sunset calls to create_seeding.R within inference

[alsnhll]

Currently in inference:initialize_mcmc_first_block, if the seeding file does not already exist in the model output directory AND if the file specified in seeding:lambda_file in the config does not exist, it will call create_seeding.R to create it. But this is a hidden option, not documented anywhere. We want it to be specified directly in the config if external scripts are going to be run to create required files.

if(!file.exists(config$seeding$lambda_file)) { print("Will create seeding lambda file using flepimop/main_scripts/create_seeding.R") #Need to document this

In the same function, there is also a hidden option for adding new seedings if it is a resume run:

additional seeding for new variants or introductions to add to fitted seeding (for resumes)

    #   need to document!!
    if (!is.null(config$seeding$added_seeding) & is_resume & block <= 1){
        if(!file.exists(config$seeding$added_seeding$added_lambda_file)) {
            err <- system(paste(
                opt$rpath,
                paste(opt$flepi_path, "flepimop", "main_scripts", "create_seeding_added.R", sep = "/"),
                "-c", opt$config
            ))
            if (err != 0) {
                stop("Could not run added seeding")
            }
        }

[saraloo]

This should be fixed with the plugin option. We need to addresshow the classical inference scripts should handle these plugins.

Currently gempyor handles these, which causes issues in inference_slot if files do not exist yet (eg if a plugin creates seeding files, they do not yet exist if gempyor hasn't been called yet but sometimes inference_slot looks for these).

Another action item is to move these scripts to the COVID19_USA repo.

• seeding scripts
• any initialisation/resume scripts that are currently called in the batch scripts.