From bf9a65ef112b628c2dccce3cebd3bc80f1090a49 Mon Sep 17 00:00:00 2001
From: saraloo <45245630+saraloo@users.noreply.github.com>
Date: Wed, 15 Nov 2023 09:08:29 -0500
Subject: [PATCH] allow for any variant recode contres;

---
 preprocessing/seir_recode_omicron.R | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/preprocessing/seir_recode_omicron.R b/preprocessing/seir_recode_omicron.R
index 421fa77c2..6230a9040 100644
--- a/preprocessing/seir_recode_omicron.R
+++ b/preprocessing/seir_recode_omicron.R
@@ -81,30 +81,35 @@ seir_dt <- continued_seir %>% mutate(date = lubridate::as_date(date))  %>%
   summarise(value = sum(value, na.rm = TRUE)) %>%  
   dplyr::mutate(mc_name = paste(mc_infection_stage, mc_vaccination_stage, mc_variant_type, mc_age_strata, sep = "_")) %>%
   pivot_wider(names_from = geoid, values_from = value) 
+
+# SAVE --------------------------------------------------------------------
+  
+# rewrite to new init file
+new_init_file <- opt$init_filename
+
+arrow::write_parquet(seir_dt, new_init_file)
+
+cat(paste0("\nWriting modified init file to: \n  -- ", new_init_file, "\n\n"))
+
   
 
 # PULL SEED FILES -------------------------------------------------------------------
 ## Read in SEED files from resume, and remove other variants
 
-# seir file from continued run
+# variants to keep 
+variant_comp <- config$compartments$variant_type
+
+# seed file from continued run
 continued_seed <- readr::read_csv(opt$in_seed_filename) 
 
 # remove all but Omicron
 seed_dt <- continued_seed %>% mutate(date = lubridate::as_date(date))  %>%
-  filter(destination_variant_type == "OMICRON") %>%
-  mutate(source_variant_type = "OMICRON")  
+  filter(destination_variant_type %in% variant_comp) %>%
+  mutate(source_variant_type = opt$recode_variant)  
 
 
 # SAVE --------------------------------------------------------------------
   
-# rewrite to new init file
-new_init_file <- opt$init_filename
-
-arrow::write_parquet(seir_dt, new_init_file)
-
-cat(paste0("\nWriting modified init file to: \n  -- ", new_init_file, "\n\n"))
-
-  
 # rewrite to SAME seed file
 rewrite_seed_filename <- opt$in_seed_filename