Merge pull request #3262 from DongchenZ/develop

Bug fixes for the progress bar in the qub_parallel function and Q type identification in the analysis_SDA_block function.

base/remote/R/qsub_parallel.R

@@ -103,7 +103,6 @@ qsub_parallel <- function(settings, files = NULL, prefix = "sipnet.out", sleep =
   folders <- file.path(settings$host$outdir, run_list)
   L_folder <- length(folders)
   pb <- utils::txtProgressBar(min = 0, max = L_folder, style = 3)
-  pbi <- 0
   #here we not only detect if the target files are generated.
   #we also detect if the jobs are still existed on the server.
   if (is_rabbitmq) {
@@ -121,7 +120,6 @@ qsub_parallel <- function(settings, files = NULL, prefix = "sipnet.out", sleep =
   } else {
     L_jobid <- length(jobids)
     pb1 <- utils::txtProgressBar(min = 0, max = L_jobid, style = 3)
-    pb1 <- 0
     if (hybrid) {
       while ((L_folder - length(folders)) < L_folder & 
              (L_jobid - length(jobids)) < L_jobid) {

modules/assim.sequential/R/Analysis_sda_block.R

@@ -339,11 +339,11 @@ MCMC_Init <- function (block.list, X) {
     }
     #initialize q.
     #if we want the vector q.
-    if (block.list[[i]]$constant$q.type == 1) {
+    if (block.list[[i]]$constant$q.type == 3) {
       for (j in seq_along(block.list[[i]]$data$y.censored)) {
         block.list[[i]]$Inits$q <- c(block.list[[i]]$Inits$q, stats::rgamma(1, shape = block.list[[i]]$data$aq[j], rate = block.list[[i]]$data$bq[j]))
       }
-    } else if (block.list[[i]]$constant$q.type == 2) {
+    } else if (block.list[[i]]$constant$q.type == 4) {
       #if we want the wishart Q.
       if ("try-error" %in% class(try(block.list[[i]]$Inits$q <- 
                                      stats::rWishart(1, df = block.list[[i]]$data$bq, Sigma = block.list[[i]]$data$aq)[,,1], silent = T))) {