Dynamic Modeling and Parameter Estimation in ODE Models

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Documentation for package ‘dMod’ version 0.1

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%o% Concatenation of parameter transformations
+.obj Add two lists element by element
addObservable Add observables to ODEs
addReaction Add reaction to reaction table
as.obj Generate dummy list of class 'obj' from named numeric
blockdiagSymb Embed two matrices into one blockdiagonal matrix
combine Combine several data.frames from csv read-in
concatenation Concatenation of parameter transformations
constraintExp2 Compute a differentiable box prior
constraintL2 Soft L2 constraint on parameters
datapointL2 L2 objective function for validation data point
expand.grid.alt Alternative version of expand.grid
forcingsSymb Return some useful forcing functions as strings
funC0 Evaluation of algebraic expressions defined by characters
generateEquations Generate equations from data.frame(s)
generateModel Generate the model objects for use in Xs (models with sensitivities)
getCoefficients Get coefficients from a character
lbind Bind named list of data.frames into one data.frame
loadTemplate Load a template file in the editor
long2wide Translate long to wide format (inverse of wide2long.matrix)
P Parameter transformation
Pi Parameter transformation (implicit)
plotCombined Plot a list of model predictions and a list of data points in a combined plot
plotData Plot a list data points
plotPaths Profile likelihood: plot of the parameter paths.
plotPrediction Plot a list of model predictions
plotProfile Profile likelihood plot
print.eqnList Print function for eqnList
print0 Print without attributes
priorL2 L2 objective function for prior value
profile Profile-likelihood (PL) computation
progressBar Progress bar
res Compare data and model prediction by computing residuals
resolveRecurrence Place top elements into bottom elemens
subset.eqnList subset of an equation list
summation Add two lists element by element
symmetryDetection Search for symmetries in the loaded model
variableTransformation Do a variable transformation in the ODE
wide2long Translate wide output format (e.g. from ode) into long format
wide2long.data.frame Translate wide output format (e.g. from ode) into long format
wide2long.list Translate wide output format (e.g. from ode) into long format
wide2long.matrix Translate wide output format (e.g. from ode) into long format
wrss Compute the weighted residual sum of squares
Xf Model evaluation without sensitivities.
Xs Model evaluation.
Y Observation functions.