scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based application. It 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.

AuthorSebastien Bihorel
Date of publication2014-08-22 08:26:44
MaintainerSebastien Bihorel <sb.pmlab@gmail.com>
LicenseGPL-3
Version1.1-3

View on CRAN

Man pages

bound.parameters: Forces parameter estimates between defined boundaries.

compute.secondary: Computes secondary parameter values

convert.infusion: Process Infusion Information

dde.model: Delay Differential Equations

dde.utils: Utility Functions for Delay Differential Equation Systems

estimation.plot: Create Summary Estimation Plots

examples.data: Datasets for scaRabee demo.

explicit.model: Explicit Equations

finalize.grid.report: Finalize Direct Grid Search Report

finalize.report: Finalize Estimation Report

fitmle: Maximum Likelihood Estimator

fitmle.cov: Computation of the Covariance Matrix

get.cov.matrix: Computation of the Covariance Matrix

get.events: Create events from bolus dosing records.

get.layout: Layout for Lattice Functions

get.parms.data: Extract data from scaRabee parameter table

get.secondary: Computation of Secondary Parameter Estimates

initialize.report: Initialize Report Files

ode.model: Ordinary Differential Equations

ode.utils: Utility Functions for Ordinary Differential Equation Systems

order.parms.list: Sort a scaRabee parameter table

pder: Compute Matrix of Partial Derivatives

problem.eval: Evaluation of structural and residual variability models

residual.report: Creation of Prediction & Residual Report

scarabee.analysis: Run a scaRabee Analysis

scarabee.check.model: Check scaRabee Models

scarabee.check.reserved: Check for Reserved Variable Names

scarabee.clean: Cleaning of the Run Directory

scarabee.directory: Creation of the Run Directory

scarabee.gridsearch: Direct Grid Search Utility

scarabee.new: Create a scaRabee Analysis Folder

scaRabee-package: scaRabee toolkit

scarabee.read.data: Read scaRabee Data File

scarabee.read.model: Read scaRabee Model File

scarabee.read.parms: Read scaRabee Parameter File

simulation.plot: Create Simulation Plots

simulation.report: Simulations

weighting: Residual Variability

Files in this package

scaRabee
scaRabee/inst
scaRabee/inst/doc
scaRabee/inst/doc/scaRabee.R
scaRabee/inst/doc/scaRabee.pdf
scaRabee/inst/doc/scaRabee.Rnw
scaRabee/NAMESPACE
scaRabee/demo
scaRabee/demo/example5.R
scaRabee/demo/example4.R
scaRabee/demo/example3.R
scaRabee/demo/example8.R
scaRabee/demo/example1.R
scaRabee/demo/00Index
scaRabee/demo/example7.R
scaRabee/demo/example2.R
scaRabee/demo/example6.R
scaRabee/data
scaRabee/data/example8.data.rda
scaRabee/data/example3.initials.rda
scaRabee/data/example2.initials.rda
scaRabee/data/example2.data.rda
scaRabee/data/example8.initials.rda
scaRabee/data/example1.initials.rda
scaRabee/data/example4.data.rda
scaRabee/data/example1.data.rda
scaRabee/data/example6.data.rda
scaRabee/data/example6.initials.rda
scaRabee/data/example4.initials.rda
scaRabee/data/example3.data.rda
scaRabee/Changelog
scaRabee/R
scaRabee/R/derived.parms.R scaRabee/R/scarabee.analysis.R scaRabee/R/get.layout.R scaRabee/R/init.update.R scaRabee/R/ode.model.R scaRabee/R/bound.parameters.R scaRabee/R/input.scaling.R scaRabee/R/order.parms.list.R scaRabee/R/compute.secondary.R scaRabee/R/create.intervals.R scaRabee/R/weighting.R scaRabee/R/fitmle.cov.R scaRabee/R/convert.infusion.R scaRabee/R/scarabee.read.model.R scaRabee/R/scarabee.check.model.R scaRabee/R/dde.model.R scaRabee/R/dde.lags.R scaRabee/R/estimation.plot.R scaRabee/R/ode.syst.R scaRabee/R/scarabee.read.data.R scaRabee/R/make.dosing.R scaRabee/R/fitmle.R scaRabee/R/scarabee.new.R scaRabee/R/initialize.report.R