Merge updates from develop branch

rstan/rstan/R/stan_csv.R

@@ -107,10 +107,11 @@ parse_stancsv_comments <- function(comments) {
   } 
   names1 <- intersect(c("thin", "iter", "warmup", "chain_id", "max_depth", 
                         "num_samples", "num_warmup", "id",
-                        "max_treedepth", "save_warmup"), names0)
+                        "max_treedepth"), names0)
   names2 <- intersect(c("stepsize", "stepsize_jitter", "adapt_gamma", "adapt_kappa", 
                         "adapt_delta", "gamma", "kappa", "delta", "t0",
                         "adapt_t0"), names0) 
+  if ("save_warmup" %in% names(values)) values[["save_warmup"]] <- as.integer(as.logical(values[["save_warmup"]]))
   for (z in names1) values[[z]] <- as.integer(values[[z]])
   for (z in names2) values[[z]] <- as.numeric(values[[z]])
   if (compute_iter) values[["iter"]] <- values[["iter"]] + values[["warmup"]]