Package: nmw 0.3.1

Kyun-Seop Bae

nmw: Understanding Nonlinear Mixed Effects Modeling for Population Pharmacokinetics

This shows how 'NONMEM' (Beal SL, Sheiner LB, Boeckmann AJ, Bauer RJ. NONMEM 7.5 Users Guides. Icon plc, 2020) software works. 'NONMEM' classical estimation methods such as 'First Order (FO) approximation', 'First Order Conditional Estimation (FOCE)', and 'Laplacian approximation' are explained. Functions are also provided for post-run processing of NONMEM output files, generating PDF diagnostic reports including objective function value analysis, parameter estimates, prediction and residual diagnostics, empirical Bayes estimate (EBE) analysis, input data summary, and individual pharmacokinetic parameter distributions. Helper utilities for building NONMEM-ready datasets from SDTM-style source tables are also included.

Authors:Kyun-Seop Bae [aut, cre]

nmw_0.3.1.tar.gz
nmw_0.3.1.tar.gz(r-4.7-any)nmw_0.3.1.tar.gz(r-4.6-any)
nmw_0.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nmw/json (API)

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

On CRAN:

Conda:

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

1.60 score 1 stars 9 scripts 459 downloads 77 exports 2 dependencies

Last updated from:0321043939. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK116
source / vignettesOK249
linux-release-x86_64OK121
wasm-releaseOK101

Exports:add_crcl_cgAddCoxAddDoNoTaLDAddPageBtwTagMatBtwTagValsbuild_dose_recordsbuild_nm_datasetbuild_obs_recordsCalcSmatClosePDFcode_racecode_sexCombDmExPcCovStepcrcl_cgdat2_time_to_posixDECNDesclVarDxPlotPostEBEpairEstStepExpandDoseHistGetAICcGetCountEpsGetCountEtaGetCountObsGetCountParaGetEstMethodGetOFVInitSteplocf_valueLogDVLogDV2ltv2matmat2ltvmat2utvmerge_cov_locfMinSuccessmlr2Mxnm_to_molarNMIDStatNMVarStatnmw_report_ebenmw_report_indipknmw_report_inputnmw_report_ofvnmw_report_outputnmw_report_paramnmw_report_prednmw_report_residnmw_runObjObjEtaOiOi0Oi1OiS0OiS1Outlineparse_dtcParseOutPostHocEtaPrepPDFPrinMTxtPrinTxtRemoveNAResTestrun.test.nmScaleVarSESuccessSqrtInvCovSumOutTabStepTrimOututv2mat

Dependencies:MASSnumDeriv

Readme and manuals

Help Manual

Help pageTopics
Understanding Nonlinear Mixed Effects Modeling for Population Pharmacokineticsnmw-package nmw
Add CRCL Column via Cockcroft-Gaultadd_crcl_cg
Add a Covariate Column to an Existing NONMEM datasetAddCox
Add Dose Number, Time of Latest Dose, and Time after Latest DoseAddDoNoTaLD
Add a New Page to PDFAddPage
Extract Matrix from NONMEM XML OutputBtwTagMat
Extract Vector of Values Between XML TagsBtwTagVals
Build NONMEM Dose Recordsbuild_dose_records
Build a NONMEM-Format Dataset from DM/EX/PCbuild_nm_dataset
Build NONMEM Observation Recordsbuild_obs_records
Close PDF OutputClosePDF
Code RACE as Integercode_race
Code SEX as Integercode_sex
Combine the demographics(DM), dosing(EX), and DV(PC) tables into a new NONMEM datasetCombDmExPc
Covariance StepCovStep
Cockcroft-Gault Creatinine Clearancecrcl_cg
Combine Date and Time Strings into POSIXctdat2_time_to_posix
Diagnostic Plot for Post-ProcessingDxPlotPost
EBE Pair PlotEBEpair
Estimation StepEstStep
Expand Dose History with ADDL/II RecordsExpandDoseHist
Get Corrected AIC (AICc)GetAICc
Get Count of EpsilonsGetCountEps
Get Count of EtasGetCountEta
Get Count of ObservationsGetCountObs
Get Count of ParametersGetCountPara
Get Estimation MethodGetEstMethod
Get Objective Function ValueGetOFV
Initialization StepInitStep
LOCF / LOCB Lookuplocf_value
Check if Model Uses Log-Transformed DV (from Control File)LogDV
Check if Model Uses Log-Transformed DV (from FSUBS)LogDV2
Merge Time-Varying Covariates by LOCFmerge_cov_locf
Check Minimization SuccessMinSuccess
Multiple Linear Regression with Influence Diagnosticsmlr2
Convert NM Dataset from Mass to Molar Unitsnm_to_molar
NONMEM Individual (ID) StatisticsNMIDStat
NONMEM Variable StatisticsNMVarStat
Generate EBE Diagnostics Report (S5-EBE.PDF)nmw_report_ebe
Generate Individual PK Parameter Report (SC-IndiPK.PDF)nmw_report_indipk
Generate Input Data Summary Report (SA-Input.PDF)nmw_report_input
Generate OFV Diagnostic Report (S1-OFV.PDF)nmw_report_ofv
Generate NONMEM Output Report (SB-Output.PDF)nmw_report_output
Generate Parameter Estimates Report (S2-Parameters.PDF)nmw_report_param
Generate Prediction Diagnostics Report (S3-Predictions.PDF)nmw_report_pred
Generate Residual Diagnostics Report (S4-Residuals.PDF)nmw_report_resid
Run All NONMEM Post-Processing Reportsnmw_run
Draw Model Development Flow DiagramOutline
Parse SDTM-Style DTC Strings into POSIXctparse_dtc
Parse Value After Tag from NONMEM OutputParseOut
Prepare PDF OutputPrepPDF
Print Multiple Lines of TextPrinMTxt
Print Text at PositionPrinTxt
Remove Rows with NA ValuesRemoveNA
Residual Count Test Using Binomial DistributionResTest
Runs Test for NONMEM Residualsrun.test.nm
Check Standard Error SuccessSESuccess
Summarize Multiple NONMEM RunsSumOut
Table StepTabStep
Trimming and beautifying NONMEM original OUTPUT fileTrimOut