From 8a76d84fcd1b1dff569b57ef8963c9f22b24fa02 Mon Sep 17 00:00:00 2001 From: Shaun Truelove Date: Tue, 14 Nov 2023 17:06:22 -0500 Subject: [PATCH] remove unused `initialize` in GempyorSimulator call --- flepimop/main_scripts/inference_slot.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/flepimop/main_scripts/inference_slot.R b/flepimop/main_scripts/inference_slot.R index 8e9b0be0c..54a05f657 100644 --- a/flepimop/main_scripts/inference_slot.R +++ b/flepimop/main_scripts/inference_slot.R @@ -429,12 +429,10 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) { seir_modifiers_scenario=seir_modifiers_scenario, outcome_modifiers_scenario=outcome_modifiers_scenario, stoch_traj_flag=opt$stoch_traj_flag, - initialize=TRUE, # Shall we pre-compute now things that are not pertubed by inference run_id=opt$run_id, prefix=reticulate::py_none(), # we let gempyor create setup prefix inference_filepath_suffix=global_intermediate_filepath_suffix, inference_filename_prefix=slotblock_filename_prefix - #index = ) }, error = function(e) { print("GempyorSimulator failed to run (call on l. 426 of inference_slot.R).") @@ -544,7 +542,7 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) { ## Using the prefixes, create standardized files of each type (e.g., seir) of the form ## {variable}/{prefix}{block-1}.{run_id}.{variable}.{ext} ## N.B.: prefix should end in "{block}." - this_global_files <- inference::create_filename_list(run_id=opt$run_id, prefix = setup_prefix, filepath_suffix=global_intermediate_filepath_suffix,filename_prefix=slotblock_filename_prefix, index=this_index) + this_global_files <- inference::create_filename_list(run_id=opt$run_id, prefix = setup_prefix, filepath_suffix=global_intermediate_filepath_suffix, filename_prefix=slotblock_filename_prefix, index=this_index) this_chimeric_files <- inference::create_filename_list(run_id=opt$run_id, prefix = setup_prefix, filepath_suffix=chimeric_intermediate_filepath_suffix, filename_prefix=slotblock_filename_prefix, index=this_index) ### Do perturbations from accepted parameters to get proposed parameters ----