R/plot_prep.R

In cstawitz/RMAS: Read and Write Input and Output for MAS Model

plot_output_object<- function(json_output){
years <- json_output$nyears
ages <- json_output$nages
popdy <- json_output$population_dynamics
observed_catch_data <- popdy$fleet$observed
expected_catch_data <- popdy$fleet$undifferentiated
expected_surv_data <- popdy$survey$undifferentiated
observed_surv_data <- popdy$survey$observed

names(expected_catch_data)[c(2,4)] <- names(observed_catch_data)

ind_surv <- names(expected_surv_data[which(names(expected_surv_data) %in% names(observed_surv_data))])

ind_catch <- names(expected_catch_data[which(names(expected_catch_data) %in% names(observed_catch_data))])

make_mat <- function(data_list) {
  if(length(unlist(data_list))==years*ages){
    return(matrix(unlist(data_list), nrow=ages, ncol=years, byrow=FALSE))}
    else{
      return(unlist(data_list))
    }
  }

e_catch <- lapply((1:length(ind_catch)), function(x) make_mat(expected_catch_data[[ind_catch[x]]]$values))
o_catch <- lapply((1:length(ind_catch)), function(x) make_mat(observed_catch_data[[ind_catch[x]]]$values))

e_surv <- lapply((1:length(ind_surv)), 
                 function(x) make_mat(expected_surv_data[[ind_surv[x]]]$values))
o_surv <- lapply((1:length(ind_surv)), 
                 function(x) make_mat(observed_surv_data[[ind_surv[x]]]$values))


  plot_obs_vs_exp(o_surv, e_surv)
  return(invisible(1))
}