Read a LiBbi Model

Read results of a LibBi run from a folder. This completely reconstructs the saved LibBi object This reads all options, files and outputs of a LibBi run from a specified folder

read_libbi(folder, ...)

Arguments

folder	Name of the folder containing the Libbi output as formated by save_libbi.
...	any extra options to pass to read_libbi when creating the new object

Value

a libbi object#'

Examples

## Function code
ModelTBBCGEngland::read_libbi
#> function(folder, ...) {
#>   if (missing(folder)) {
#>     stop("Need to specify a folder to read")
#>   }
#>   
#>   files <- list.files(folder)
#>   
#>   read_obj <- map(files, function(x) {
#>     if (x == "output") {
#>       files <- list.files(file.path(folder, x))
#>       file <- map(files, ~readRDS(file.path(folder, x, .)))
#>       names(file) <-  str_replace(files,".rds", "")
#>                           
#>     }else{
#>       file <- readRDS(file.path(folder, x))
#>       file <- file[[1]]
#>     }
#>     
#>     return(file)
#>   })
#>   
#>   names(read_obj) <- str_replace(files,".rds", "")
#>   
#>   libbi_options <- list(...)
#>   pass_options <- c("model", "dims", "time_dim", "coord_dims", 
#>                     "thin", "output-every", "init", "input", "obs")
#>   for (option in pass_options) {
#>     if (!(option %in% names(libbi_options)) && option %in% 
#>         names(read_obj)) {
#>       libbi_options[[option]] <- read_obj[[option]]
#>     }
#>   }
#>   if ("options" %in% names(read_obj)) {
#>     for (option in names(read_obj[["options"]])) {
#>       if (!(option %in% names(libbi_options))) {
#>         libbi_options[[option]] <- read_obj[["options"]][[option]]
#>       }
#>     }
#>   }
#>   new_obj <- do.call(libbi, libbi_options)
#>   new_obj <- attach_data(new_obj, file = "output", data = read_obj$output, 
#>                          time_dim = libbi_options$time_dim)
#>   if ("log" %in% names(read_obj)) {
#>     writeLines(read_obj[["log"]], new_obj$log_file_name)
#>   }
#>   new_obj$supplement <- read_obj$supplement
#>   
#>   return(new_obj)
#> }
#> <environment: namespace:ModelTBBCGEngland>