fixing problem with dorng

biodiverse · Dec 13, 2024 · 5a77298 · 5a77298
1 parent e251a2b
commit 5a77298
Show file tree

Hide file tree

Showing 24 changed files with 205 additions and 284 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,7 +16,6 @@ URL: https://www.doserlab.com/files/spoccupancy-web,
         https://github.com/biodiverse/spOccupancy
 BugReports: https://github.com/biodiverse/spOccupancy/issues
 Depends: R (>= 3.5.0)
-Imports: stats, coda, abind, RANN, lme4, foreach, doParallel, doRNG,
-        parallel, spAbundance, methods
+Imports: stats, coda, abind, RANN, lme4, foreach, doParallel, spAbundance, methods
 Suggests: testthat
 NeedsCompilation: yes
diff --git a/NAMESPACE b/NAMESPACE
@@ -203,8 +203,6 @@ importFrom("abind", "abind")
 importFrom("RANN", "nn2")
 importFrom("lme4", "findbars", "mkReTrms", "nobars")
 importFrom("foreach", "foreach", "%do%", "%dopar%")
-importFrom("doRNG", "%dorng%")
 importFrom("doParallel", "registerDoParallel", "stopImplicitCluster")
-importFrom("parallel", "makePSOCKcluster", "stopCluster")
 importFrom("methods", "is")
 importFrom("spAbundance", "msAbund")
diff --git a/R/PGOcc.R b/R/PGOcc.R
@@ -785,9 +785,8 @@ if (length(sigma.sq.p.inits) != p.det.re) {
     # Number of sites in each hold out data set. 
     sites.random <- sample(1:J)    
     sites.k.fold <- split(sites.random, sites.random %% k.fold)
-    par.k <- parallel::makePSOCKcluster(k.fold.threads)
-    registerDoParallel(par.k)
-    model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+    registerDoParallel(k.fold.threads)
+    model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
       curr.set <- sort(sites.random[sites.k.fold[[i]]])
       if (binom) {
         y.indx <- !(1:J %in% curr.set)
@@ -986,10 +985,7 @@ if (length(sigma.sq.p.inits) != p.det.re) {
     model.deviance <- -2 * model.deviance
     # Return objects from cross-validation
     out$k.fold.deviance <- model.deviance
-    parallel::stopCluster(par.k)
-    # Remove attributes from doRNG
-    attr(out$k.fold.deviance, 'rng') <- NULL
-    attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+    stopImplicitCluster()
   }
   class(out) <- "PGOcc"
   out$run.time <- proc.time() - ptm

diff --git a/R/intPGOcc.R b/R/intPGOcc.R
diff --git a/R/lfJSDM.R b/R/lfJSDM.R
@@ -660,9 +660,8 @@ lfJSDM <- function(formula, data, inits, priors, n.factors, n.samples,
     # Number of sites in each hold out data set. 
     sites.random <- sample(1:J)    
     sites.k.fold <- split(sites.random, sites.random %% k.fold)
-    par.k <- parallel::makePSOCKcluster(k.fold.threads)
-    registerDoParallel(par.k)
-    model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+    registerDoParallel(k.fold.threads)
+    model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
       curr.set <- sort(sites.random[sites.k.fold[[i]]])
       y.fit <- c(y.big[, -curr.set, drop = FALSE])
       y.fit <- y.fit[!is.na(y.fit)]
@@ -797,10 +796,7 @@ lfJSDM <- function(formula, data, inits, priors, n.factors, n.samples,
     model.deviance <- -2 * model.deviance
     # Return objects from cross-validation
     out$k.fold.deviance <- model.deviance
-    parallel::stopCluster(par.k)
-    # Remove attributes from doRNG
-    attr(out$k.fold.deviance, 'rng') <- NULL
-    attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+    stopImplicitCluster()
   }
 
   class(out) <- "lfJSDM"

diff --git a/R/lfMsPGOcc.R b/R/lfMsPGOcc.R
@@ -1113,9 +1113,8 @@ lfMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
     # Number of sites in each hold out data set. 
     sites.random <- sample(1:J)    
     sites.k.fold <- split(sites.random, sites.random %% k.fold)
-    par.k <- parallel::makePSOCKcluster(k.fold.threads)
-    registerDoParallel(par.k)
-    model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+    registerDoParallel(k.fold.threads)
+    model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
       curr.set <- sort(sites.random[sites.k.fold[[i]]])
       if (binom) {
         y.indx <- !(1:J %in% curr.set)
@@ -1350,10 +1349,7 @@ lfMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
     model.deviance <- -2 * model.deviance
     # Return objects from cross-validation
     out$k.fold.deviance <- model.deviance
-    parallel::stopCluster(par.k)
-    # Remove attributes from doRNG
-    attr(out$k.fold.deviance, 'rng') <- NULL
-    attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+    stopImplicitCluster()
   }
 
   class(out) <- "lfMsPGOcc"

diff --git a/R/msPGOcc.R b/R/msPGOcc.R
@@ -1022,9 +1022,8 @@ msPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
         if (binom) {
           y.indx <- !(1:J %in% curr.set)
@@ -1252,10 +1251,7 @@ msPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     }
     class(out) <- "msPGOcc"
     out$run.time <- proc.time() - ptm

diff --git a/R/sfJSDM.R b/R/sfJSDM.R
@@ -1247,9 +1247,8 @@ sfJSDM <- function(formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
         y.fit <- c(y.big[, -curr.set, drop = FALSE])
         y.fit <- y.fit[!is.na(y.fit)]
@@ -1443,10 +1442,7 @@ sfJSDM <- function(formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     }
 
     class(out) <- "sfJSDM"

