Package: Pmetrics 3.0.9

Michael Neely

Pmetrics: Pmetrics for Population Modeling and Simulation

Pmetrics is short for pharmacometrics, the discipline of modeling drug kinetics and effects on biologic systems, including disease progression. Models can be used to simulate novel therapeutic dosing regimens and/or populations, informing trial design and dosing strategies. The package supports primarily non-parametric but also parametric pharmacometric modeling and simulation with functions to run and analyze the output from all three components of the Pmetrics software suite for population pharmacometric data analysis: 1) IT2B (Iterative Two-Stage Bayesian) for parametric models; 2) NPAG (Non-parametric Adaptive Grid) for non-paramametric models; 3) Simulator for semi-parametric Monte-Carlo simulations.

Authors:Michael Neely [aut, cre], JuliÃĄn OtÃĄlvaro [aut], Markus Hovd [aut], Walter Yamada [ctb], Alan Schumitzky [ctb], Rong Chen [ctb], Michael van Guilder [ctb], David Bayard [ctb], Robert Leary [ctb]

Pmetrics_3.0.9.tar.gz
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Pmetrics_3.0.9.tgz(r-4.6-x86_64)Pmetrics_3.0.9.tgz(r-4.6-arm64)Pmetrics_3.0.9.tgz(r-4.5-x86_64)Pmetrics_3.0.9.tgz(r-4.5-arm64)
Pmetrics_3.0.9.tar.gz(r-4.6-arm64)Pmetrics_3.0.9.tar.gz(r-4.6-x86_64)Pmetrics_3.0.9.tar.gz(r-4.5-arm64)Pmetrics_3.0.9.tar.gz(r-4.5-x86_64)
Pmetrics.pdf |Pmetrics.html✨
Pmetrics/json (API)
NEWS

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

Bug tracker:https://github.com/lapkb/pmetrics_rust/issues

Pkgdown/docs site:https://lapkb.github.io

Datasets:
  • NPex - Example NPAG Output with validation
  • badData - Pmetrics data file with errors
  • cdc_bmi - CDC Pediatric and Adolescent BMI Table
  • dataEx - Pmetrics data file
  • ger_bmi - CDC Pediatric and Adolescent BMI Table
  • growth - CDC Pediatric and Adolescent Growth Data Table
  • locales - Pmetrics locales
  • mic1 - Example MIC data
  • modEx - Pmetrics model object
  • simEx - Example simulator output

On CRAN:

Conda:

modelingpharmacokineticssimulationrustcargo

5.86 score 26 stars 36 scripts 106 exports 129 dependencies

Last updated from:8ff3a91dbc (on v3.0.9). Checks:11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING362
linux-devel-x86_64WARNING382
source / vignettesOK475
linux-release-arm64WARNING394
linux-release-x86_64WARNING380
macos-devel-arm64WARNING305
macos-devel-x86_64WARNING773
macos-release-arm64WARNING451
macos-release-x86_64WARNING471
windows-develWARNING475
windows-releaseWARNING480
windows-oldrelWARNING567
wasm-releaseFAIL243

Exports:%>%abab_lineadd_renaladd_shapesadd_smoothadditiveall_is_numericbuild_modelbuild_plotclear_buildcli_askcli_dfclick_plotcompile_modelcor2covcreate_pmetrics_projectdummy_compileexport_plotlyfitgetCovgetDefaultColorsgetFixedColNumgetPalettesgetPMoptionsinterpis_cargo_installedITloadITreportmake_NCAmake_validmakeAUCmakeErrorPolymakeNCAmakeNPDEmakePTAtargetmakeValidmodel_libmodel_parametersmodifyList2msdNM2PMNPloadNPreportNPrunopposite_colorplotlyggPM_batchPM_buildPM_comparePM_covPM_cyclePM_dataPM_finalPM_fitPM_helpPM_loadPM_manualPM_modelPM_opPM_optPM_parsePM_popPM_postPM_ptaPM_reportPM_resultPM_simPM_stepPM_treePM_tutorialPM_validPMbuildPMcheckPMcheckMatrixPMcomparePMdiagPMfixMatrixPMFortranConfigPMgetCRCLPMloadPMmatrixRelTimePMnewsPMpatchPMreadDefaultsPMreportPMsavePMtestPMtreePMwriteDefaultsPMwriteMatrixPMwrk2csvpos_defproportionalqgrowthrgba_to_rgbround2save_flextablesetPMoptionssetup_logssimulate_allsimulate_oness.PKsub_plottemporary_pathzBMI

Dependencies:askpassautocogsbackportsbase64encbitbit64broombslibcachemcallrcheckmateclicliprcommonmarkcpp11crayoncrosstalkcurldata.tabledigestdiptestDistributionUtilsdplyrDTevaluatefarverfastmapfideliusflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehexbinhighrhmshtmltoolshtmlwidgetshttpuvhttrigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmclustmemoisemimemomentsofficeropensslopenxlsxotelpanderpillarpkgconfigplotlypolyclipprettyunitsprocessxprogresspromisespspurrrR6raggrappdirsRColorBrewerRcppRcppArmadilloreadrremotesrlangrmarkdownrstudioapiS7sassscalesshinysodiumsourcetoolsstringistringrsyssystemfontstextshapingtibbletidygraphtidyrtidyselecttimechangetinytextrelliscopejstweenrtzdbutf8uuidvctrsviridisviridisLitevroomwebshotwhiskerwithrxfunxml2xtableyamlzip

