rbi (version 0.9.1)

bi_read: Bi Read

Description

This function reads all variable from a NetCDF file or the output of a libbi object. The file can be specified as a string to the filepath, in which case a NetCDF connection is opened, or directly as a NetCDF connection.

Usage

bi_read(x, vars, dims, model, type, file, missval.threshold, coord_dims, vector,
  thin, verbose, clear_cache, init.to.param = FALSE)

Arguments

x

either a path to a NetCDF file, or a NetCDF connection created using nc_open, or a libbi object from which to read the output

vars

variables to read; if not given, all will be read

dims

factors for dimensions

model

model file or a bi_model object (if x is not a libbi object)

type

vector of types of variable to read (out of "param", "state", "noise", "obs"). This needs 'x' to be a libbi object or model to be specified

file

which file to read (if x is given as a libbi object): one of "output" (default), "init", "input", "obs"

missval.threshold

upper threshold for the likelihood

coord_dims

any coord dimensions, given as a named list of character vectors, where each element corresponds to the variable of the same name, and the character vector are the coord dimensions

vector

if TRUE, will return results as vectors, not data.frames

thin

thinning (keep only 1/thin of samples)

verbose

if TRUE, will print variables as they are read

clear_cache

if TRUE, will clear the cache and re-read the file even if cached data exists

init.to.param

logical; if TRUE, convert states to initial values

Value

list of results

Examples

# NOT RUN {
example_output_file <- system.file(package="rbi", "example_output.nc")
d <- bi_read(example_output_file)
# }