Merge pull request #42 from ncn-foreigners/dev

switch from doSNOW on doParallel
ncn-foreigners · Mar 11, 2024 · 2abd6a2 · 2abd6a2
2 parents 446e349 + 9744666
commit 2abd6a2
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Showing 6 changed files with 38 additions and 38 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -43,7 +43,7 @@ Imports:
     RANN,
     Rcpp (>= 1.0.12),
     nleqslv,
-    doSNOW,
+    doParallel,
     progress,
     foreach,
     parallel

diff --git a/NAMESPACE b/NAMESPACE
@@ -31,7 +31,7 @@ importFrom(Matrix,Matrix)
 importFrom(RANN,nn2)
 importFrom(Rcpp,evalCpp)
 importFrom(Rcpp,sourceCpp)
-importFrom(doSNOW,registerDoSNOW)
+importFrom(doParallel,registerDoParallel)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
 importFrom(maxLik,maxLik)

diff --git a/R/boot_dr.R b/R/boot_dr.R
@@ -260,7 +260,7 @@ bootDR <- function(outcome,
 #' @importFrom foreach foreach
 #' @importFrom parallel makeCluster
 #' @importFrom parallel stopCluster
-#' @importFrom doSNOW registerDoSNOW
+#' @importFrom doParallel registerDoParallel
 bootDR_multicore <- function(outcome,
                              data,
                              svydesign,
@@ -340,15 +340,15 @@ bootDR_multicore <- function(outcome,
     rep_weights <- survey::as.svrepdesign(svydesign, type = rep_type, replicates = num_boot)$repweights$weights
 
     cl <- parallel::makeCluster(cores)
-    doSNOW::registerDoSNOW(cl)
+    doParallel::registerDoParallel(cl)
     on.exit(parallel::stopCluster(cl))
     ## progress bar
-    if (verbose) {
-      pb <- progress::progress_bar$new(total = num_boot)
-      opts <- list(progress = \(n) pb$tick())
-    } else {
-      opts <- NULL
-    }
+    # if (verbose) {
+    #   pb <- progress::progress_bar$new(total = num_boot)
+    #   opts <- list(progress = \(n) pb$tick())
+    # } else {
+    #   opts <- NULL
+    # }
     parallel::clusterExport(cl = cl, varlist = c(
       "internal_selection", "internal_outcome", "logit_model_nonprobsvy", "start_fit", "get_method", "controlSel", "theta_h_estimation",
       "mle", "mu_hatDR", "probit_model_nonprobsvy", "cloglog_model_nonprobsvy", "glm_nonprobsvy", "nn_nonprobsvy", "pmm_nonprobsvy",
@@ -359,7 +359,7 @@ bootDR_multicore <- function(outcome,
 
       k <- 1:num_boot
       mu_hats <- foreach::`%dopar%`(
-        obj = foreach::foreach(k = k, .combine = c, .options.snow = opts),
+        obj = foreach::foreach(k = k, .combine = c),
         ex = {
           estimation_method <- get_method(est_method)
           strap_nons <- sample.int(replace = TRUE, n = n_nons, prob = 1 / weights)

diff --git a/R/boot_dr_sel.R b/R/boot_dr_sel.R
@@ -113,7 +113,7 @@ bootDR_sel <- function(X,
 #' @importFrom foreach foreach
 #' @importFrom parallel makeCluster
 #' @importFrom parallel stopCluster
-#' @importFrom doSNOW registerDoSNOW
+#' @importFrom doParallel registerDoParallel
 bootDR_sel_multicore <- function(X,
                                  svydesign,
                                  R,
@@ -142,15 +142,15 @@ bootDR_sel_multicore <- function(X,
   rep_weights <- survey::as.svrepdesign(svydesign, type = rep_type, replicates = num_boot)$repweights$weights
 
   cl <- parallel::makeCluster(cores)
-  doSNOW::registerDoSNOW(cl)
+  doParallel::registerDoParallel(cl)
   on.exit(parallel::stopCluster(cl))
   ## progress bar
-  if (verbose) {
-    pb <- progress::progress_bar$new(total = num_boot)
-    opts <- list(progress = \(n) pb$tick())
-  } else {
-    opts <- NULL
-  }
+  # if (verbose) {
+  #   pb <- progress::progress_bar$new(total = num_boot)
+  #   opts <- list(progress = \(n) pb$tick())
+  # } else {
+  #   opts <- NULL
+  # }
   parallel::clusterExport(cl = cl, varlist = c(
     "internal_selection", "logit_model_nonprobsvy", "start_fit", "get_method", "controlSel", "mle",
     "probit_model_nonprobsvy", "cloglog_model_nonprobsvy", "mm", "u_theta_beta_dr",
@@ -159,7 +159,7 @@ bootDR_sel_multicore <- function(X,
 