scaRabee/R/get.parms.data.R scaRabee/R/pder.R scaRabee/R/get.secondary.R scaRabee/R/problem.eval.R scaRabee/R/get.events.R scaRabee/R/explicit.model.R scaRabee/R/scarabee.gridsearch.R scaRabee/R/scarabee.read.parms.R scaRabee/R/init.cond.R scaRabee/R/dde.syst.R scaRabee/R/get.cov.matrix.R scaRabee/R/finalize.report.R scaRabee/R/scarabee.directory.R scaRabee/R/scarabee.check.reserved.R scaRabee/R/simulation.plot.R scaRabee/R/de.output.R scaRabee/R/finalize.grid.report.R scaRabee/R/simulation.report.R scaRabee/R/scarabee.clean.R scaRabee/R/residual.report.R
scaRabee/vignettes
scaRabee/vignettes/ode.utils.tex
scaRabee/vignettes/convert.infusion.tex
scaRabee/vignettes/Rd2latex.sh
scaRabee/vignettes/scarabee.read.model.tex
scaRabee/vignettes/dde.model.tex
scaRabee/vignettes/simulation.plot.tex
scaRabee/vignettes/simulation.report.tex
scaRabee/vignettes/estimation.plot.tex
scaRabee/vignettes/pder.tex
scaRabee/vignettes/leuko.pdf
scaRabee/vignettes/get.secondary.tex
scaRabee/vignettes/explicit.model.tex
scaRabee/vignettes/bound.parameters.tex
scaRabee/vignettes/problem.eval.tex
scaRabee/vignettes/order.parms.list.tex
scaRabee/vignettes/get.parms.data.tex
scaRabee/vignettes/finalize.grid.report.tex
scaRabee/vignettes/dde.utils.tex
scaRabee/vignettes/scaRabee.Rnw
scaRabee/vignettes/compute.secondary.tex
scaRabee/vignettes/scarabee.check.model.tex
scaRabee/vignettes/residual.report.tex
scaRabee/vignettes/finalize.report.tex
scaRabee/vignettes/examples.data.tex
scaRabee/vignettes/scarabee_R.pdf
scaRabee/vignettes/fitmle.tex
scaRabee/vignettes/ode.model.tex
scaRabee/vignettes/deinputs.png
scaRabee/vignettes/scarabee.clean.tex
scaRabee/vignettes/precursor.pdf
scaRabee/vignettes/scarabee.read.data.tex
scaRabee/vignettes/get.layout.tex
scaRabee/vignettes/get.events.tex
scaRabee/vignettes/scarabee.analysis.tex
scaRabee/vignettes/tmdd.pdf
scaRabee/vignettes/get.cov.matrix.tex
scaRabee/vignettes/scarabee.gridsearch.tex
scaRabee/vignettes/scaRabee_network_2.pdf
scaRabee/vignettes/initialize.report.tex
scaRabee/vignettes/scaRabee_network_1.pdf
scaRabee/vignettes/scaRabee.bib
scaRabee/vignettes/scaRabee-package.tex
scaRabee/vignettes/scarabee.check.reserved.tex
scaRabee/vignettes/scarabee.new.tex
scaRabee/vignettes/fitmle.cov.tex
scaRabee/vignettes/scarabee.directory.tex
scaRabee/vignettes/weighting.tex
scaRabee/vignettes/scarabee.read.parms.tex
scaRabee/MD5
scaRabee/build
scaRabee/build/vignette.rds
scaRabee/DESCRIPTION
scaRabee/man
scaRabee/man/scarabee.analysis.Rd scaRabee/man/scarabee.gridsearch.Rd scaRabee/man/convert.infusion.Rd scaRabee/man/get.cov.matrix.Rd scaRabee/man/residual.report.Rd scaRabee/man/fitmle.cov.Rd scaRabee/man/bound.parameters.Rd scaRabee/man/order.parms.list.Rd scaRabee/man/explicit.model.Rd scaRabee/man/get.layout.Rd scaRabee/man/scarabee.check.model.Rd scaRabee/man/ode.utils.Rd scaRabee/man/scarabee.clean.Rd scaRabee/man/finalize.grid.report.Rd scaRabee/man/scarabee.directory.Rd scaRabee/man/estimation.plot.Rd scaRabee/man/dde.model.Rd scaRabee/man/examples.data.Rd scaRabee/man/finalize.report.Rd scaRabee/man/initialize.report.Rd scaRabee/man/simulation.plot.Rd scaRabee/man/get.secondary.Rd scaRabee/man/scarabee.read.data.Rd scaRabee/man/scaRabee-package.Rd scaRabee/man/weighting.Rd scaRabee/man/scarabee.check.reserved.Rd scaRabee/man/dde.utils.Rd scaRabee/man/scarabee.read.model.Rd scaRabee/man/fitmle.Rd scaRabee/man/pder.Rd scaRabee/man/compute.secondary.Rd scaRabee/man/scarabee.new.Rd scaRabee/man/problem.eval.Rd scaRabee/man/scarabee.read.parms.Rd scaRabee/man/get.events.Rd scaRabee/man/simulation.report.Rd scaRabee/man/get.parms.data.Rd scaRabee/man/ode.model.Rd

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