;
 };
 
-//' @export
 // [[Rcpp::export(.mackPairsBoot)]]
 Rcpp::List mackPairsBoot(Rcpp::NumericMatrix trngl, int n_boot = 1e3,
                          int n_sim = 1e3, bool progress = true) {
@@ -305,20 +302,20 @@ Rcpp::List mackSim(arma::mat triangle, options::SimType sim_type, int n_boot,
         case options::ORIGIN: {
             if (progress) {
                 pb = new CliProgressBar;
-                pgb = new Progress(n_dev * n_boot * n_sim, true, *pb);
+                pgb = new Progress((n_dev - 1) * n_boot * n_sim, true, *pb);
             } else {
                 pb = nullptr;
                 pgb = nullptr;
             }
 
-            reserves = arma::mat(n_boot * n_sim, n_dev);
+            reserves = arma::mat(n_boot * n_sim, n_dev - 1);
             // clang-format off
             #pragma omp parallel for num_threads(n_threads) default(none) \
                 shared(reserves, pgb, col_mapping_) \
                 firstprivate(boot_type, mask, triangle, n_boot, n_sim, n_dev) \
                 firstprivate(dist_type, resid_type, cond, progress)
             // clang-format on
-            for (int i = 0; i < n_dev; i++) {
+            for (int i = 0; i < n_dev - 1; i++) {
                 bool abort_check;
                 if (progress) {
                     abort_check = !Progress::check_abort();
@@ -335,6 +332,7 @@ Rcpp::List mackSim(arma::mat triangle, options::SimType sim_type, int n_boot,
                     Mask mask_in = mask;
                     mask_in.row(i) = false;
                     mask_in(i, 0) = true;
+
                     if (boot_type == options::PAIRS ||
                         boot_type == options::PARAM)
                         mask_in(0, n_dev - 1) = true;
@@ -387,7 +385,6 @@ Rcpp::List mackSim(arma::mat triangle, options::SimType sim_type, int n_boot,
     return res;
 };
 
-//' @export
 // [[Rcpp::export(.mackPairsSim)]]
 Rcpp::List mackPairsSim(Rcpp::NumericMatrix trngl, Rcpp::String sim_type,
                         int n_boot, int n_sim, bool progress) {
@@ -397,7 +394,6 @@ Rcpp::List mackPairsSim(Rcpp::NumericMatrix trngl, Rcpp::String sim_type,
                    options::Dist::NORMAL, options::STANDARD);
 }
 
-//' @export
 // [[Rcpp::export(.mackParamSim)]]
 Rcpp::List mackParamSim(Rcpp::NumericMatrix trngl, Rcpp::String sim_type,
                         bool cond, Rcpp::String dist, int n_boot, int n_sim,
@@ -408,7 +404,6 @@ Rcpp::List mackParamSim(Rcpp::NumericMatrix trngl, Rcpp::String sim_type,
                    options::dist_mapping.at(dist), options::STANDARD);
 }
 
-//' @export
 // [[Rcpp::export(.mackResidSim)]]
 Rcpp::List mackResidSim(Rcpp::NumericMatrix trngl, Rcpp::String sim_type,
                         bool cond, Rcpp::String resid_type, int n_boot,