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Attach a new file or data set to a libbi object

Source: R/libbi.R
attach_data.Rd

Adds an (output, obs, etc.) file to a libbi object. This is useful to recreate a libbi object from the model and output files of a previous run

The bi_write options append and overwrite determine what exactly the file will contain at the end of this. If they are both FALSE (the default), any existing file will be ignored. If append is TRUE, the existing data in the file will be preserved, and any data set passed as data and not already in the file will be added. If overwrite is TRUE, existing data in the file will be preserved except for variables that exist in the passed data.

Usage

# S3 method for libbi
attach_data(
  x,
  file,
  data,
  in_place = FALSE,
  append = FALSE,
  overwrite = FALSE,
  quiet = FALSE,
  time_dim = character(0),
  coord_dims = list(),
  ...
)

Arguments

x

a libbi object

file

the type of the file to attach, one of "output", "obs", "input" or "init"

data

name of the file to attach, or a list of data frames that contain the outputs; it will be assumed that this is already thinned

in_place

if TRUE, replace the file in place if it already exists in the libbi object; this can speed up the operation if append=TRUE as otherwise the file will have to be read and used again; it should be used with care, though, as it can render existing libbi objects invalid as the files they are pointing to are changed.

append

if TRUE, will append variables if file exists; default: FALSE

overwrite

if TRUE, will overwrite variables if file exists; default: FALSE

quiet

if TRUE, will suppress the warning message normally given if replace=TRUE and the file exists already

time_dim

the name of the time dimension, if one exists; default: "time"

coord_dims

the names of the coordinate dimension, if any; should be a named list of character vectors, they are matched to variables names

...

any options to bi_write (e.g., 'time_dim')

Value

an updated libbi object

Examples

bi <- libbi(model = system.file(package = "rbi", "PZ.bi"))
example_output <- bi_read(system.file(package = "rbi", "example_output.nc"))
bi <- attach_data(bi, "output", example_output)