Package: mrgsolve 1.5.2.9000

Kyle T Baron

mrgsolve: Simulate from ODE-Based Models

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Authors:Kyle T Baron [aut, cre], Bill Gillespie [ctb], Charles Margossian [ctb], Devin Pastoor [ctb], Bill Denney [ctb], Dilawar Singh [ctb], Felicien Le Louedec [ctb], Timothy Waterhouse [ctb], Kyle Meyer [ctb], Metrum Research Group [cph]

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NEWS

# Install 'mrgsolve' in R:
install.packages('mrgsolve', repos = c('https://metrumresearchgroup.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/metrumresearchgroup/mrgsolve/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

mrgsolveode

11.13 score 130 stars 3 packages 1.2k scripts 1.3k downloads 11 mentions 126 exports 19 dependencies

Last updated 19 days agofrom:e1778eb1ac. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
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R-4.5-linux-x86_64OKOct 18 2024
R-4.4-win-x86_64OKOct 18 2024
R-4.4-mac-x86_64OKOct 18 2024
R-4.4-mac-aarch64OKOct 18 2024
R-4.3-win-x86_64OKOct 18 2024
R-4.3-mac-x86_64OKOct 18 2024
R-4.3-mac-aarch64OKOct 18 2024

Exports:%>%%then%allparamas_bmatas_cmatas_data_frame.mrgsimsas_data_setas_deslistas_dmatas.data.frameas.evas.evdas.listas.matrixas.tbl.mrgsimsassign_evblocksbmatcamacarry_outcarry.outcheck_data_namescmatcmtncollapse_matrixcollapse_omegacollapse_sigmacvecdata_setdesigndmatdo_mrgsimenv_evalenv_getenv_get_envenv_lsenv_updateevev_assignev_daysev_expandev_repev_repeatev_rxev_seqevdevd_expandexpand_observationsexpand.evexpand.evdexpand.idatafile_showfilterfilter_simsheadhouseidata_setinitinventoryis.mrgmodis.mrgsimsknobslabelslctranloadsomcodemcode_cachemcRNGmodelparsemodelparse_rmdmodlibmodMATRIXmreadmread_cachemread_filemread_yamlmrgsimmrgsim_0mrgsim_dmrgsim_dfmrgsim_dimrgsim_emrgsim_eimrgsim_imrgsim_qmutate_simsmvgaussmwrite_cppmwrite_yamlnrownumerics_onlyobsaugobsonlyomatoutvarsparamparam_tagsparse_rxplotplot_simsqsimread_nmextrealize_addlreqReqrevars_seeselect_simsshowsimargssmatsolocstimetailtgridtouch_funstscaleuctranupdatevalid_data_setvalid_data_set.matrixvalid_idata_setwf_sweepyaml_to_cppzero_re

