From 9d53f979dd696819ad81506a584438958f23d8e2 Mon Sep 17 00:00:00 2001
From: kellijohnson-NOAA <kelli.johnson@noaa.gov>
Date: Fri, 15 Apr 2022 06:13:50 -0700
Subject: [PATCH] fix: Provides `fit` to `FishStatsUtils::plot_biomass_index()`

if `fit = NULL` which is the default, then the function doesn't work.
This change provides the model output, which is labelled `out`,
to the `fit` input argument.

Closes #41
---
 R/VAST_do.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/VAST_do.R b/R/VAST_do.R
index c3c3231..8f08297 100644
--- a/R/VAST_do.R
+++ b/R/VAST_do.R
@@ -143,6 +143,7 @@ VAST_do <- function(Database, settings, conditiondir, compiledir,
     error = function(e) e)
 
   index <- suppressWarnings(FishStatsUtils::plot_biomass_index(
+    fit = out,
     DirName = file.path(conditiondir, .Platform$file.sep),
     TmbData = out$data_list, Sdreport = out$parameter_estimates$SD,
     use_biascorr = TRUE,