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.

Install the latest version of this package by entering the following in R:
install.packages("scaRabee")
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

Functions

bound.parameters Man page
compute.secondary Man page
convert.infusion Man page
create.intervals Man page
dde.lags Man page
dde.model Man page
dde.syst Man page
de.output Man page
derived.parms Man page
estimation.plot Man page
example1.data Man page
example1.initials Man page
example2.data Man page
example2.initials Man page
example3.data Man page
example3.initials Man page
example4.data Man page
example4.initials Man page
example6.data Man page
example6.initials Man page
example8.data Man page
example8.initials Man page
explicit.model Man page
finalize.grid.report Man page
finalize.report Man page
fitmle Man page
fitmle.cov Man page
get.cov.matrix Man page
get.events Man page
get.layout Man page
get.parms.data Man page
get.secondary Man page
init.cond Man page
initialize.report Man page
init.update Man page
input.scaling Man page
make.dosing Man page
ode.model Man page
ode.syst Man page
order.parms.list Man page
pder Man page
problem.eval Man page
residual.report Man page
scaRabee Man page
scarabee.analysis Man page
scarabee.check.model Man page
scarabee.check.reserved Man page
scarabee.clean Man page
scarabee.directory Man page
scarabee.gridsearch Man page
scarabee.new Man page
scaRabee-package Man page
scarabee.read.data Man page
scarabee.read.model Man page
scarabee.read.parms Man page
simulation.plot Man page
simulation.report Man page
weighting Man page

Files

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

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