Merge pull request #241 from HopkinsIDD/fix-sample-configs

Some small fixes to errors in aggregation stuff
HopkinsIDD · Jun 25, 2024 · 530afbc · 530afbc
2 parents 9e0ad95 + bb207a2
commit 530afbc
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/..._library/config_sample_2pop_inference.yml → ..._subpops/config_sample_2pop_inference.yml b/..._library/config_sample_2pop_inference.yml → ..._subpops/config_sample_2pop_inference.yml
@@ -47,7 +47,7 @@ seir:
 
 seir_modifiers:
   scenarios:
-    - Ro_all
+    - inference
   modifiers:
     Ro_mod: # assume same for all subpopulations
       method: SinglePeriodModifier
@@ -86,7 +86,7 @@ seir_modifiers:
         sd: 0.025
         a: -0.1
         b: 0.1
-    Ro_all:
+    inference:
       method: StackedModifier
       modifiers: ["Ro_mod","Ro_lockdown"]
 
@@ -122,10 +122,10 @@ outcomes:
 
 outcome_modifiers:
   scenarios:
-    - test_limits
+    - all
   modifiers:
     # assume that due to limitations in testing, initially the case detection probability was lower
-    test_limits:
+    all:
       method: SinglePeriodModifier
       parameter: incidCase
       subpop: "all"

diff --git a/flepimop/main_scripts/inference_slot.R b/flepimop/main_scripts/inference_slot.R
@@ -91,6 +91,7 @@ if (opt$config == ""){
 }
 config = flepicommon::load_config(opt$config)
 
+opt$total_ll_multiplier <- 1
 if (!is.null(config$inference$incl_aggr_likelihood)){
     print("Using config option for `incl_aggr_likelihood`.")
     opt$incl_aggr_likelihood <- config$inference$incl_aggr_likelihood
@@ -450,7 +451,7 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
         autowrite_seir = TRUE
       )
     }, error = function(e) {
-      print("GempyorInference failed to run (call on l. 405 of inference_slot.R).")
+      print("GempyorInference failed to run (call on l. 443 of inference_slot.R).")
       print("Here is all the debug information I could find:")
       for(m in reticulate::py_last_error()) print(m)
       stop("GempyorInference failed to run... stopping")
@@ -637,8 +638,8 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
             sim_hosp <- sim_hosp %>%
                 dplyr::bind_rows(
                     sim_hosp %>%
-                        dplyr::select(-tidyselect::all_of(obs_subpop), -tidyselect::starts_with("date")) %>%
-                        dplyr::group_by(time) %>%
+                        dplyr::select(-tidyselect::all_of(obs_subpop)) %>%
+                        dplyr::group_by(date) %>%
                         dplyr::summarise(dplyr::across(tidyselect::everything(), sum)) %>% # no likelihood is calculated for time periods with missing data for any subpop
                         dplyr::mutate(!!obs_subpop := "Total")
                 )