Function reference • rbi

Run LibBi and analyse results

LibBi operations

Functions for running LibBi.

filter(<libbi>) filter(<bi_model>): Using the LibBi wrapper to filter

generate_dataset(): Generate Dataset

optimise(<libbi>) optimise(<bi_model>): Using the LibBi wrapper to optimise

libbi(): LibBi Wrapper

predict(<libbi>): Using the LibBi wrapper to predict

run(<libbi>): Using the LibBi wrapper to launch LibBi

sample(<libbi>) sample(<bi_model>): Using the LibBi wrapper to sample

sample_obs(): Sample observations from a LibBi model that has been run

simulate(<libbi>) simulate(<bi_model>): Using the LibBi wrapper to simulate

Read and write LibBi inputs/outputs

Functions for interacting with the NetCDF files used by LibBi.

bi_contents(): Bi contents

bi_file_summary(): NetCDF File Summary

bi_read(): Bi Read

bi_write(): Create (e.g., init or observation) files for LibBi

Analyse LibBi outputs

Functions for analysing LibBi results.

extract_sample(): Extract a sample from a LibBi run.

get_traces(): Get the parameter traces

summary(<libbi>): Print summary information about a libbi object

logLik(<libbi>): Using the LibBi wrapper to logLik

Manipulate LibBi inputs/outputs

Functions for updating and saving LibBi objects.

attach_data(<libbi>): Attach a new file or data set to a libbi object

join(<libbi>): Join multiple libbi objects

read_libbi(): Read results of a LibBi run from an RDS file or from a folder. This completely reconstructs the saved LibBi object

save_libbi(<libbi>): Write results of a LibBi run to an RDS file

update(<libbi>): Update a libbi object

Construct, show and manipulate LibBi models

Create a model

Function for creating a LibBi model.

bi_model(): Bi Model

Show models

Functions for getting information from LibBi models.

get_block(<bi_model>): Get the contents of a block in a LibBi model

get_const(): Get constants in a LibBi model

get_dims(): Get dimensions in a LibBi model

get_name(<bi_model>): Get the name of a bi model

rewrite(<libbi>) rewrite(<bi_model>): Using the LibBi wrapper to rewrite

var_names(): Get variable names in a LibBi model

Manipulate models

Functions for manipulating LibBi models.

add_block(<bi_model>): Add a block to a LibBi model

enable_outputs(): Enable outputting variables in a bi_model

fix(<bi_model>): Fix noise term, state or parameter of a libbi model

insert_lines(<bi_model>): Insert lines in a LibBi model

remove_lines(<bi_model>): Remove line(s) and/or block(s) in a libbi model

remove_vars(): Remove variables

replace_all(<bi_model>): Replace all instances of a string with another in a model

set_name(<bi_model>): Set the name of a bi model

write_model(<bi_model>) write_model(<libbi>): Writes a bi model to a file.

Model operators

Operators for LibBi models

`==`(<bi_model>): Check if two models are equal

`[`(<bi_model>): Subset model lines

`[<-`(<bi_model>): Subset and replace model lines

`!=`(<bi_model>): Check if two models are unequal

Other functions

Utility functions

Useful additional functions.

flatten(): Flatten list of data frames This function takes a list of data frames (such as, for example, returned by bi_read) and converts it to a flat data frame

print_log(): Print the log file a libbi object

Deprecated functions

To be removed in the next version of rbi.

bi_generate_dataset(): Bi Generate Dataset