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scaRabee: Optimization toolkit for pharmacometric 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 pharmacometric 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.

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Version

Install

install.packages('scaRabee')

Monthly Downloads

330

Version

1.1-5

License

GPL-3

Maintainer

Sebastien Bihorel

Last Published

January 25th, 2026

Functions in scaRabee (1.1-5)

fitmle

Maximum Likelihood Estimator
ode.utils

Utility Functions for Ordinary Differential Equation Systems
get.parms.data

Extract data from scaRabee parameter table
get.cov.matrix

Computation of the Covariance Matrix
initialize.report

Initialize Report Files
get.secondary

Computation of Secondary Parameter Estimates
fitmle.cov

Computation of the Covariance Matrix
ode.model

Ordinary Differential Equations
get.layout

Layout for Lattice Functions
get.events

Create events from bolus dosing records.
order.parms.list

Sort a scaRabee parameter table
scaRabee-package

scaRabee toolkit
scarabee.check.model

Check scaRabee Models
scarabee.analysis

Run a scaRabee Analysis
scarabee.clean

Cleaning of the Run Directory
scarabee.check.reserved

Check for Reserved Variable Names
problem.eval

Evaluation of structural and residual variability models
pder

Compute Matrix of Partial Derivatives
residual.report

Creation of Prediction & Residual Report
scarabee.directory

Creation of the Run Directory
scarabee.read.data

Read scaRabee Data File
scarabee.read.model

Read scaRabee Model File
weighting

Residual Variability
simulation.report

Simulations
scarabee.new

Create a scaRabee Analysis Folder
scarabee.gridsearch

Direct Grid Search Utility
simulation.plot

Create Simulation Plots
scarabee.read.parms

Read scaRabee Parameter File
bound.parameters

Forces parameter estimates between defined boundaries.
dde.utils

Utility Functions for Delay Differential Equation Systems
compute.secondary

Computes secondary parameter values
convert.infusion

Process Infusion Information
finalize.report

Finalize Estimation Report
explicit.model

Explicit Equations
dde.model

Delay Differential Equations
finalize.grid.report

Finalize Direct Grid Search Report
examples.data

Datasets for scaRabee demo.
estimation.plot

Create Summary Estimation Plots