   k <- 1:num_boot
   mu_hats <- foreach::`%dopar%`(
-    obj = foreach::foreach(k = k, .combine = c, .options.snow = opts),
+    obj = foreach::foreach(k = k, .combine = c),
     ex = {
       strap_nons <- sample.int(replace = TRUE, n = n_nons, prob = 1 / weights)
       # strap_rand <- sample.int(replace = TRUE, n = n_rand, prob = 1/weights_rand)

diff --git a/R/boot_ipw.R b/R/boot_ipw.R
@@ -182,7 +182,7 @@ bootIPW <- function(X_rand,
 #' @importFrom foreach foreach
 #' @importFrom parallel makeCluster
 #' @importFrom parallel stopCluster
-#' @importFrom doSNOW registerDoSNOW
+#' @importFrom doParallel registerDoParallel
 bootIPW_multicore <- function(X_rand,
                               X_nons,
                               svydesign,
@@ -220,15 +220,15 @@ bootIPW_multicore <- function(X_rand,
   boot_vars <- numeric(length = mu_len)
 
   cl <- parallel::makeCluster(cores)
-  doSNOW::registerDoSNOW(cl)
+  doParallel::registerDoParallel(cl)
   on.exit(parallel::stopCluster(cl))
   ## progress bar
-  if (verbose) {
-    pb <- progress::progress_bar$new(total = num_boot)
-    opts <- list(progress = \(n) pb$tick())
-  } else {
-    opts <- NULL
-  }
+  # if (verbose) {
+  #   pb <- progress::progress_bar$new(total = num_boot)
+  #   opts <- list(progress = \(n) pb$tick())
+  # } else {
+  #   opts <- NULL
+  # }
   ###
   parallel::clusterExport(cl = cl, varlist = c(
     "internal_selection", "logit_model_nonprobsvy", "start_fit", "get_method", "controlSel",
@@ -239,7 +239,7 @@ bootIPW_multicore <- function(X_rand,
 
   k <- 1:num_boot
   mu_hats_boot <- foreach::`%dopar%`(
-    obj = foreach::foreach(k = k, .combine = c, .options.snow = opts),
+    obj = foreach::foreach(k = k, .combine = c),
     ex = {
       if (is.null(pop_totals)) {
         strap_nons <- sample.int(replace = TRUE, n = n_nons, prob = 1 / weights)

diff --git a/R/boot_mi.R b/R/boot_mi.R
@@ -433,7 +433,7 @@ bootMI <- function(X_rand,
 #' @importFrom foreach foreach
 #' @importFrom parallel makeCluster
 #' @importFrom parallel stopCluster
-#' @importFrom doSNOW registerDoSNOW
+#' @importFrom doParallel registerDoParallel
 bootMI_multicore <- function(X_rand,
                              X_nons,
                              weights,
@@ -469,16 +469,16 @@ bootMI_multicore <- function(X_rand,
   }
 
   cl <- parallel::makeCluster(cores)
-  doSNOW::registerDoSNOW(cl)
+  doParallel::registerDoParallel(cl)
   on.exit(parallel::stopCluster(cl))
 
   ## progress bar
-  if (verbose) {
-    pb <- progress::progress_bar$new(total = num_boot)
-    opts <- list(progress = \(n) pb$tick())
-  } else {
-    opts <- NULL
-  }
+  # if (verbose) {
+  #   pb <- progress::progress_bar$new(total = num_boot)
+  #   opts <- list(progress = \(n) pb$tick())
+  # } else {
+  #   opts <- NULL
+  # }
   ###
   parallel::clusterExport(cl = cl, varlist = c(
     "internal_selection", "logit_model_nonprobsvy", "start_fit", "get_method", "controlSel",
@@ -496,7 +496,7 @@ bootMI_multicore <- function(X_rand,
     if (method == "glm") {
       k <- 1:num_boot
       mu_hats <- foreach::`%dopar%`(
-        obj = foreach::foreach(k = k, .combine = c, .options.snow = opts),
+        obj = foreach::foreach(k = k, .combine = c),
         ex = {
           strap <- sample.int(replace = TRUE, n = n_nons, prob = 1 / weights)
           weights_strap <- weights[strap]