rbi 1.0.0
- 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
- add
markdown Suggests to pass CRAN check
rbi 0.10.3
- 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
- better error handling
- expanded
summary function
- fix in dealing with observation times in
sample_obs
rbi 0.10.1
preserve_shell option in remove_lines to
keep block options
- new
simulate function
rbi 0.10.0
- 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
- Fixed a bug in
bi_generate_dataset
- Fixed chaining when there are no variables to chain
rbi 0.9.0
- 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
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
- 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
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$fix that ignored input
variables
rbi 0.5.0
client is now an option to libbi$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
- 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