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dMod (version 0.1)

Dynamic Modeling and Parameter Estimation in ODE Models

Description

The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.

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Version

Install

install.packages('dMod')

Monthly Downloads

192

Version

0.1

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

June 11th, 2015

Functions in dMod (0.1)

as.obj

Generate dummy list of class obj from named numeric
lbind

Bind named list of data.frames into one data.frame
plotProfile

Profile likelihood plot
wide2long.data.frame

Translate wide output format (e.g. from ode) into long format
Xs

Model evaluation.
Y

Observation functions.
datapointL2

L2 objective function for validation data point
plotPaths

Profile likelihood: plot of the parameter paths.
res

Compare data and model prediction by computing residuals
plotData

Plot a list data points
variableTransformation

Do a variable transformation in the ODE
blockdiagSymb

Embed two matrices into one blockdiagonal matrix
Xf

Model evaluation without sensitivities.
profile

Profile-likelihood (PL) computation
Pi

Parameter transformation (implicit)
print0

Print without attributes
expand.grid.alt

Alternative version of expand.grid
resolveRecurrence

Place top elements into bottom elemens
constraintL2

Soft L2 constraint on parameters
P

Parameter transformation
plotCombined

Plot a list of model predictions and a list of data points in a combined plot
priorL2

L2 objective function for prior value
wrss

Compute the weighted residual sum of squares
wide2long.matrix

Translate wide output format (e.g. from ode) into long format
print.eqnList

Print function for eqnList
wide2long.list

Translate wide output format (e.g. from ode) into long format
loadTemplate

Load a template file in the editor
funC0

Evaluation of algebraic expressions defined by characters
getCoefficients

Get coefficients from a character
addReaction

Add reaction to reaction table
subset.eqnList

subset of an equation list
constraintExp2

Compute a differentiable box prior
progressBar

Progress bar
symmetryDetection

Search for symmetries in the loaded model
plotPrediction

Plot a list of model predictions
+.obj

Add two lists element by element
%o%

Concatenation of parameter transformations
generateEquations

Generate equations from data.frame(s)
forcingsSymb

Return some useful forcing functions as strings
generateModel

Generate the model objects for use in Xs (models with sensitivities)
wide2long

Translate wide output format (e.g. from ode) into long format
addObservable

Add observables to ODEs
combine

Combine several data.frames from csv read-in
long2wide

Translate long to wide format (inverse of wide2long.matrix)