Package: SimuRg 0.2.0

Anna Mikhailova

SimuRg: Building, Fitting and Evaluating PK/PD Modeles

Provides a unified workflow for building, fitting using external engines, and evaluating ordinary differential equation (ODE)-based pharmacokinetic/pharmacodynamic (PK/PD) models. Supports generation of estimation scenarios and control files for external engines (e.g., 'Monolix'), simulation of models using 'rxode2', and creation of goodness-of-fit diagnostics. Includes tools for covariate modeling, virtual population design, and local and global sensitivity analyses.

Authors:Victor Sokolov [cph, aut], Anna Mikhailova [cre], Yaroslav Ugolkov [aut], Anatoly Pokladyuk [aut], Alina Melnikova [aut], Victoria Kulesh [aut]

SimuRg_0.2.0.tar.gz
SimuRg_0.2.0.tar.gz(r-4.7-any)SimuRg_0.2.0.tar.gz(r-4.6-any)
SimuRg_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SimuRg/json (API)
NEWS

# Install 'SimuRg' in R:
install.packages('SimuRg', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • data_pbc - Primary Biliary Cirrhosis (PBC) dataset
  • ds_covval - Warfarin covariate values dataset
  • gfo4cov - Warfarin PopPK model fitting output
  • parest - Warfarin population PK parameter estimates
  • warfarin - Warfarin PKPD dataset

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.70 score 4 scripts 26 exports 168 dependencies

Last updated from:2b7690b1f6. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK363
source / vignettesOK283
linux-release-x86_64OK354
wasm-releaseOK205

Exports:read_smrg_objsg_convertersg_covsens_simsg_covsens_vissg_fitsg_globalsens_simsg_globalsens_vissg_gof_obprsg_gof_par_covsg_gof_par_distsg_gof_ressg_gof_res_distsg_gof_tpsg_localsens_simsg_localsens_vissg_modbuildsg_modcompsg_multistartsg_parsumsg_predist_simsg_simsg_sim_tpsg_translatorsg_vpc_simsg_vpc_vissg_vpop_est

Dependencies:armadillo4rbackportsbase64encBHbitbit64bootbromanbslibcachemcheckmateclassclassIntclicliprclockclueclustercmmcodetoolscoincommonmarkcpp11cpp4rcrayondata.tabledescdiagramdigestdparserdplyrdqrngdtwdtwcluste1071farverfastDummiesfastmapflexclustFNNfontawesomeforcatsforeachforeignfsfuturefuture.applygenericsggplot2ggrepelglobalsgluegowergtablehardhathmshtmltoolshttpuvinlineipredirlbaisobanditeratorsjquerylibjsonliteKernSmoothlabelinglaterlatticelavalhslibcoinlifecyclelistenvlotrilubridatemagrittrMASSMatrixmatrixStatsmemoisemimemipfpmodeltoolsmultcompmvtnormnnetnumbersnumDerivotelparallellypartyphilentropypillarpkgconfigplyrpolsplinepoormanppcorPreciseSumsprettyunitsprodlimprogressprogressrpromisesprotoproxypurrrqs2R6randomForestrangerrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppParallelRcppProgressRcppThreadreadrrecipesreshape2rexrlangrmutilrpartRsolnpRSpectrarxode2rxode2llS7sandwichsassscalessensitivityshapeshinyshinyjssitmosourcetoolssparsevctrsSQUAREMStanHeadersstringfishstringistringrstrucchangesurvivalsynthpopsysTH.datatibbletidyrtidyselecttimechangetimeDatetruncnormtzdbutf8uwotvctrsviridisLitevroomwithrxtablezoo

Readme and manuals

Help Manual

Help pageTopics
Primary Biliary Cirrhosis (PBC) datasetdata_pbc
Warfarin covariate values datasetds_covval
Warfarin PopPK model fitting output (4-covariate model)gfo4cov
Warfarin population PK parameter estimatesparest
Convert Monolix project output to R objectssg_converter
Covariate sensitivity analysis via simulationsg_covsens_sim
Visualisation of covariate sensitivity analysis resultssg_covsens_vis
The function to store common parameters descriptionsg_dummy
Run fit with monolix/simurg/nonmem fittersg_fit
Global sensitivity analysis via PRCC or eFASTsg_globalsens_sim
Visualize global sensitivity analysis resultssg_globalsens_vis
Observed vs predicted plotsg_gof_obpr
Plot random effects or individual parameters vs covariatessg_gof_par_cov
Plot distributions of individual parameters with optional theoretical densitysg_gof_par_dist
Create residual diagnostic plotssg_gof_res
Plot distribution or QQ-plot of residuals from NONMEM/Simurg runsg_gof_res_dist
Plot time profiles of the fitted datasg_gof_tp
Perform local sensitivity analysis simulationssg_localsens_sim
Visualize Local Sensitivity Analysis Resultssg_localsens_vis
Build estimation model scenariossg_modbuild
Returns dataframe with summary statistics for model comparisonsg_modcomp
Build multistart scenarios with varying initial valuessg_multistart
Extract parameter summary (theta, eta, SE, RSE, CI, CV, shrinkage)sg_parsum
Perform simulations for prediction distribution plotssg_predist_sim
Perform simulations from an rxode2 modelsg_sim
Time-profile plotting with optional summary bandssg_sim_tp
Translate structural models between rxode2 and MLXTRAN syntaxsg_translator
Perform simulations for VPC plotsg_vpc_sim
Visual Predictive Check (VPC) Functionsg_vpc_vis
Perform generation of synthetic datasets for an empirical distributionsg_vpop_est
Warfarin PKPD datasetwarfarin