# pass from command line ---- args <- commandArgs(trailingOnly=TRUE) if (length(args) != 2) stop("Pass in suffix (sqrt or og), params (all-reg, xi-ri, sigma-ri_xi-ri, nu-ri_xi-ri, kappa-ri_xi-ri)", call.=FALSE) if (!(args[1] %in% c('sqrt', 'og'))) stop("Pass in the response data type (sqrt or og)", call.=FALSE) if (!(args[2] %in% c("all-reg", "xi-ri", "sigma-ri_xi-ri", "nu-ri_xi-ri", "kappa-ri_xi-ri"))) stop("Pass in the parameter combination (all-reg, xi-ri, sigma-ri_xi-ri, nu-ri_xi-ri, kappa-ri_xi-ri)", call.=FALSE) suffix <- args[1] params <- args[2] library(cmdstanr) set_cmdstan_path(path = "/projects/eslawler@colostate.edu/.cmdstan/cmdstan-2.31.0") # this is only relevant to Alpine check_cmdstan_toolchain(fix = TRUE, quiet = TRUE) library(MCMCvis) library(tidyverse) library(stringr) options(mc.cores = parallel::detectCores()) file_base <- paste0("g1_", suffix, "_", params, "*") csv_files <- paste0("./full-model/fire-sims/burns/g1/csv-fits/", list.files("full-model/fire-sims/burns/g1/csv-fits/", pattern = file_base)) print(csv_files) st_date <- stringr::str_extract(basename(csv_files[1]), "\\d{2}-Mar-\\d{4}") egpd_fit <- as_cmdstan_fit(csv_files, format = "draws_list") # egpd_fit$save_obj(file = paste0("./full-model/fire-sims/burns/g1/cmd-stan-fits/g1_", suffix, "_", params, "_", st_date, ".RDS")) egpd_mcmc <- as_mcmc.list(egpd_fit) # save traceplots MCMCtrace(egpd_mcmc, params = "rho", ind = TRUE, open_pdf = FALSE, filename = paste0('./full-model/figures/g1/trace/g1_', params, '_', suffix, '_rhos_', st_date, ".pdf")) MCMCtrace(egpd_mcmc, params = "beta", ind = TRUE, open_pdf = FALSE, filename = paste0('./full-model/figures/g1/trace/g1_', params, '_', suffix,'_betas_', st_date, ".pdf")) MCMCtrace(egpd_mcmc, params = "phi", ind = TRUE, open_pdf = FALSE, filename = paste0('./full-model/figures/g1/trace/g1_', params, '_', suffix,'_phis_', st_date, ".pdf"))