From 796eb08f9dbf9fb980ab19c76a2282011055d43c Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Mon, 23 Sep 2024 14:48:27 -0700
Subject: [PATCH] Add progress bar in simulate.sdmTMB() #346

Also silent = FALSE by default
---
 DESCRIPTION            |  2 +-
 NEWS.md                |  2 ++
 R/tmb-sim.R            | 23 +++++++++++++----------
 man/simulate.sdmTMB.Rd |  2 +-
 4 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 30269120..e287cdf3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9008
+Version: 0.6.0.9009
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index bca9cc51..5815ca76 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # sdmTMB (development version)
 
+* Add progress bar to `simulate.sdmTMB()`. #346
+
 * Add AUC and TSS examples to cross validation vignette. #268
 
 * Add `model` (linear predictor number) argument to coef() method. Also,
diff --git a/R/tmb-sim.R b/R/tmb-sim.R
index 724e884d..c54ff2a9 100644
--- a/R/tmb-sim.R
+++ b/R/tmb-sim.R
@@ -381,7 +381,7 @@ sdmTMB_simulate <- function(formula,
 simulate.sdmTMB <- function(object, nsim = 1L, seed = sample.int(1e6, 1L),
                             type = c("mle-eb", "mle-mvn"),
                             model = c(NA, 1, 2),
-                            re_form = NULL, mcmc_samples = NULL, silent = TRUE, ...) {
+                            re_form = NULL, mcmc_samples = NULL, silent = FALSE, ...) {
   set.seed(seed)
   type <- tolower(type)
   type <- match.arg(type)
@@ -421,18 +421,21 @@ simulate.sdmTMB <- function(object, nsim = 1L, seed = sample.int(1e6, 1L),
     new_par <- mcmc_samples
   }
 
-  # do the sim
+  # do the simulation
+  if (!silent) cli::cli_progress_bar("Simulating...", total = nsim)
+  ret <- list()
   if (!is.null(mcmc_samples)) { # we have a matrix
-    ret <- lapply(seq_len(nsim), function(i) {
-      if (!silent) cat("-")
-      newobj$simulate(par = new_par[, i, drop = TRUE], complete = FALSE)$y_i
-    })
+    for (i in seq_len(nsim)) {
+      if (!silent) cli::cli_progress_update()
+      ret[[i]] <- newobj$simulate(par = new_par[, i, drop = TRUE], complete = FALSE)$y_i
+    }
   } else {
-    ret <- lapply(seq_len(nsim), function(i) {
-      if (!silent) cat("-")
-      newobj$simulate(par = new_par, complete = FALSE)$y_i
-      })
+    for (i in seq_len(nsim)) {
+      if (!silent) cli::cli_progress_update()
+      ret[[i]] <- newobj$simulate(par = new_par, complete = FALSE)$y_i
+    }
   }
+  cli::cli_progress_done()
 
   if (isTRUE(object$family$delta)) {
     if (is.na(model[[1]])) {
diff --git a/man/simulate.sdmTMB.Rd b/man/simulate.sdmTMB.Rd
index e3cda1e8..2d8b25ca 100644
--- a/man/simulate.sdmTMB.Rd
+++ b/man/simulate.sdmTMB.Rd
@@ -12,7 +12,7 @@
   model = c(NA, 1, 2),
   re_form = NULL,
   mcmc_samples = NULL,
-  silent = TRUE,
+  silent = FALSE,
   ...
 )
 }