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R/postprocess.R

@@ -516,7 +516,7 @@ plot_abkinetics_trajectories <- function(model_summary, file_path) {
 
 #' @importFrom data.table as.data.table rbindlist setDT data.table
 #' @importFrom future plan multisession
-plot_abkinetics_trajectories_ind <- function(model_summary, file_path) {
+plot_abkinetics_trajectories_ind <- function(model_summary, file_path, parallel_i = FALSE) {
 
     fitfull <- model_summary$fit    
     outputfull <- model_summary$post
@@ -592,8 +592,9 @@ plot_abkinetics_trajectories_ind <- function(model_summary, file_path) {
     exposures_fit <- model_outline$infoModel$exposureFitted
     exposures <- model_outline$exposureTypes
 
-
-    plan(multisession, workers = 8)
+    if (parallel_i) {
+        plan(multisession, workers = 8)
+    }
 
 
     cat("\n Get order of all entries, \n")

R/postprocess_sim.R

@@ -43,7 +43,7 @@ plotPostFigsSim <- function(model_summary, sim_model, sim_res, save_info) {
 
 }
 
-plot_abkinetics_trajectories_ind_sim <- function(model_summary, sim_model, sim_res, file_path) {
+plot_abkinetics_trajectories_ind_sim <- function(model_summary, sim_model, sim_res, file_path, parallel_i = FALSE) {
 
     fitfull <- model_summary$fit    
     outputfull <- model_summary$post
@@ -119,8 +119,9 @@ plot_abkinetics_trajectories_ind_sim <- function(model_summary, sim_model, sim_r
     exposures_fit <- model_outline$infoModel$exposureFitted
     exposures <- model_outline$exposureTypes
 
-    plan(multisession, workers = 8)
-
+    if (parallel_i) {
+        plan(multisession, workers = 8)
+    }
 
     cat("\n Get order of all entries, \n")
 

R/utils_model.R

@@ -262,7 +262,7 @@ runSeroJump <- function(seroModel, settings, priorPred = FALSE, save_info = NULL
         function(i) { 
             rjmc_sero_func(model = i$model, data = i$data, settings = settings)
         },
-        mc.cores = 8
+        mc.cores = settings$numberCores
         )
     } else {
         out_pp_full <- lapply(list(seroModel), 

vignettes/model_define.Rmd

@@ -227,6 +227,7 @@ save_info <- list(
 
 rj_settings <- list(
         numberChainRuns = 4, 
+        numberCores = 2,
         iterations = 2000,
         burninPosterior = 1000,
         thin = 1

vignettes/sim_recovery.Rmd

@@ -11,10 +11,10 @@ library(devtools)
 library(tidyr)
 library(dplyr)
 library(magrittr)
-#library(serojump)
-devtools::load_all()
+library(serojump)
 library(patchwork)
 
+
 ```
 
 ## Step 2: Read Simulated Data
@@ -24,13 +24,17 @@ This data has been generated using `serosim`.
 ```{r}
 
 
-modeli <- readRDS(file = system.file("vig_data", "cesCOP", "inputs.RDS", package = "serojump"))
-res <- readRDS(file = system.file("vig_data", "cesCOP", "sim_data_0.5.RDS", package = "serojump"))
+sim_model_cop <- readRDS(file = "cesCOP_inputs.RDS")
+sim_res_cop <- readRDS(file = "cesCOP_sim_data_0.5.rds")
 
-data_titre_model <- res$observed_biomarker_states %>% select(i, t, value) %>% rename(id = i, time = t, titre = value) 
+#modeli <- readRDS(file = system.file("extdata", "vig_data", "cesCOP", "cesCOP_inputs.RDS", package = "serojump"))
+#res <- readRDS(file = system.file("extdata","vig_data", "cesCOP", "cesCOP_sim_data_0.5.RDS", package = "serojump"))
 
-data_titre_model <- data_titre_model %>% mutate(biomarker = "sVNT") %>% as.data.frame %>% rename(sVNT = titre)
+#modeli <- readRDS(file = "cesCOP_inputs.RDS")
+#modeli <- readRDS(file = "cesCOP_sin_data_0.5.RDS")
 
+data_titre_model <- sim_res_cop$observed_biomarker_states %>% select(i, t, value) %>% rename(id = i, time = t, titre = value) 
+data_titre_model <- data_titre_model %>% mutate(biomarker = "sVNT") %>% as.data.frame %>% rename(sVNT = titre)
 
 ```
 
@@ -139,11 +143,13 @@ p3
 
 ```{r}
 
+sim_model_no_cop <- readRDS(file = "cesNoCOP_inputs.RDS")
+sim_res_no_cop <- readRDS(file = "cesNoCOP_sim_data_0.5.rds")
 
-modeli <- readRDS(file = system.file("vig_data", "cesNoCOP", "inputs.RDS", package = "serojump"))
-res <- readRDS(file = system.file("vig_data", "cesNoCOP", "sim_data_0.5.RDS", package = "serojump"))
+#modeli <- readRDS(file = system.file("extdata", "vig_data", "cesNoCOP", "cesNoCOP_inputs.RDS", package = "serojump"))
+#res <- readRDS(file = system.file("extdata", "vig_data", "cesNoCOP", "cesNoCOP_sim_data_0.5.RDS", package = "serojump"))
 
-data_titre_model <- res$observed_biomarker_states %>% select(i, t, value) %>% rename(id = i, time = t, titre = value) 
+data_titre_model <- sim_res_no_cop$observed_biomarker_states %>% select(i, t, value) %>% rename(id = i, time = t, titre = value) 
 data_titre_model <- data_titre_model %>% mutate(biomarker = "sVNT") %>% as.data.frame %>% rename(sVNT = titre)
 
 
@@ -268,20 +274,12 @@ save_info_no_cop <- list(
 #model_summary_cop <- runInfRJMCMC(model_cop, rj_settings, save_info = save_info_cop)
 #model_summary_no_cop <- runInfRJMCMC(model_no_cop, rj_settings, save_info = save_info_no_cop)
 
-model_summary_cop <-  readRDS(here::here("outputs", "fits", save_info_cop$file_name, save_info_cop$model_name, paste0("model_summary.RDS")))
-model_summary_no_cop <-  readRDS(here::here("outputs", "fits", save_info_no_cop$file_name, save_info_no_cop$model_name, paste0("model_summary.RDS")))
-
-modelname_sim <- "cesCOP_notd"
-sim_model_cop <- readRDS(here::here("outputs", "sim_data", modelname_sim, "inputs.RDS"))
-sim_res_cop <- readRDS(file = here::here("outputs", "sim_data", modelname_sim, paste0("sim_data_", "0.5", ".rds")))
+model_summary_cop <-  readRDS("cop_model_summary.RDS")
+model_summary_no_cop <-  readRDS("no_cop_model_summary.RDS")
 
 plotMCMCDiagnosis(model_summary_cop, save_info = save_info_cop)
 plotPostFigsSim(model_summary_cop, sim_model_cop, sim_res_cop, save_info = save_info_cop)
 
-modelname_sim <- "cesNoCOP_notd"
-sim_model_no_cop <- readRDS(here::here("outputs", "sim_data", modelname_sim, "inputs.RDS"))
-sim_res_no_cop <- readRDS(file = here::here("outputs", "sim_data", modelname_sim, paste0("sim_data_", "0.5", ".rds")))
-
 plotMCMCDiagnosis(model_summary_no_cop, save_info = save_info_no_cop)
 plotPostFigsSim(model_summary_no_cop, sim_model_no_cop, sim_res_no_cop, save_info = save_info_no_cop)