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dMod (version 1.0.2)

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. The methods used in dMod were published in Kaschek et al, 2019, .

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Version

Install

install.packages('dMod')

Monthly Downloads

232

Version

1.0.2

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

January 27th, 2021

Functions in dMod (1.0.2)

An identity function which vanishes upon concatenation of fns

Parameter transformation

Observation functions.

Model prediction function from data.frame

Add reaction to reaction table

Generate a parameter transformation function

Model prediction function for ODE models without sensitivities.

Model prediction function for ODE models.

Parameter transformation (implicit)

Generate objective list from numeric vector

Generate a prediction function that returns times

Select attributes.

as.parvec.parframe

Select a parameter vector from a parameter frame.

confint.parframe

Profile uncertainty extraction

Embed two matrices into one blockdiagonal matrix

Combine several data.frames by rowbind

as.data.frame.eqnlist

Coerce equation list into a data frame

Soft L2 constraint on parameters

Compute a differentiable box prior

as.data.frame.datalist

Coerce to a Data Frame

Coerce to an equation vector

Extract the equations of an object

Coerce to eventlist

List, get and set controls for different functions

as.parframe.parlist

Coerce object to a parameter frame

Fit an error model

Construct fitlist from temporary files.

expand.grid.alt

Alternative version of expand.grid

Extract the parameters of an object

Generate a table of reactions (data.frame) from an equation list

conservedQuantities

Determine conserved quantites by finding the kernel of the stoichiometric matrix

Access the covariates in the data

Symbolic time derivative of equation vector given an equation list

Coordinate transformation for data frames

Generate list of fluxes from equation list

Compare two objects and return differences

Parameter transformation function

Load shared object for a dMod object

Objective frame

Generate objective list

Return some useful forcing functions as strings

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

Prediction frame

Print list of dMod objects in .GlobalEnv

Plot a list of model predictions

Profile likelihood: plot of the parameter paths.

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

Observation function

Generate eqnlist object

Compile one or more prdfn, obsfn or parfn objects

Determine loaded DLLs available in working directory

Prediction list

L2 objective function for validation data point

Generate a datalist object

Extract the observables of an object

Define parameter transformations by define(), branch() and insert()

Time-course data for the JAK-STAT cell signaling pathway

Generate equation vector object

Encode equation vector in format with sufficient spaces

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

Plot Fluxes given a list of flux Equations

L2 norm between data and model prediction

Find integer-null space of matrix A

Evaluation of algebraic expressions defined by characters

Extract the conditions of an object

plotProfile.parframe

Profile likelihood plot

plotPars.parframe

Plot parameter values for a fitlist

Gather statistics of a fitlist

Non-Linear Optimization

Pretty printing for a parameter vector

Plot residuals for a fitlist

Print object and its "default" attributes only.

unique.parframe

Extract those lines of a parameter frame with unique elements in the value column

Calculate analytical steady states.

Extract the derivatives of an object

getCoefficients

Get coefficients from a character

Reparameterization

Summary of an equation vector

symmetryDetection

Search for symmetries in the loaded model

Compute the weighted residual sum of squares

Write equation list into a csv file

Generate a parameter frame

Compare data and model prediction by computing residuals

Get modelname from single object (used internally)

dMod match function arguments

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

wide2long.matrix

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

Non-Linear Optimization, multi start

Open last plot in external pdf viewer

L2 objective function for prior value

Prediction function

Profile-likelihood (PL) computation

Multiplication of objective functions with scalars

Parameter vector

Add two lists element by element

Get and set modelname

Compute the negative log-likelihood

Plot a list data points

Reproducibly construct "random" parframes

plotValues.parframe

Plotting objective values of a collection of fits

Direct sum of datasets

Model Predictions

Plot a parameter list.

Direct sum of objective functions

Direct sum of functions

plotData.datalist

Plot a list data points

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

Print equation vector

Pretty printing parameter transformations

Print or pander equation list

Submatrix of a matrix returning ALWAYS a matrix

reduceReplicates

Reduce replicated measurements to mean and standard deviation

subset of an equation list

Standard plotting theme of dMod

scale_fill_dMod

Standard dMod color scheme

Concatenation of functions

scale_color_dMod

Standard dMod color palette

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

Transform matrix A into reduced row echelon form this function is written along the lines of the rref-matlab function.

Elide character vector

resolveRecurrence

Place top elements into bottom elemens

Pad string to desired width