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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

300

Version

1.1-4

License

GPL-3

Maintainer

Sebastien Bihorel

Last Published

February 4th, 2022

Functions in scaRabee (1.1-4)

convert.infusion

Process Infusion Information
dde.utils

Utility Functions for Delay Differential Equation Systems
bound.parameters

Forces parameter estimates between defined boundaries.
finalize.report

Finalize Estimation Report
finalize.grid.report

Finalize Direct Grid Search Report
examples.data

Datasets for scaRabee demo.
dde.model

Delay Differential Equations
estimation.plot

Create Summary Estimation Plots
compute.secondary

Computes secondary parameter values
ode.model

Ordinary Differential Equations
explicit.model

Explicit Equations
initialize.report

Initialize Report Files
residual.report

Creation of Prediction & Residual Report
ode.utils

Utility Functions for Ordinary Differential Equation Systems
problem.eval

Evaluation of structural and residual variability models
get.events

Create events from bolus dosing records.
scarabee.clean

Cleaning of the Run Directory
scarabee.check.model

Check scaRabee Models
get.cov.matrix

Computation of the Covariance Matrix
scarabee.check.reserved

Check for Reserved Variable Names
fitmle

Maximum Likelihood Estimator
get.secondary

Computation of Secondary Parameter Estimates
scarabee.analysis

Run a scaRabee Analysis
get.parms.data

Extract data from scaRabee parameter table
scarabee.read.parms

Read scaRabee Parameter File
get.layout

Layout for Lattice Functions
scaRabee-package

scaRabee toolkit
simulation.plot

Create Simulation Plots
scarabee.directory

Creation of the Run Directory
scarabee.new

Create a scaRabee Analysis Folder
scarabee.gridsearch

Direct Grid Search Utility
simulation.report

Simulations
weighting

Residual Variability
scarabee.read.data

Read scaRabee Data File
order.parms.list

Sort a scaRabee parameter table
fitmle.cov

Computation of the Covariance Matrix
pder

Compute Matrix of Partial Derivatives
scarabee.read.model

Read scaRabee Model File