Readme and manuals

Help Manual

Help pageTopics
Initial range for primary parameter valuesab
Add lines to plotly plotab_line
Estimate renal function using various equationsadd_renal
Add shapes to plotly plotadd_shapes
Add regression to plotly plotadd_smooth
Additive error modeladditive
Check if all values are numericall_is_numeric
Pmetrics data file with errorsbadData
Launch Model Builder appbuild_model
Launch Plot Builder appbuild_plot
CDC Pediatric and Adolescent BMI Tablecdc_bmi
Click on plotly plot to highlight tracesclick_plot
Compiles the text representation of a model into a binary file.compile_model
Convert correlation matrix to covariance matrixcor2cov
Pmetrics data filedataEx
Dummy function to cache compilation artifacts.dummy_compile
Export plotly plotexport_plotly
Fits the model at the given path to the data at the given path using the provided parameters.fit
CDC Pediatric and Adolescent BMI Tableger_bmi
Extract covariate informationgetCov
Get a list of default colorsgetDefaultColors
Number of fixed columnsgetFixedColNum
Get color palettegetPalettes
Get Pmetrics User OptionsgetPMoptions
CDC Pediatric and Adolescent Growth Data Tablegrowth
Model covariate declarationinterp
Checks if Cargo is installed on the system.is_cargo_installed
Pmetrics localeslocales
Non-compartmental analysismake_NCA
Calculation of AUCsmakeAUC
Assay error polynomial coefficientsmakeErrorPoly
Non-compartmental analysismakeNCA
Make a Percent Target Attainment (PTA) TargetmakePTAtarget
Example MIC datamic1
Model Librarymodel_lib
Retrieves the model parameters from the compiled model at the given path.model_parameters
Pmetrics model objectmodEx
Initial mean/SD for primary parameter valuesmsd
Compare discrete distributionsmtsknn.eq
Convert NONMEM to Pmetrics Data FilesNM2PM
Example NPAG Output with validationNPex
Find opposite color with max contrastopposite_color
Plot Pmetrics Covariate objectsplot.PM_cov
Plot Cycle Informationplot.PM_cycle
Plot PM_cycle_data objectsplot.PM_cycle_data
Plot PM_data Time-Output Dataplot.PM_data
Plot Pmetrics Final Cycle Parameter Value Distributionsplot.PM_final
Plot PM_final_data objectsplot.PM_final_data
Plot PM_model objectsplot.PM_model
Plot Pmetrics Observed vs. Predicted Objectsplot.PM_op
Plot PM_op_data objectsplot.PM_op_data
Plot Pmetrics Multiple-Model Optimal Sampling Objectsplot.PM_opt
Plot PM_pop Prediction Dataplot.PM_pop
Plot PM_post Prediction Dataplot.PM_post
Plot PM_pta Percent Target Attainment objectsplot.PM_pta
Plot Pmetrics Simulation Objectsplot.PM_sim
Plot Pmetrics Validation Objectsplot.PM_valid
Plot Pmetrics Validation Objectsplot.PMvalid
Convert a plotly object to ggplotplotlygg
Build PmetricsPM_build
Compare runsPM_compare
Contains covariate dataPM_cov
Pmetrics Run Cycle InformationPM_cycle
Defines the PM_data objectPM_data
Final Cycle Population ValuesPM_final
Get Help and Report IssuesPM_help
Load Pmetrics NPAG or IT2B outputPM_load
Open user and function manuals. *[Stable]*PM_manual
Defines the PM_model classPM_model
Observed vs. predicted dataPM_op
Optimal Sample TimesPM_opt
Population predictions at short intervalsPM_pop
Individual Bayesian posterior predictions at short intervalsPM_post
Generate a reportPM_report
Stepwise covariate-parameter regressionsPM_step
Create a new Pmetrics folder treePMtree PM_tree
Pmetrics tutorialPM_tutorial
Pmetrics validation objectPM_valid
Check Pmetrics Inputs for ErrorsPMcheck
Convert Absolute Dates and Times to Relative HoursPMmatrixRelTime
Download and install Pmetrics patchesPMpatch
Read a Pmetrics data filePMreadMatrix
Test PmetricsPMtest
Write a Pmetrics .csv Matrix FilePMwriteMatrix
Convert Old .wrk Files to .csv Matrix FilePMwrk2csv
Print method for PM_compare objectsprint.PM_compare
Print Data Errorsprint.PMerr
Print NPCprint.PMnpc
Print Summary of Cycle Statisticsprint.summary.PM_cycle
Print Summary of Pmetrics Dataprint.summary.PM_data
Print Summary of Parameter Values and Credibility Intervalsprint.summary.PM_final
Print Summary of Observations and Predictionsprint.summary.PM_op
Print Summary of Simulationsprint.summary.PM_sim
Proportional error modelproportional
Extract CDC pediatric growth chartsqgrowth
Convert RGBA to RGBrgba_to_rgb
Set Pmetrics User OptionssetPMoptions
Example simulator outputsimEx
Simulates all subjects in the data set using the model at the given path.simulate_all
Simulates the first subject in the data set using the model at the given path.simulate_one
Sample size calculations for Phase 1 PK study designss.PK
Display multiple plotly plotssub_plot
Summarize Covariates and Bayesian Posterior Parameter Valuessummary.PM_cov
Summarize Final Cycle Statisticssummary.PM_cycle
Summarize PM_cycle_data objectssummary.PM_cycle_data
Summarize PM_data objectssummary.PM_data
Summary Statistics for Final Cyclesummary.PM_final
Summarize PM_final_data objectssummary.PM_final_data
Summarize Observations and Predictionssummary.PM_op
Summarize PM_op_data objectssummary.PM_op_data
Summarize Observations and Predictionssummary.PM_pop
Summarize Observations and Predictionssummary.PM_post
Summarize Percent Target Attainmentsummary.PM_pta
Summarize Pmetrics Simulation Objectssummary.PM_sim
Retrieves the temporary path used for building models.temporary_path
Extract CDC pediatric BMI z-scoreszBMI