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@shauntruelove
shauntruelove committed Mar 21, 2024
1 parent b73cefa commit 0d71d32
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Showing 2 changed files with 59 additions and 65 deletions.
10 changes: 5 additions & 5 deletions flepimop/R_packages/inference/R/inference_slot_runner_funcs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -707,14 +707,14 @@ initialize_mcmc_first_block <- function(
if (!is.null(config$initial_conditions)){
if ("init_filename" %in% global_file_names) {

if (config$initial_conditions$method %in% c("FromFile", "SetInitialConditions")){
if (config$initial_conditions$method == "SetInitialConditions"){

if (is.null(config$initial_conditions$initial_conditions_file)) {
stop("ERROR: Initial conditions file needs to be specified in the config under `initial_conditions:initial_conditions_file`")
}
initial_init_file <- config$initial_conditions$initial_conditions_file

if (!file.exists(initial_init_file)) {
if (!file.exists(config$initial_conditions$initial_conditions_file)) {
stop("ERROR: Initial conditions file specified but does not exist.")
}
if (grepl(".csv", initial_init_file)){
Expand All @@ -728,9 +728,9 @@ initialize_mcmc_first_block <- function(
stop("Could not copy initial conditions file")
}

# } else if (config$initial_conditions$method == "FromFile") {
# # stop("ERROR: Method 'FromFile' Initial conditions has not been implemented yet for Inference.")
# }
} else if (config$initial_conditions$method == "FromFile") {
# stop("ERROR: Method 'FromFile' Initial conditions has not been implemented yet for Inference.")
}
}
}

Expand Down
114 changes: 54 additions & 60 deletions flepimop/main_scripts/inference_slot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -498,10 +498,10 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
initial_spar <- arrow::read_parquet(first_chimeric_files[['spar_filename']])
initial_hpar <- arrow::read_parquet(first_chimeric_files[['hpar_filename']])

# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("FromFile", "SetInitialConditions", "SetInitialConditionsFolderDraw", "InitialConditionsFolderDraw"))){
# # initial_init <- arrow::read_parquet(first_global_files[['init_filename']])
# initial_init <- arrow::read_parquet(first_chimeric_files[['init_filename']])
# }
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditions","SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
# initial_init <- arrow::read_parquet(first_global_files[['init_filename']])
initial_init <- arrow::read_parquet(first_chimeric_files[['init_filename']])
}


chimeric_likelihood_data <- arrow::read_parquet(first_chimeric_files[['llik_filename']])
Expand Down Expand Up @@ -552,74 +552,71 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {

### Do perturbations from accepted parameters to get proposed parameters ----

if (!is.null(config$seeding)){
proposed_seeding <- inference::perturb_seeding(
seeding = initial_seeding,
date_sd = config$seeding$date_sd,
date_bounds = c(gt_start_date, gt_end_date),
amount_sd = config$seeding$amount_sd,
continuous = !(opt$stoch_traj_flag)
)
} else {
proposed_seeding <- initial_seeding
}
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditions","SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
if (infer_initial_conditions) {
proposed_init <- inference::perturb_init(initial_init, config$initial_conditions$perturbation)
} else {
proposed_init <- initial_init
}
}
if (!is.null(config$seir_modifiers$modifiers)){
proposed_snpi <- inference::perturb_snpi(initial_snpi, config$seir_modifiers$modifiers)
}
# TODO we need a hnpi for inference
proposed_hnpi <- inference::perturb_hnpi(initial_hnpi, config$outcome_modifiers$modifiers)
if (!is.null(config$outcome_modifiers$modifiers)){
proposed_hnpi <- inference::perturb_hnpi(initial_hnpi, config$outcome_modifiers$modifiers)# NOTE: no scenarios possible right now
}
proposed_spar <- initial_spar
proposed_hpar <- inference::perturb_hpar(initial_hpar, config$outcomes$outcomes) # NOTE: no scenarios possible right now



# since the first iteration is accepted by default, we don't perturb it
if ((opt$this_block == 1) && (current_index == 0)) {

proposed_snpi <- initial_snpi
proposed_hnpi <- initial_hnpi
proposed_spar <- initial_spar
proposed_hpar <- initial_hpar

# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("FromFile", "SetInitialConditions", "SetInitialConditionsFolderDraw", "InitialConditionsFolderDraw"))){
# proposed_init <- initial_init
# }
if (!is.null(config$seeding)){
proposed_seeding <- initial_seeding
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditions","SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
proposed_init <- initial_init
}
} else {

if (!is.null(config$seeding)){
proposed_seeding <- inference::perturb_seeding(
seeding = initial_seeding,
date_sd = config$seeding$date_sd,
date_bounds = c(gt_start_date, gt_end_date),
amount_sd = config$seeding$amount_sd,
continuous = !(opt$stoch_traj_flag)
)
} else {
proposed_seeding <- initial_seeding
}
# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("FromFile","SetInitialConditions","SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
# if (infer_initial_conditions) {
# proposed_init <- inference::perturb_init(initial_init, config$initial_conditions$perturbation)
# } else {
# proposed_init <- initial_init
# }
# }
if (!is.null(config$seir_modifiers$modifiers)){
proposed_snpi <- inference::perturb_snpi(initial_snpi, config$seir_modifiers$modifiers)
}
# TODO we need a hnpi for inference
proposed_hnpi <- inference::perturb_hnpi(initial_hnpi, config$outcome_modifiers$modifiers)
if (!is.null(config$outcome_modifiers$modifiers)){
proposed_hnpi <- inference::perturb_hnpi(initial_hnpi, config$outcome_modifiers$modifiers)# NOTE: no scenarios possible right now
}
proposed_spar <- initial_spar
proposed_hpar <- inference::perturb_hpar(initial_hpar, config$outcomes$outcomes) # NOTE: no scenarios possible right now

