rbi (version 0.7.0)

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, missval.threshold, coord_name, vector, thin,
  verbose, clear_cache)

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

missval.threshold

upper threshold for the likelihood

coord_name

name of coord dimension (if any)

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

Value

list of results

Examples

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