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Changelog

Source: NEWS.md

rbi (development version)

rbi 1.0.0

CRAN release: 2023-08-15

  • add github actions for package checking and testing
  • add a vignette with example implementations of the SIR epidemic model
  • enable sparse input data
  • hard deprecate functions and arguments

rbi 0.10.4

CRAN release: 2021-11-08

  • add markdown Suggests to pass CRAN check

rbi 0.10.3

CRAN release: 2020-04-17

  • updates to work with the latest version of LibBi
  • errors fixed in sample_obs and chaining
  • errors fixed in reading and saving libbi object

rbi 0.10.2

CRAN release: 2019-07-10

  • better error handling
  • expanded summary function
  • fix in dealing with observation times in sample_obs

rbi 0.10.1

CRAN release: 2019-01-08

  • preserve_shell option in remove_lines to keep block options
  • new simulate function

rbi 0.10.0

CRAN release: 2018-12-11

  • Replaced the sample_obs argument with a sample_obs function
  • output_every argument for outputs at every n-th time step
  • Better handling of the external libbi call via the processx package
  • Improved error/output handling
  • print_log function to inspect the LibBi log
  • Speed up re-running libbi objects by writing to the same model file
  • Big clean-up of code and arguments, deprecating a few obsolete arguments
  • get_traces now also reports initial states if they are treated as parameters
  • read_libbi and save_libbi now have an option to split the files up
  • improved summary function that can now also print summaries of time-varying variables
  • new attach_data, replacing attach_file but offering vastly improved functionality
  • improved rewrite function to provide correct output

rbi 0.9.1

CRAN release: 2018-05-14

  • Fixed a bug in bi_generate_dataset
  • Fixed chaining when there are no variables to chain

rbi 0.9.0

CRAN release: 2018-03-06

  • Fixed a few bugs when working with multiple dimensions
  • New functions: join and logLik
  • Save supplement when saving a libbi option
  • Fixed the dry option
  • Fixed handling of without options
  • Fixed handling of predict function

rbi 0.8.0

CRAN release: 2017-08-14

  • supplement option to save_libbi to store supplementary information
  • Temporary directories are now removed when quitting R or collecting garbage
  • Improved chaining of libbi calls
  • New attach_file function, a more general version of the former add_output
  • New file option for bi_read
  • Fixed problems with predict
  • Fixed add_output when passed a list
  • Fixed a bug in writing observation files; extra dimensions are now written in the correct order
  • Improved writing of observation files with ns or other dimensions
  • Improved error handling: libbi calls now finish and yield a warning if the call to the libbi executable fails; this makes it possible to inspect the object to diagnose the problem

rbi 0.7.0

CRAN release: 2017-02-06

  • The class is now based on S3 classes. Because of this, it plays much nicer with the magrittr and related packages. There are now str and summary methods defined for libbi objects, and sample, filter and optimise commands for running LibBi
  • Caching is now supported: multiple calls to bi_read are much faster
  • added a testing suite
  • Fixed bug in bi_read when reading variables with one dimension
  • bi_generate_dataset now has a seed option
  • extract_sample function for extracting a single sample from a NetCDF file
  • new add_output option for reconstructing libbi objects
  • cleaned up code and removed obsolete functions
  • Many smaller bug fixes

rbi 0.6.0

CRAN release: 2016-12-23

  • bi_contents to quickly get the variables in an NetCDF file
  • generate_seed to generate a seed for a libbi run
  • new sample_obs option to libbi$run, to sample posterior observations
  • improved option handling; there is now only one ‘options’ option
  • overloaded subset operators in bi_model
  • no more result field in the libbi object
  • new vignette: Introduction to rbi
  • Fixed bug in bi_model$get_vars that didn’t remove all spaces
  • Fixed bug in reading in the coord dimension(s) in bi_read
  • Fixed bug in bi_model$fix that ignored input variables

rbi 0.5.0

CRAN release: 2016-11-18

  • client is now an option to libbi$run
  • Fix bug in parsing options in libbi$initialize
  • Fix bug in get_traces if there is only one sample
  • bi_model$insert_lines can now work with blocks
  • Improve cloning, where all initialising parameters can now be passed

rbi 0.4.1

CRAN release: 2016-10-18

  • Change package name to lower case
  • Tidy up for CRAN submission
  • Fix finding libbi path
  • Fix handling of config options (#2, @tyler-abbot)
  • Fix options in bi_generate_dataset (#3, #5, @tyler-abbot)
  • Fix demos (#1, #6, @tyler-abbot)
  • Remove stringr dependency

rbi 0.4

  • Guess time dimension in netCDF files
  • Bug fixes to better deal with multiple coordinate variables
  • burnin option to get_traces
  • Reduce memory use when thinning

rbi 0.3

  • Bug fixes in bi_write
  • Improve dealing with different types of dimensions, including introduction of the coord_dim option in bi_write
  • bi_generate_dataset now returns observations
  • Remove Rcpp dependency

rbi 0.2

  • Remove C code and use ncdf4 package for interaction with netCDF files
  • Introduce the bi_model class to manipulate models
  • Allow giving init, obs and input as R objects
  • Rename bi_wrapper to libbi
  • Improved bi_read function to directly read from libbi objects

rbi 0.1

  • initial version