# proposed_snpi <- inference::perturb_snpi_from_file(initial_snpi, config$seir_modifiers$settings, chimeric_likelihood_data)
# proposed_hnpi <- inference::perturb_hnpi_from_file(initial_hnpi, config$seir_modifiers$settings, chimeric_likelihood_data)
# proposed_spar <- inference::perturb_spar_from_file(initial_spar, config$seir_modifiers$settings, chimeric_likelihood_data)
# proposed_hpar <- inference::perturb_hpar_from_file(initial_hpar, config$seir_modifiers$settings, chimeric_likelihood_data)

}

# proposed_snpi <- inference::perturb_snpi_from_file(initial_snpi, config$seir_modifiers$settings, chimeric_likelihood_data)
# proposed_hnpi <- inference::perturb_hnpi_from_file(initial_hnpi, config$seir_modifiers$settings, chimeric_likelihood_data)
# proposed_spar <- inference::perturb_spar_from_file(initial_spar, config$seir_modifiers$settings, chimeric_likelihood_data)
# proposed_hpar <- inference::perturb_hpar_from_file(initial_hpar, config$seir_modifiers$settings, chimeric_likelihood_data)


## Write files that need to be written for other code to read
# writes to file of the form variable/name/seir_modifiers_scenario/outcome_modifiers_scenario/run_id/global/intermediate/slot.block.iter.run_id.variable.ext


arrow::write_parquet(proposed_snpi,this_global_files[['snpi_filename']])
arrow::write_parquet(proposed_hnpi,this_global_files[['hnpi_filename']])
arrow::write_parquet(proposed_spar,this_global_files[['spar_filename']])
arrow::write_parquet(proposed_hpar,this_global_files[['hpar_filename']])
if (!is.null(config$seeding)){
readr::write_csv(proposed_seeding, this_global_files[['seed_filename']])
}
# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditionsFolderDraw"))){
# arrow::write_parquet(proposed_init, this_global_files[['init_filename']])
# }
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
arrow::write_parquet(proposed_init, this_global_files[['init_filename']])
}


## Run the simulator
Expand Down Expand Up @@ -745,9 +742,9 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {

print("Resetting chimeric files to global")

# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditionsFolderDraw"))){
# initial_init <- proposed_init
# }
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
initial_init <- proposed_init
}
initial_seeding <- proposed_seeding
initial_snpi <- proposed_snpi
initial_hnpi <- proposed_hnpi
Expand All @@ -760,9 +757,6 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
## Chimeric likelihood acceptance or rejection decisions (one round) -----
# "Chimeric" means Subpopulation-specific (i.e., each state or county in the US has a chimeric likelihood)

proposed_init <- NULL
initial_init <- proposed_init

seeding_npis_list <- inference::accept_reject_proposals(
init_orig = initial_init,
init_prop = proposed_init,
Expand All @@ -779,9 +773,9 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
)

# Update accepted parameters to start next simulation
# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("FromFile", "SetInitialConditions", "SetInitialConditionsFolderDraw", "InitialConditionsFolderDraw"))){
# initial_init <- seeding_npis_list$init
# }
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditions", "SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
initial_init <- seeding_npis_list$init
}
initial_seeding <- seeding_npis_list$seeding
initial_snpi <- seeding_npis_list$snpi
initial_hnpi <- seeding_npis_list$hnpi
Expand All @@ -800,9 +794,9 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
if (!is.null(config$seeding)){
readr::write_csv(initial_seeding,this_chimeric_files[['seed_filename']])
}
# if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
# arrow::write_parquet(initial_init, this_chimeric_files[['init_filename']])
# }
if (!is.null(config$initial_conditions) & (config$initial_conditions$method %in% c("SetInitialConditionsFolderDraw","InitialConditionsFolderDraw"))){
arrow::write_parquet(initial_init, this_chimeric_files[['init_filename']])
}
arrow::write_parquet(initial_snpi,this_chimeric_files[['snpi_filename']])
arrow::write_parquet(initial_hnpi,this_chimeric_files[['hnpi_filename']])
arrow::write_parquet(initial_spar,this_chimeric_files[['spar_filename']])
Expand All @@ -812,7 +806,7 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
print(paste("Current index is ",current_index))

###Memory management
# rm(proposed_init)
rm(proposed_init)
rm(proposed_snpi)
rm(proposed_hnpi)
rm(proposed_hpar)
Expand Down

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