markdown
Suggests to pass CRAN checksample_obs
and chaininglibbi
objectsummary
functionsample_obs
preserve_shell
option in remove_lines
to keep block optionssimulate
functionsample_obs
argument with a sample_obs
functionoutput_every
argument for outputs at every n-th time stepprint_log
function to inspect the LibBi logget_traces
now also reports initial states if they are treated as parametersread_libbi
and save_libbi
now have an option to split the files upsummary
function that can now also print summaries of time-varying variablesattach_data
, replacing attach_file
but offering vastly improved functionalityrewrite
function to provide correct outputbi_generate_dataset
join
and logLik
libbi
optiondry
optionwithout
optionspredict
functionsupplement
option to save_libbi
to store supplementary informationlibbi
callsattach_file
function, a more general version of the former add_output
file
option for bi_read
predict
ns
or other dimensionslibbi
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 problemstr
and summary
methods defined for libbi
objects, and sample
, filter
and optimise
commands for running LibBibi_read
are much fasterbi_read
when reading variables with one dimensionbi_generate_dataset
now has a seed optionextract_sample
function for extracting a single sample from a NetCDF fileadd_output
option for reconstructing libbi
objectsbi_contents
to quickly get the variables in an NetCDF filegenerate_seed
to generate a seed for a libbi
runsample_obs
option to libbi$run
, to sample posterior observationsbi_model
result
field in the libbi
objectbi_model$get_vars
that didn't remove all spacesbi_read
bi_model$fix
that ignored input variablesclient
is now an option to libbi$run
libbi$initialize
get_traces
if there is only one samplebi_model$insert_lines
can now work with blocksbi_generate_dataset
(#3, #5, @tyler-abbot)stringr
dependencyburnin
option to get_traces
bi_write
coord_dim
option in bi_write
bi_generate_dataset
now returns observationsRcpp
dependencyncdf4
package for interaction with netCDF filesbi_model
class to manipulate modelsinit
, obs
and input
as R objectsbi_wrapper
to libbi
bi_read
function to directly read from libbi
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