From 3f5d32e9448bedcd48a18219d371c34f2194e40c Mon Sep 17 00:00:00 2001
From: Luna Fazio <boris.fazio@outlook.com>
Date: Thu, 9 Nov 2023 02:53:00 +0100
Subject: [PATCH 1/2] Special casing for lp_approx__

- Replace lp_approx__ with log_g__
- Assign then return stanfit object instead of implicit return
---
 R/backends.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/backends.R b/R/backends.R
index bcfb201df..c03b2044d 100644
--- a/R/backends.R
+++ b/R/backends.R
@@ -298,6 +298,7 @@ fit_model <- function(model, backend, ...) {
   variables <- repair_variable_names(metadata$metadata$variables)
   variables <- unique(sub("\\[.+", "", variables))
   variables <- setdiff(variables, exclude)
+  variables <- ifelse(variables == "lp_approx__", "log_g__", variables)
   # transform into stanfit object for consistent output structure
   out <- read_csv_as_stanfit(out$output_files(), variables = variables)
   out <- repair_stanfit(out)
@@ -941,7 +942,7 @@ read_csv_as_stanfit <- function(files, variables = NULL,
   sdate <- do.call(max, lapply(files, function(csv) file.info(csv)$mtime))
   sdate <- format(sdate, "%a %b %d %X %Y")
 
-  new(
+  out <- new(
     "stanfit",
     model_name = model_name,
     model_pars = svars,
@@ -954,4 +955,5 @@ read_csv_as_stanfit <- function(files, variables = NULL,
     date = sdate,  # not the time of sampling
     .MISC = new.env(parent = emptyenv())
   )
+  return(out)
 }

From 1ce56d0ecfd008ff7306fc6dd560ab6c1966eaa0 Mon Sep 17 00:00:00 2001
From: Luna Fazio <boris.fazio@outlook.com>
Date: Thu, 9 Nov 2023 15:25:46 +0100
Subject: [PATCH 2/2] Explain temp fix, clean code up

Add comment to temp fix for cmdstanr
Removed stanfit explicit return as it turns out it wasn't needed
---
 R/backends.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/backends.R b/R/backends.R
index c03b2044d..dcfc512e7 100644
--- a/R/backends.R
+++ b/R/backends.R
@@ -298,6 +298,7 @@ fit_model <- function(model, backend, ...) {
   variables <- repair_variable_names(metadata$metadata$variables)
   variables <- unique(sub("\\[.+", "", variables))
   variables <- setdiff(variables, exclude)
+  # temp fix for cmdstanr not recognizing the variable names it produces  #1473
   variables <- ifelse(variables == "lp_approx__", "log_g__", variables)
   # transform into stanfit object for consistent output structure
   out <- read_csv_as_stanfit(out$output_files(), variables = variables)
@@ -942,7 +943,7 @@ read_csv_as_stanfit <- function(files, variables = NULL,
   sdate <- do.call(max, lapply(files, function(csv) file.info(csv)$mtime))
   sdate <- format(sdate, "%a %b %d %X %Y")
 
-  out <- new(
+  new(
     "stanfit",
     model_name = model_name,
     model_pars = svars,
@@ -955,5 +956,4 @@ read_csv_as_stanfit <- function(files, variables = NULL,
     date = sdate,  # not the time of sampling
     .MISC = new.env(parent = emptyenv())
   )
-  return(out)
 }