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dMod (version 0.3.1)

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

232

Version

0.3.1

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

May 18th, 2016

Functions in dMod (0.3.1)

Symbolic time derivative of equation vector given an equation list

Extract the derivatives of an object

Evaluation of algebraic expressions defined by characters

Fit an error model

Model prediction function for ODE models.

Generate a parameter transformation function

Select attributes.

Open a unit test template.

Parameter vector

Parameter transformation

Plot a parameter list.

L2 objective function for validation data point

Print list of dMod objects in .GlobalEnv

as.data.frame.eqnlist

Coerce equation list into a data frame

Non-Linear Optimization, multi start

Extract an example from a unit test file.

Encode equation vector in format with sufficient spaces

Parameter transformation function

Plot an array of model predictions for a list of parameters

Pretty printing parameter transformations

Direct sum of functions

Soft L2 constraint on parameters

conservedQuantities

Determine conserved quantites by finding the kernel of the stoichiometric matrix

Model prediction function from data.frame

Return some useful forcing functions as strings

Prediction function

Load a template file in the editor

extractExamples

Extract example from unit tests.

Observation function

Combine several data.frames by rowbind

Construct fitlist from temporary files.

Generate objective list

Coerce object to a parameter frame

Parameter transformation (implicit)

python.version.request

Check if rPython comes with the correct Python version

python.version.rpython

Get the Python version to which rPython is linked

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

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

Elide character vector

Coerce to an equation vector

L2 norm between data and model prediction

resolveRecurrence

Place top elements into bottom elemens

Prediction frame

Compare data and model prediction by computing residuals

Extract the conditions of an object

Generate sample for multi-start fit

Plot a list data points

Generate a datalist object

Plot a list of model predictions

Observation functions.

Generate objective list from numeric vector

subset of an equation list

Extract the parameters of an object

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

Profile-likelihood (PL) computation

Generate equation vector object

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

Compare two objects and return differences

as.parvec.parframe

Select a parameter vector from a parameter frame.

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

Plot a list data points

expand.grid.alt

Alternative version of expand.grid

wide2long.matrix

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

Named repititions

Write equation list into a csv file

Run an R expression in the background (only on UNIX)

Compute the negative log-likelihood

Plot Fluxes given a list of flux Equations

wide2long.data.frame

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

Objective frame

Standard plotting theme of dMod

Print equation vector

getCoefficients

Get coefficients from a character

python.version.sys

Check which Python versions are installed on the system

Gather statistics of a fitlist

Generate eqnlist object

Generate list of fluxes from equation list

Open last plot in external pdf viewer

Coordinate transformation for data frames

detectFreeCores

Detect number of free cores (on UNIX)

Concatenation of functions

Pretty printing for a parameter vector

symmetryDetection

Search for symmetries in the loaded model

L2 objective function for prior value

Generate a prediction function that returns times

Direct sum of objective functions

Profile likelihood: plot of the parameter paths.

Add reaction to reaction table

Calculate analytical steady states

List, get and set controls for different functions

scale_color_dMod

Standard dMod color palette

Embed two matrices into one blockdiagonal matrix

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

Print object and its "default" attributes only.

Print or pander equation list

scale_fill_dMod

Standard dMod color scheme

Generate a paramter frame

Add two lists element by element

reduceReplicates

Reduce replicated measurements to mean and standard deviation

Plot parameter values for a fitlist

Plotting objective values of a collection of fits

Profile likelihood plot

Summary of an equation vector

Model prediction function for ODE models without sensitivities.

Direct sum of datasets

Pad string to desired width

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

Submatrix of a matrix returning ALWAYS a matrix

Compute the weighted residual sum of squares

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

Find integer-null space of matrix A

Prediction list