Make data prep and post-processing more generic (#66)

* Split prep_data.py into functions and make it a bit more configurable * use parser output as dictionary * Fix misnamed variable * Working prep_data script * Fix output path bug * Add right_truncation_offset calculation to python prep_data.py * Make post_process.R more generic * Quiet read_csv, progress messages * Format files * only run main if we're running in main * clear up temporary code info for post_process * remove duckdb * actually remove duckdb import * make param_estimates lazy * use Path for argument typs where appropriate --------- Co-authored-by: Damon Bayer <[email protected]> Co-authored-by: Damon Bayer <[email protected]>
CDCgov · Oct 21, 2024 · 7253f9b · 7253f9b
1 parent cc7f156
commit 7253f9b
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diff --git a/nssp_demo/post_process.R b/nssp_demo/post_process.R
@@ -7,6 +7,10 @@ library(scales)
 library(here)
 library(argparser)
 
+theme_set(theme_minimal_grid())
+
+disease_name_formatter <- c("covid-19" = "COVID-19", "influenza" = "Flu")
+
 # Create a parser
 p <- arg_parser("Generate forecast figures") %>%
   add_argument(p, "--model_dir",
@@ -29,9 +33,7 @@ good_chain_tol <- argv$good_chain_tol
 
 base_dir <- path_dir(model_dir)
 
-theme_set(theme_minimal_grid())
 
-disease_name_formatter <- c("covid-19" = "COVID-19", "influenza" = "Flu")
 
 read_pyrenew_samples <- function(inference_data_path,
                                  filter_bad_chains = TRUE,
@@ -178,8 +180,9 @@ save_plot(
   device = cairo_pdf, base_height = 6
 )
 
-
-# Temp code while command line version doesn't work
+# File will end here once command line version is working
+# Temp code to run for all states while command line version doesn't work
+# Command line version is dependent on https://github.com/rstudio/renv/pull/2018
 base_dir <- path(
   "nssp_demo",
   "private_data",