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.

Author
Pierre E. Jacob [aut], Anthony Lee [ctb], Lawrence M. Murray [ctb], Sebastian Funk [aut, cre]
Date of publication
2016-12-23 13:42:28
Maintainer
Sebastian Funk <sebastian.funk@lshtm.ac.uk>
License
GPL-3
Version
0.6.0
URLs

View on CRAN

Man pages

absolute_path
Absolute Path
bi_contants
Bi contents
bi_dim_len
NetCDF dimension length
bi_dim_values
NetCDF dimension values
bi_file_summary
NetCDF File Summary
bi_generate_dataset
Bi Generate Dataset
bi_init_file
Create init files for LibBi, retained for backwards...
bi_model
Bi Model
bi_model_clone
Clones a model (returning a new object with the same...
bi_model_fix
Fix noise term, state or parameter of a libbi model
bi_model_get_lines
Get lines in a libbi model
bi_model_insert_lines
Insert lines in a libbi model
bi_model_propose_prior
Propose from the prior in a libbi model
bi_model_remove_lines
Remove line(s) in a libbi model
bi_model_replace_all
replace all instances of one string with another
bi_model_set_name
Set the name of a bi model
bi_model_update_lines
Update line(s) in a libbi model
bi_model_write
Writes a bi model to a file.
bi_open
Bi open
bi_read
Bi Read
bi_write
Create (init or observation) files for LibBi
generate_seed
Generate a random seed
get_traces
Get the parameter traces
libbi
LibBi Wrapper
libbi_clone
Clone a libbi object
libbi_run
Using the LibBi wrapper to launch LibBi
log2normw
Normalize log weights
merge_by_name
Merge lists by name
netcdf_create_from_list
Create NetCDF File from R list
option_list
Convert string to option list
option_string
Convert Options
rbi-package
RBi - R interface for 'libbi'
read_var_input
Read variable from NetCDF file.
tick-subset-tick
Subset assignment to mode lines
tick-sub-tick
Subset of model lines

Files in this package

rbi
rbi/inst
rbi/inst/SIR.bi
rbi/inst/PZ.bi
rbi/inst/doc
rbi/inst/doc/introduction.Rmd.rsp
rbi/inst/doc/introduction.html
rbi/inst/example_output.nc
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/util_get_traces.R
rbi/R/util_nc_var_has_dim.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/util_generate_seed.R
rbi/R/bi_read.R
rbi/R/util_option_string.R
rbi/R/util_log2normw.R
rbi/R/util_nc_var_get_dim.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/util_merge_by_name.R
rbi/R/bi_file_summary.R
rbi/R/bi_open.R
rbi/R/util_absolute_path.R
rbi/R/bi_dim_values.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/libbi_clone.Rd
rbi/man/bi_open.Rd
rbi/man/bi_model_clone.Rd
rbi/man/bi_init_file.Rd
rbi/man/option_string.Rd
rbi/man/option_list.Rd
rbi/man/bi_model_insert_lines.Rd
rbi/man/bi_contants.Rd
rbi/man/rbi-package.Rd
rbi/man/get_traces.Rd
rbi/man/bi_model_replace_all.Rd
rbi/man/tick-sub-tick.Rd
rbi/man/bi_generate_dataset.Rd
rbi/man/bi_model.Rd
rbi/man/netcdf_create_from_list.Rd
rbi/man/bi_model_fix.Rd
rbi/man/bi_model_set_name.Rd
rbi/man/read_var_input.Rd
rbi/man/bi_model_get_lines.Rd
rbi/man/bi_file_summary.Rd
rbi/man/bi_model_update_lines.Rd
rbi/man/bi_read.Rd
rbi/man/generate_seed.Rd
rbi/man/merge_by_name.Rd
rbi/man/bi_dim_len.Rd
rbi/man/bi_model_remove_lines.Rd
rbi/man/tick-subset-tick.Rd
rbi/man/log2normw.Rd
rbi/man/bi_model_write.Rd
rbi/man/absolute_path.Rd
rbi/man/bi_dim_values.Rd
rbi/man/libbi_run.Rd
rbi/man/bi_model_propose_prior.Rd