Dependencies:BHclidplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigR6RcppRcppArmadillorlangtibbletidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
mrgsolve: Simulate from ODE-Based Modelsmrgsolve-package mrgsolve
Select columns from an ev object$,ev-method [[,ev-method
Select parameter values from a model object$,mrgmod-method [,mrgmod-method [[,mrgmod-method
About the lsoda differential equation solver used by mrgsolveaboutsolver
Coerce R objects to block or diagonal matricesas_bmat as_bmat,ANY-method as_bmat,data.frame-method as_bmat,list-method as_bmat,numeric-method as_cmat as_dmat as_dmat,ANY-method as_dmat,data.frame-method as_dmat,list-method as_dmat,numeric-method
Create a simulation data set from ev objects or data framesas_data_set as_data_set,data.frame-method as_data_set,ev-method
Create a list of designs from a data frameas_deslist
Coerce an object to class evas.ev as.ev,data.frame-method as.ev,ev-method
Coerce a model object to listas.list,mrgmod-method
Coerce an mrgsims object to listas.list,mrgsims-method
Functions to parse code blocksBLOCK_PARSE CAPTURE CMT FIXED HANDLEMATRIX INIT PARAM THETA
Return the code blocks from a model specification fileblocks blocks,character-method blocks,mrgmod-method
Operations with matlist objectsc,matlist-method
Operations with tgrid objects*,tgrid,numeric-method *,tgrids,numeric-method +,tgrid,numeric-method +,tgrids,numeric-method c,tgrid-method c,tgrids-method tgrids_*_numeric tgrids_+_numeric tgrid_*_numeric tgrid_+_numeric
Select items to carry into simulated outputcarry.out carry_out
Check input data set names against model parameterscheck_data_names
Get the compartment number from a compartment namecmtn cmtn,mrgmod-method
Extract the code from a modelcode
Collapse the matrices of a matlist objectcollapse_matrix
Collapse OMEGA or SIGMA matrix listscollapse_omega collapse_sigma
Select and modify a data set for simulationdata_set data_set,mrgmod,ANY-method data_set,mrgmod,data.frame-method data_set,mrgmod,ev-method data_set,mrgmod,missing-method
Set observation designs for the simulationdesign
Extract model detailsdetails
Re-evaluate the code in the ENV blockenv_eval
Return model environmentenv_get env_get_env
List objects in the model environmentenv_ls
Update objects in model environmentenv_update
Event objects for simulating PK and other interventionsev ev,ev-method ev,missing-method ev,mrgmod-method
Replicate a list of events into a data setassign_ev ev_assign
Schedule dosing events on days of the weekev_days
Replicate an event objectev_rep
Repeat a block of dosing eventsev_repeat
Create intervention objects from Rx inputev_rx ev_rx,character,missing-method ev_rx,mrgmod,character-method parse_rx
Schedule a series of event objectsev_seq seq.ev
Create an event object with data-like namesas.evd evd evd,ev-method evd,missing-method evd,mrgmod-method
Example input data setsexBoot exdatasets exidata exTheoph extran1 extran2 extran3
Insert observations into a data setexpand_observations
Create template data sets for simulationevd_expand ev_expand expand.ev expand.evd expand.idata
Select and modify a idata set for simulationidata_set idata_set,mrgmod,ANY-method idata_set,mrgmod,data.frame-method idata_set,mrgmod,missing-method
Methods for working with the model compartment listinit init,ANY-method init,list-method init,missing-method init,mrgmod-method init,mrgsims-method
Check whether all required parameters needed in a model are present in an objectinventory
Check if an object is a model objectis.mrgmod
Check if an object is mrgsims outputis.mrgsims
Change the case of nmtran-like data itemslctran lctran.data.frame lctran.ev uctran uctran.data.frame uctran.ev
Load the model shared objectloadso loadso.mrgmod
Create matrices from vector inputbmat cmat dmat matrix_helpers
Write, compile, and load model codemcode mcode_cache
Set RNG to use L'Ecuyer-CMRGmcRNG
Internal model librarymodlib
modlib: PK/PD Model parameters, compartments, and output variablesmodlib_details
modlib: Pharmacokinetic modelsmodlib_pk
modlib: Pharmacokinetic / pharmacodynamic modelsmodlib_pkpd
modlib: Target mediated disposition modelmodlib_tmdd
modlib: HCV viral dynamics modelsmodlib_viral
Read a model specification filemread mread_cache mread_file
Read a model from yaml formatmread_yaml yaml_to_cpp
Simulate from a model objectdo_mrgsim mrgsim mrgsim_df
Simulate from a model object with quicker turnaroundmrgsim_q
mrgsim variant functionsmrgsim_0 mrgsim_d mrgsim_di mrgsim_e mrgsim_ei mrgsim_i mrgsim_variants
Methods for handling output with dplyr verbsas.tbl.mrgsims as_data_frame.mrgsims as_tibble.mrgsims distinct.mrgsims do.mrgsims filter.mrgsims group_by.mrgsims mrgsims_dplyr mutate.mrgsims pull.mrgsims select.mrgsims slice.mrgsims summarise.each summarise.mrgsims
Methods for modifying mrgsims objectsfilter_sims mrgsims_modify mutate_sims select_sims
dplyr verbs for event objectsfilter.ev mutate.ev select.ev
Write a model to native mrgsolve formatmwrite_cpp
Write model code to yaml formatmwrite_yaml
Get all names from a model objectnames,mrgmod-method
Import model estimates from a NONMEM ext filenmext
Import model estimates from a NONMEM xml fileNMXML nmxml
Prepare data.frame for input to mrgsim()numerics_only
Augment observations in the simulated outputobsaug
Collect only observation records in the simulated outputobsonly
Manipulate OMEGA matricesomat omat,list-method omat,matrix-method omat,missing-method omat,mrgmod-method omat,mrgsims-method omat,NULL-method omat,omegalist-method OMEGA omega
Show names of current output variablesoutvars
Create and work with parameter objectsallparam param param,ANY-method param,list-method param,missing-method param,mrgmod-method param,mrgsims-method
Return parameter tagsparam_tags
Parse PKMODEL BLOCK dataPKMODEL
Generate a quick plot of simulated dataplot,mrgsims,character-method plot,mrgsims,formula-method plot,mrgsims,missing-method plot_mrgsims
Plot data as an mrgsims objectplot_sims
Plot method for mrgsims objectsplot,batch_mrgsims,formula-method plot,batch_mrgsims,missing-method
Basic, simple simulation from model objectqsim
Extract estimates from NONMEM ext fileread_nmext
Make addl doses explicit in an event object or data setrealize_addl realize_addl.data.frame realize_addl.ev
Render a model to a documentdorender render render,character-method render,mrgmod-method
Request simulated outputReq req req.mrgmod
Reserved wordsreserved
Get model random effect variances and covariancesrevar revar,mrgmod-method
Print model code to the consolesee see,mrgmod-method
Manipulate SIGMA matricesSIGMA sigma smat smat,list-method smat,matrix-method smat,missing-method smat,mrgmod-method smat,mrgsims-method smat,NULL-method smat,sigmalist-method
Access or clear arguments for calls to mrgsim()simargs
Return the location of the model shared objectsoloc
Optional inputs for lsodasolversettings
Print summary of a mrgmod objectsummary.mrgmod
Re-scale time in the simulated outputtscale
Update the model objectupdate update,mrgmod-method update,omegalist-method update,parameter_list-method update,sigmalist-method
Validate and prepare data sets for simulationvalid_data_set valid_data_set.matrix
Validate and prepare idata data sets for simulationvalid_idata_set
Update parameters, initials, and settings within a model objectwithin within,mrgmod-method within.mrgmod
Zero out random effects in a model objectzero_re zero_re,mrgmod-method