NEWS.md
Fixed a major issue with addExperiments()
, where some experimetal data was lost or misassigned.
addExperiments()
is also used by runParameterEstimation()
and setParameterEstimationSettings()
.
Deprecate the name
parameter of setParameters()
.
Renaming parameters on a per reaction basis is not supported by COPASI.
Improved consistency of fetching of models from URLs.
Adjust for new BioModels URL scheme.
Added biomodels_url()
helper function to assist with generating URLs where desirable.
Added support for Combine archives via loadCombineArchive()
and saveCombineArchive()
.
Minor fixes and code cleanups.
runParameterEstimation()
output, in some cases, listing incorrect parameter start values.Hotfix for windows build having an incorrect COPASI Version annotation.
The COPASI version was incorrectly reported to be 4.12.
Fix system compatility with various linux distros.
CoRC used to crash on various untested linux distros. Compatibility has now been confirmed with Ubuntu (16.04, 18.04, 20.04), CentOS (6, 7, 8), and Fedora (30, 32).
Use ‘readr’ package for write out of experimental data, to prevent erroneous conversion of NaN
to NA
.
Fix behaviour of autoplot.copasi_ts()
function when a timeseries output named ‘Time’ exists.
‘Time’ output used to confilict with the invariant time column.
Rework tidyverse dependencies to be more light weight.
Minor fixes and code cleanups.
soft_error
to runTimeCourse()
to allow for readout of incomplete result tables for failed time courses.preserve_concentrations
argument to setCompartments()
to preserve species concentrations instead of particle numbers on adjustment of compartment sizes.getCopasi()
to fall back on github as a download mirror.parallel::parLapplyLB()
for parallel processing as it was fixed in R version 3.5.NaN
, Inf
and -Inf
for many values.getVersion()
for retrieving the version of the COPASI backend.newReaction()
from scheme
to reaction
.loadSBMLFromString()
, saveSBMLToString()
).event()
, event_strict()
, getEvents()
, setEvents()
, newEvent()
, deleteEvent()
).""
instead of NA
to denote unset or empty expressions.getValue(1)
instead of getValue("1")
.type
of setCompartments()
and setGlobalQuantities()
.