c++ initialization with OpenMP support

DESCRIPTION

@@ -1,10 +1,12 @@
 Package: learner
 Type: Package
 Title: Latent Space-Based Transfer Learning
-Version: 0.2.0
+Version: 1.0.0
 Authors@R: c(person("Sean", "McGrath", role = c("aut", "cre"), 
                      email = "sean.mcgrath514@gmail.com",
                      comment = c(ORCID = "0000-0002-7281-3516")),
+              person("Ryan", "ODea", role = c("aut"),
+                     email = "ryanodea@hsph.harvard.edu"),
               person("Cenhao", "Zhu", role = c("aut"),
                       email = "cenhaoz@mit.edu"),
               person("Rui", "Duan", role = c("aut"), 
@@ -22,7 +24,10 @@ LazyData: true
 RoxygenNote: 7.3.2
 URL: https://github.com/stmcg/learner
 BugReports: https://github.com/stmcg/learner/issues
-Imports: doParallel, foreach, ScreeNOT
+Imports: ScreeNOT,
+         Rcpp (>= 1.0.11),
+         RcppEigen
+LinkingTo: Rcpp, RcppEigen
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -3,5 +3,6 @@
 export(cv.learner)
 export(dlearner)
 export(learner)
-import(doParallel)
-import(foreach)
+import(RcppEigen)
+importFrom(Rcpp,sourceCpp)
+useDynLib(learner, .registration = TRUE)

NEWS.md

@@ -1,5 +1,6 @@
-### learner version 0.2.0 (TBD)
+### learner version 1.0.0 (TBD)
 
+* Implemented the optimization algorithm in Rcpp, resulting in significant computational speed-ups.
 * Fixed a bug in `cv.learner` when `Y_target` has missing entries.
 
 ### learner version 0.1.0 (2025-01-08)

R/RcppExports.R

@@ -0,0 +1,15 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+learner_cpp <- function(Y_source, Y_target, r, lambda1, lambda2, step_size, max_iter, threshold, max_value) {
+    .Call(`_learner_learner_cpp`, Y_source, Y_target, r, lambda1, lambda2, step_size, max_iter, threshold, max_value)
+}
+
+cv_learner_cpp <- function(Y_source, Y_target, lambda1_all, lambda2_all, step_size, n_folds, max_iter, threshold, n_cores, r, max_value, index_set) {
+    .Call(`_learner_cv_learner_cpp`, Y_source, Y_target, lambda1_all, lambda2_all, step_size, n_folds, max_iter, threshold, n_cores, r, max_value, index_set)
+}
+
+omp_max_threads <- function() {
+    .Call(`_learner_omp_max_threads`)
+}
+

R/dlearner.R

@@ -54,8 +54,9 @@ dlearner <- function(Y_source, Y_target, r){
   }
 
   svd_source <- svd(Y_source, nu = r, nv = r)
-  dlearner_estimate <- (svd_source$u %*% t(svd_source$u)) %*%
-    Y_target %*% (svd_source$v %*% t(svd_source$v))
+  dlearner_estimate <- svd_source$u %*%
+    (t(svd_source$u) %*% Y_target %*% svd_source$v) %*%
+    t(svd_source$v)
 
   colnames(dlearner_estimate) <- colnames(Y_source)
   rownames(dlearner_estimate) <- rownames(Y_source)

R/globals.R

@@ -2,3 +2,14 @@ if(getRversion() >= "2.15.1"){
   # To remove 'no visible binding for global variable ...' notes
   utils::globalVariables(c('lambda_1_ind', 'lambda_2_ind'))
 }
+
+.onAttach <- function(libname, pkgname) {
+  max_threads <- tryCatch(omp_max_threads(), error = function(e) 1)
+  if (max_threads < 2) {
+    packageStartupMessage("*******\n
+                          This installation of learner has not detected OpenMP support\n
+                          It will still work but will not support multithreading via the `n_cores` argument
+                          If you plan to use multithreading, please ensure you are using R>=3.4.0 and have OpenMP installed\n
+                          *******")
+  }
+}

R/learner-package.R

@@ -0,0 +1,6 @@
+## usethis namespace: start
+#' @import RcppEigen
+#' @importFrom Rcpp sourceCpp
+#' @useDynLib learner, .registration = TRUE
+## usethis namespace: end
+NULL