diff --git a/R/sfMsPGOcc.R b/R/sfMsPGOcc.R
@@ -1520,9 +1520,8 @@ sfMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J.w)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set.small <- sort(sites.random[sites.k.fold[[i]]])
         curr.set <- which(grid.index.r %in% curr.set.small)
         if (binom) {
@@ -1818,10 +1817,7 @@ sfMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     }
 
     class(out) <- "sfMsPGOcc"

diff --git a/R/spIntPGOcc.R b/R/spIntPGOcc.R
@@ -1241,9 +1241,8 @@ spIntPGOcc <- function(occ.formula, det.formula, data, inits, priors,
         sites.random <- sample(1:J)    
       }
       sites.k.fold <- split(sites.random, rep(1:k.fold, length.out = length(sites.random)))
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set <- sort(sites.k.fold[[i]])
         curr.set.pred <- curr.set
 	# curr.set.fit are the rows of X.fit that are included in the fitted model
@@ -1589,10 +1588,7 @@ spIntPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     }
   } else {
 
@@ -1917,9 +1913,8 @@ spIntPGOcc <- function(occ.formula, det.formula, data, inits, priors,
         sites.random <- sample(1:J)    
       }
       sites.k.fold <- split(sites.random, rep(1:k.fold, length.out = length(sites.random)))
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set <- sort(sites.k.fold[[i]])
         curr.set.pred <- curr.set
 	# curr.set.fit are the rows of X.fit that are included in the fitted model
@@ -2289,10 +2284,7 @@ spIntPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     }
   }
   class(out) <- "spIntPGOcc"

diff --git a/R/spMsPGOcc.R b/R/spMsPGOcc.R
@@ -1404,9 +1404,8 @@ spMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
         if (binom) {
           y.indx <- !(1:J %in% curr.set)
@@ -1653,10 +1652,7 @@ spMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     } # Cross-validation
   } else {
 
@@ -2042,9 +2038,8 @@ spMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = "+") %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
         if (binom) {
           y.indx <- !(1:J %in% curr.set)
@@ -2317,10 +2312,7 @@ spMsPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     } # Cross-validation
   } # NNGP
   class(out) <- "spMsPGOcc"

diff --git a/R/spPGOcc.R b/R/spPGOcc.R
@@ -1154,9 +1154,8 @@ spPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
         if (binom) {
           y.indx <- !(1:J %in% curr.set)
@@ -1373,10 +1372,7 @@ spPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     } # cross-validation
 
   } else {
@@ -1705,9 +1701,8 @@ spPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J.w)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
         curr.set.small <- sort(sites.random[sites.k.fold[[i]]])
         curr.set <- which(grid.index.r %in% curr.set.small)
         if (binom) {
@@ -1963,10 +1958,6 @@ spPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
     } # cross-validation
   } # NNGP or GP
   class(out) <- "spPGOcc"

diff --git a/R/stPGOcc.R b/R/stPGOcc.R
@@ -1365,9 +1365,8 @@ stPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J.w)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
         curr.set.small <- sort(sites.random[sites.k.fold[[i]]])
         curr.set <- which(grid.index.r %in% curr.set.small)
         y.indx <- !((z.long.site.indx + 1) %in% curr.set)
@@ -1634,10 +1633,7 @@ stPGOcc <- function(occ.formula, det.formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     } # cross-validation
   } # NNGP
   class(out) <- "stPGOcc"

diff --git a/R/svcPGBinom.R b/R/svcPGBinom.R
@@ -909,9 +909,8 @@ svcPGBinom <- function(formula, data, inits, priors, tuning,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
         y.fit <- y[-curr.set]
 	y.0 <- y[curr.set]
@@ -1065,10 +1064,7 @@ svcPGBinom <- function(formula, data, inits, priors, tuning,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     } # cross-validation
   } # NNGP or GP
   class(out) <- "svcPGBinom"

diff --git a/R/svcPGOcc.R b/R/svcPGOcc.R
@@ -1296,8 +1296,8 @@ svcPGOcc <- function(occ.formula, det.formula, data, inits, priors, tuning,
       sites.random <- sample(1:J.w)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
       par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
         curr.set.small <- sort(sites.random[sites.k.fold[[i]]])
         curr.set <- which(grid.index.r %in% curr.set.small)
         if (binom) {
@@ -1560,10 +1560,7 @@ svcPGOcc <- function(occ.formula, det.formula, data, inits, priors, tuning,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()
     } # cross-validation
   } # NNGP or GP
   class(out) <- "svcPGOcc"

diff --git a/R/svcTPGBinom.R b/R/svcTPGBinom.R
@@ -1011,9 +1011,8 @@ svcTPGBinom <- function(formula, data, inits, priors,
       # Number of sites in each hold out data set. 
       sites.random <- sample(1:J)    
       sites.k.fold <- split(sites.random, sites.random %% k.fold)
-      par.k <- parallel::makePSOCKcluster(k.fold.threads)
-      registerDoParallel(par.k)
-      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dorng% {
+      registerDoParallel(k.fold.threads)
+      model.deviance <- foreach (i = 1:k.fold, .combine = sum) %dopar% {
         curr.set <- sort(sites.random[sites.k.fold[[i]]])
 	year.indx <- !((z.site.indx + 1) %in% curr.set)
         y.fit <- y[year.indx]
@@ -1200,10 +1199,7 @@ svcTPGBinom <- function(formula, data, inits, priors,
       model.deviance <- -2 * model.deviance
       # Return objects from cross-validation
       out$k.fold.deviance <- model.deviance
-      parallel::stopCluster(par.k)
-      # Remove attributes from doRNG
-      attr(out$k.fold.deviance, 'rng') <- NULL
-      attr(out$k.fold.deviance, 'doRNG_version') <- NULL
+      stopImplicitCluster()  
     } # cross-validation
   } # NNGP
   class(out) <- "svcTPGBinom"