From 35ece2f09c38eace7ba1c121535445d4c0dae600 Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Thu, 21 Mar 2024 13:37:35 -0700
Subject: [PATCH] Improve update_version checks [skip ci]

---
 R/utils.R               | 12 ++++++------
 scratch/test-versions.R | 19 +++++++++++++++++++
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index e6e7734f1..da225a9a3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -593,7 +593,7 @@ get_fitted_time <- function(x) {
 }
 
 update_version <- function(object) {
-  if (object$version < '0.4.3') {
+  if (object$version < "0.4.3") {
     cli::cli_abort("`update_version()` only works with models fit with version 0.4.3 or later.")
   }
   if (!"fitted_time" %in% names(object)) { # < 0.4.3.9004
@@ -606,13 +606,13 @@ update_version <- function(object) {
     object$offset <- o
 
     y <- object$response
-    y <- y[seq(1, real_data_n),,drop=FALSE]
+    y <- y[seq(1, real_data_n), , drop = FALSE]
     object$response <- y
 
     d <- object$data
-    d[['__fake_data__']] <- d[['__weight_sdmTMB__']] <-
-      d[['__sdmTMB_offset__']] <- d[['__dcens_upr__']] <- NULL
-    d <- d[seq(1, real_data_n),,drop=FALSE]
+    d[["__fake_data__"]] <- d[["__weight_sdmTMB__"]] <-
+      d[["__sdmTMB_offset__"]] <- d[["__dcens_upr__"]] <- NULL
+    d <- d[seq(1, real_data_n), , drop = FALSE]
     object$data <- d
 
     # add gengamma_Q
@@ -634,6 +634,6 @@ update_version <- function(object) {
       object$tmb_obj$env$last.par.best <- ee$last.par.best
       object$tmb_map <- map
     }
-    object
   }
+  object
 }
diff --git a/scratch/test-versions.R b/scratch/test-versions.R
index f0def8e17..40394f33f 100644
--- a/scratch/test-versions.R
+++ b/scratch/test-versions.R
@@ -81,3 +81,22 @@ check_version(f)
 
 f <- "scratch/version-checks/fit-0.4.3.9003.rds"
 check_version(f)
+
+## current
+mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 15)
+pcod$os <- rep(log(0.01), nrow(pcod)) # offset
+f <- "scratch/version-checks/fit-main.rds"
+fit <- sdmTMB(
+  data = pcod,
+  formula = density ~ s(depth_scaled, k = 3),
+  mesh = mesh,
+  offset = pcod$os,
+  family = tweedie(link = "log"),
+  time = "year",
+  time_varying = ~ 1,
+  time_varying_type = 'ar1',
+  extra_time = c(2006, 2008, 2010, 2012, 2014, 2016),
+  spatiotemporal = "off"
+)
+saveRDS(fit, f)
+check_version(f)