Added support for macOS on ARM (aarch64)
Rebased on COPASI release 4.39 sources.
Included a further fix to prevent a crashing bug in this version of COPASI
Fixed errors due to breaking changes in package dependency 'stringr' version 1.5.0.
Minor changes to keep up with function deprecations in tidyverse packages.
Minor upgrades.
Rebased on COPASI release 4.34 sources.
Enabled the COPASI just in time compilation that was added in version 4.30.
Enabled setting event assignment_target
to model properties such as 'Time'.
This can be useful e.g. for stopping timecourses after an event, like the runaway accumulation of a model species, which could trigger an error for stochastic simulation due to 'Internal step limit exceeded'. Such an event can be created like so:
newEvent(name = "abort", trigger_expression = "{Prey.ParticleNumber} > 1e5", assignment_target = "Time", assignment_expression = 1e9)
.
NaN
in experimental data was lost and converted to NA
.It is now correctly exported to the '.txt' experimental data.
This matters because COPASI handles NaN
differently than NA
.
Disabled JIT compilation for now as it seems to cause crashes.
This makes getCopasi()
obsolete. The function has been deprecated.
Package installation now requires an internet connection by default, which can be circumvented by providing the correct libraries locally with the COPASI_LIB_PATH
environment variable.
One option to set this variable is with the configure.vars
argument of install.packages()
.
defineExperiments()
has new parameters weights
and normalize_weights_per_experiment
.
Fixed a bug in setSpecies()
where adjusting species initial concentration in conjunction with species type always defaulted to a initial concentration of 0.
Various internal adjustments according to R CMD check notes and warnings.
Minor additions for package stability tests.
addExperiments()
, where some experimental data was lost or misassigned.addExperiments()
is also used by runParameterEstimation()
and setParameterEstimationSettings()
.
name
parameter of setParameters()
.Renaming parameters on a per reaction basis is not supported by COPASI.
Added biomodels_url()
helper function to assist with generating URLs where desirable.
loadCombineArchive()
and saveCombineArchive()
.runParameterEstimation()
output, in some cases, listing incorrect parameter start values.The COPASI version was incorrectly reported to be 4.12.
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).
NaN
to NA
.autoplot.copasi_ts()
function when a timeseries output named 'Time' exists.'Time' output used to confilict with the invariant time column.
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()
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