Package: scaRabee 1.1-4

Sebastien Bihorel

scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

A port of the Scarabee toolkit originally written as a Matlab-based application. scaRabee provides a framework for simulation and optimization of pharmacokinetic-pharmacodynamic models at the individual and population level. It is built on top of the neldermead package, which provides the direct search algorithm proposed by Nelder and Mead for model optimization.

Authors:Sebastien Bihorel [aut, cre]

scaRabee_1.1-4.tar.gz
scaRabee_1.1-4.tar.gz(r-4.5-noble)scaRabee_1.1-4.tar.gz(r-4.4-noble)
scaRabee_1.1-4.tgz(r-4.4-emscripten)scaRabee_1.1-4.tgz(r-4.3-emscripten)
scaRabee.pdf |scaRabee.html
scaRabee/json (API)

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

Peer review:

Datasets:

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

2.70 score 3 scripts 208 downloads 44 exports 6 dependencies

Last updated 3 years agofrom:c329982527. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-linuxNOTEDec 17 2024

Exports:bound.parameterscompute.secondaryconvert.infusioncreate.intervalsdde.lagsdde.modeldde.systde.outputderived.parmsestimation.plotexplicit.modelfinalize.grid.reportfinalize.reportfitmlefitmle.covget.cov.matrixget.eventsget.layoutget.parms.dataget.secondaryinit.condinit.updateinitialize.reportinput.scalingmake.dosingode.modelode.systorder.parms.listpderproblem.evalresidual.reportscarabee.analysisscarabee.check.modelscarabee.check.reservedscarabee.cleanscarabee.directoryscarabee.gridsearchscarabee.newscarabee.read.datascarabee.read.modelscarabee.read.parmssimulation.plotsimulation.reportweighting

Dependencies:deSolvelatticeMatrixneldermeadoptimbaseoptimsimplex

scaRabee: An R-based Tool for Model Simulation and Optimization in Pharmacometrics

Rendered frommanual.Rmdusingknitr::rmarkdownon Dec 17 2024.

Last update: 2022-02-04
Started: 2022-02-04

Readme and manuals

Help Manual

Help pageTopics
scaRabee toolkitscaRabee-package scaRabee
Forces parameter estimates between defined boundaries.bound.parameters
Computes secondary parameter valuescompute.secondary
Process Infusion Informationconvert.infusion
Delay Differential Equationsdde.model
Utility Functions for Delay Differential Equation Systemsdde.lags dde.syst
Create Summary Estimation Plotsestimation.plot
Datasets for scaRabee demo.example1.data example1.initials example2.data example2.initials example3.data example3.initials example4.data example4.initials example6.data example6.initials example8.data example8.initials
Explicit Equationsexplicit.model
Finalize Direct Grid Search Reportfinalize.grid.report
Finalize Estimation Reportfinalize.report
Maximum Likelihood Estimatorfitmle
Computation of the Covariance Matrixfitmle.cov
Computation of the Covariance Matrixget.cov.matrix
Create events from bolus dosing records.get.events
Layout for Lattice Functionsget.layout
Extract data from scaRabee parameter tableget.parms.data
Computation of Secondary Parameter Estimatesget.secondary
Initialize Report Filesinitialize.report
Ordinary Differential Equationsode.model
Utility Functions for Ordinary Differential Equation Systemscreate.intervals de.output derived.parms init.cond init.update input.scaling make.dosing ode.syst
Sort a scaRabee parameter tableorder.parms.list
Compute Matrix of Partial Derivativespder
Evaluation of structural and residual variability modelsproblem.eval
Creation of Prediction & Residual Reportresidual.report
Run a scaRabee Analysisscarabee.analysis
Check scaRabee Modelsscarabee.check.model
Check for Reserved Variable Namesscarabee.check.reserved
Cleaning of the Run Directoryscarabee.clean
Creation of the Run Directoryscarabee.directory
Direct Grid Search Utilityscarabee.gridsearch
Create a scaRabee Analysis Folderscarabee.new
Read scaRabee Data Filescarabee.read.data
Read scaRabee Model Filescarabee.read.model
Read scaRabee Parameter Filescarabee.read.parms
Create Simulation Plotssimulation.plot
Simulationssimulation.report
Residual Variabilityweighting