rbi: R Interface to LibBi

Provides a complete R interface to LibBi, a library for Bayesian inference (see <http://libbi.org> for more information). This includes functions for manipulating LibBi models, for reading and writing LibBi input/output files, for converting LibBi output to provide traces for use with the coda package, and for running LibBi from R.

Install the latest version of this package by entering the following in R:
install.packages("rbi")
AuthorPierre E. Jacob [aut], Anthony Lee [ctb], Lawrence M. Murray [ctb], Sebastian Funk [aut, cre]
Date of publication2017-02-06 12:24:18
MaintainerSebastian Funk <sebastian.funk@lshtm.ac.uk>
LicenseGPL-3
Version0.7.0
https://github.com/libbi/RBi

View on CRAN

Man pages

absolute_path: Absolute Path

add_block: Add a block to a LibBi model

add_output: Add output file to a 'libbi' object

assert_output: Check that a LibBi wrapper has valid output

bi_contants: Bi contents

bi_dim_len: NetCDF dimension length

bi_file_summary: NetCDF File Summary

bi_generate_dataset: Bi Generate Dataset

bi_model: Bi Model

bi_open: Bi open

bi_read: Bi Read

bi_write: Create (init or observation) files for LibBi

clean_model: Strip model code to its bare bones

Extract.bi_model: Subset and replace model lines

extract_sample: Extract a sample from a 'LibBi' run.

filter: Using the LibBi wrapper to filter

find_block: Find a block in a LibBi model

fix: Fix noise term, state or parameter of a libbi model

get_block: Get the contents of a block in a LibBi model

get_name: Get the name of a bi model

get_traces: Get the parameter traces

insert_lines: Insert lines in a LibBi model

is_empty: Check if a model is empty

libbi: LibBi Wrapper

netcdf_create_from_list: Create NetCDF File from R list

obs_to_noise: Copy obs variables to state variables (with '__sample_'...

optimise: Using the LibBi wrapper to optimise

option_list: Convert string to option list

option_string: Convert Options

predict: Using the LibBi wrapper to predict

print: Print the lines of a LibBi model

propose_prior: Propose from the prior in a libbi model

rbi-package: RBi - R interface for 'libbi'

read_libbi: Read results of a 'LibBi' run from an RDS file. This...

read_var_input: Read variable from NetCDF file.

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

replace_all: Replace all instances of a string with another in a model

rewrite: Using the LibBi wrapper to rewrite

run: Using the LibBi wrapper to launch LibBi

sample: Using the LibBi wrapper to sample

save_libbi: Write results of a 'LibBi' run to an RDS file

set_name: Set the name of a bi model

summary: Print summary information about a 'libbi' object

var_names: Get variables

write_file: Writes a bi model to a file.

Functions

absolute_path Man page
add_block Man page
add_block.bi_model Man page
add_output Man page
add_output.libbi Man page
assert_output Man page
bi_contents Man page
bi_dim_len Man page
bi_file_summary Man page
bi_generate_dataset Man page
`[<-.bi_model` Man page
[<-.bi_model Man page
bi_model Man page
bi_open Man page
bi_read Man page
bi_write Man page
clean_model Man page
Extract.bi_model Man page
extract_sample Man page
filter Man page
filter.bi_model Man page
filter.character Man page
filter.libbi Man page
find_block Man page
fix Man page
fix.bi_model Man page
get_block Man page
get_block.bi_model Man page
get_name Man page
get_name.bi_model Man page
get_traces Man page
insert_lines Man page
insert_lines.bi_model Man page
is_empty Man page
libbi Man page
netcdf_create_from_list Man page
obs_to_noise Man page
optimise Man page
optimise.bi_model Man page
optimise.character Man page
optimise.libbi Man page
option_list Man page
option_string Man page
predict Man page
predict.libbi Man page
print Man page
print.bi_model Man page
print.libbi Man page
propose_prior Man page
rbi Man page
RBi Man page
rbi-package Man page
read_libbi Man page
read_var_input Man page
remove_lines Man page
remove_lines.bi_model Man page
replace_all Man page
replace_all.bi_model Man page
rewrite Man page
rewrite.bi_model Man page
rewrite.character Man page
rewrite.libbi Man page
run Man page
run.libbi Man page
sample Man page
sample.bi_model Man page
sample.character Man page
sample.libbi Man page
save_libbi Man page
save_libbi.libbi Man page
set_name Man page
set_name.bi_model Man page
summary Man page
summary.libbi Man page
var_names Man page
var_names.bi_model Man page
write_file Man page
write_file.bi_model Man page

Files

inst
inst/SIR.bi
inst/PZ.bi
inst/example_dataset.nc
inst/doc
inst/doc/introduction.Rmd.rsp
inst/doc/introduction.html
inst/example_output.nc
tests
tests/testthat.R
tests/testthat
tests/testthat/test-io.r tests/testthat/test-libbi.r tests/testthat/test-bi-model.r tests/testthat/test-samples.r
NAMESPACE
demo
demo/PZ_generate_dataset.R demo/PZ_SMC2.R demo/PZ_filtering.R
demo/00Index
demo/PZ_PMMH.R
NEWS.md
R
R/bi_generate_dataset.R R/get_traces.R R/bi_dim_len.R R/libbi.R R/util_nc_create_from_list.R R/read_var_input.R R/extract_sample.R R/bi_read.R R/util_option_string.R R/bi_write.R R/rbi-package.R R/bi_contents.R R/util_option_list.R R/bi_model.R R/bi_file_summary.R R/bi_open.R R/util_absolute_path.R R/zzz.R
vignettes
vignettes/introduction.Rmd.rsp
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/bi_write.Rd man/libbi.Rd man/rewrite.Rd man/run.Rd man/get_block.Rd man/bi_open.Rd man/Extract.bi_model.Rd man/set_name.Rd man/clean_model.Rd man/option_string.Rd man/option_list.Rd man/bi_contants.Rd man/rbi-package.Rd man/optimise.Rd man/get_traces.Rd man/insert_lines.Rd man/is_empty.Rd man/bi_generate_dataset.Rd man/bi_model.Rd man/get_name.Rd man/predict.Rd man/netcdf_create_from_list.Rd man/obs_to_noise.Rd man/fix.Rd man/add_output.Rd man/assert_output.Rd man/find_block.Rd man/read_var_input.Rd man/remove_lines.Rd man/bi_file_summary.Rd man/var_names.Rd man/save_libbi.Rd man/replace_all.Rd man/bi_read.Rd man/add_block.Rd man/filter.Rd man/bi_dim_len.Rd man/read_libbi.Rd man/write_file.Rd man/extract_sample.Rd man/print.Rd man/propose_prior.Rd man/sample.Rd man/summary.Rd man/absolute_path.Rd

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