The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
For the first time NMsim works on Windows. There may still be some limitations but initial testing looks very promising. Make sure to set path.nonmem. See the configuration vignette on the website: NMsim-config.html
0.1.0 is also an important upgrade that solidifies the way NMsim reads results from simulations. In addition to important bug fixes, it allows for NMsim to wait on Nonmem to complete simulations - even when they are run on a cluster. This means even large simulations with NMsim can be integrated in scripts.
Works on Windows - at least most features do.
NMsim() and NMreadSim() now have wait arguments which controls if they will wait for Nonmem to finish simulating. This will also work if jobs were sent to the cluster.
NMsim() respects the reuse.results argument. If TRUE it will use results file on the file system. This can be used in stead of putting NMsim() calls inside an if-statement to disable the simulation but read results on file.
NMsim() looks for a couple of features of the provided control streams that are known to be able to cause issues. Warnings will be issued if these are found.
addEVID2 has a new argument, EVID to specify what value the EVID column should have. It can be useful sometimes to use EVID=0 for simulation records.
NMreadSim() would not get the path right to the simulation results leading to failures in reading simulation results. Fixed.NMreadExt and NMreadPhi have been removed from NMsim. They live and are being maintained in the NMdata package. In NMsim, were deprecated and unmaintained functions.NMsim 0.0.9 had an unfortunate bug in NMreadSim() which has been fixed. That bugfix is difference between 0.0.9 and 0.0.10.
NMsim 0.0.9 is almost identical to 0.0.8 but ensures compatibility with older R versions.
NMreadSim would not be able to read and combine results from models that returned different data variables. Fixed.NMsim 0.0.7 would generate an rds file with paths to simulation files and results for each model+data set simulated. This has been changed to now only generate one table per model. This makes it simpler to read simulation results in some cases.
NMreadSim should now be the best and only way for the user to read NMsim simulation results. It interprets rds files (which are the ones intended for reading), fst files, tables of NMsim runs, and NMsim results. This makes it less confusing what can be processed by NMreadSim and also it sometimes easier to generalize code reading simulation results. Also, NMsim now always reads results using NMreadSim. This has the advantage that an fst file will always be produced if NMsim waits to read the results.
NMreadSim has a new argument, check.time by default disabling checking whether a collected fst file is newer than the results files generated by NMsim. Normally, it’s a good thing to check this but some ways of sharing file files may not retain file modification times needed to check for this. NMsim will delete the fst files if it finds any so normally it should not be a problem to skip this check.
NMsim now tries to reuse stored results if reuse.results=TRUE. It does so in a simple way - if they exist, they will be attempted read - so be careful to rerun simulations without this option if you change any arguments.
The transform option has been integrated into the table of simulations created by NMsim(). This means even if the results are not read by NMsim (because the simulation is not executed or it is submitted to a cluster), the transformation will still be applied by NMreadSim() later.
NMsim()'s dir.sims and dir.res arguments can be controlled using NMdata::NMdataConf(). Often these two arguments are used all the time, so it’s convenient to be able to configure those once and for all in a script.
NMreadSim was only able to read results if the current working directory was the same as when NMsim was executed. Now fixed.
In some cases NMsim would fail on models with multiple output tables when the table.vars argument was not used. Fixed.
NMsim’s sim.dir.from.scratch argument was not respected due to a simple bug, leading to dir.sims growing each time a simulation was rerun.
In case simulation data is a list of data sets NMsim would not order columns when order.columns was TRUE. Now fixed.
In case of lists of data sets, and the list element (data set) names included spaces, NMsim() would throw and error. Spaces in data set names are now replaced with under scores ("_") to avoid that. It will often happen when data sets are split into lists using data.table::split.data.table() - which is an excellent way to do this, by the way.
Function simPopEtas() was not exported, so only available as NMsim:::simPopEtas(). Fixed.
Function simPopEtas() to generate a population from a model. The population can be saved as a phi file to be reused in subsequent simulations. The function is by mistake not exported in 0.0.7 so for now you must use NMsim:::simPopEtas() to use it.
Function NMreadSim() provides a very simple interface to reading simulation results. Especailly in cases where the simulation is being parallelized or otherwise spawns multiple Nonmem jobs, this is a useful feature.
A list of simulation data sets will now be simulated with separate Nonmem runs. This is an efficient way to parellelize large simulation runs.
sge type clusters (using qsub). See arguments sge and nc.genPhiFile() when having more than 10 ETAs in a model. Now fixed.Full support for models estimated with SAEM. Especially, simulation of “known” subjects, i.e. re-using emperical Bayes estimates, is slightly different with these models.
Experimental support for windows with PsN. dir.psn argument has to point to a directory where executables execute and update_inits are found. Thanks to Sjoerd Koopman for debugging and testing this. Hopefully in future versions, PsN will not be needed on Windows (like it is not needed on Linux).
The simulation method called NMsim_known now accepts other .phi files to use than the .phi file generated by the estimation run. This is useful if one wants to reuse subjects generated in a previous simulation.
xml, ext, cov, cor, coi, phi, shk - in addition to output table files and the archived input data of course.NMsim supports type.sim="typical" which means all OMEGAS will be fixed to zero. This requires the ext file to be present.
Experimental support for simulation of estimated subjects using type.sim="known".
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.