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.

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

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

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