From 04b68f31bf3226d2b84b1dba1e27a5a1c318d8fd 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/gempyor_pkg/docs/Rinterface.Rmd | 1 - flepimop/main_scripts/inference_slot.R | 4 +--- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/flepimop/gempyor_pkg/docs/Rinterface.Rmd b/flepimop/gempyor_pkg/docs/Rinterface.Rmd index c7c871fa0..9a6278e26 100644 --- a/flepimop/gempyor_pkg/docs/Rinterface.Rmd +++ b/flepimop/gempyor_pkg/docs/Rinterface.Rmd @@ -68,7 +68,6 @@ Here we specified that the data folder specified in the config lies in the `test stoch_traj_flag=False, rng_seed=None, nslots=1, - initialize=True, out_run_id=None, # if out_run_id should be different from in_run_id, put it here out_prefix=None, # if out_prefix should be different from in_prefix, put it here spatial_path_prefix="", # in case the data folder is on another directory 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 ----