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dMod (version 0.3.2)

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.

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Version

Install

install.packages('dMod')

Monthly Downloads

232

Version

0.3.2

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

September 30th, 2016

Functions in dMod (0.3.2)

Select attributes.

as.data.frame.eqnlist

Coerce equation list into a data frame

as.parvec.parframe

Select a parameter vector from a parameter frame.

Compare two objects and return differences

Add reaction to reaction table

Embed two matrices into one blockdiagonal matrix

Generate objective list from numeric vector

Coerce object to a parameter frame

Coerce to an equation vector

Combine several data.frames by rowbind

Generate eqnlist object

Symbolic time derivative of equation vector given an equation list

L2 objective function for validation data point

conservedQuantities

Determine conserved quantites by finding the kernel of the stoichiometric matrix

detectFreeCores

Detect number of free cores (on UNIX)

Soft L2 constraint on parameters

List, get and set controls for different functions

Coordinate transformation for data frames

Open a unit test template.

Generate a datalist object

getCoefficients

Get coefficients from a character

expand.grid.alt

Alternative version of expand.grid

Evaluation of algebraic expressions defined by characters

Encode equation vector in format with sufficient spaces

Extract an example from a unit test file.

Generate equation vector object

Fit an error model

extractExamples

Extract example from unit tests.

Return some useful forcing functions as strings

Extract the conditions of an object

Open last plot in external pdf viewer

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

Construct fitlist from temporary files.

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

Print list of dMod objects in .GlobalEnv

Extract the derivatives of an object

Generate list of fluxes from equation list

Load a template file in the editor

Extract the parameters of an object

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

L2 norm between data and model prediction

Objective frame

Non-Linear Optimization, multi start

Find integer-null space of matrix A

Compute the negative log-likelihood

Generate a parameter transformation function

Generate objective list

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

Observation function

Generate sample for multi-start fit

Plot an array of model predictions for a list of parameters

Parameter transformation

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

Parameter transformation (implicit)

Generate a paramter frame

Parameter transformation function

Plot a list data points

Plot a parameter list.

Parameter vector

Plot parameter values for a fitlist

Direct sum of objective functions

Direct sum of functions

Profile likelihood: plot of the parameter paths.

Plot Fluxes given a list of flux Equations

Plotting objective values of a collection of fits

Plot a list data points

Direct sum of datasets

Plot a list of model predictions

Profile likelihood plot

Print or pander equation list

resolveRecurrence

Place top elements into bottom elemens

Compare data and model prediction by computing residuals

Print equation vector

Elide character vector

Calculate analytical steady states

wide2long.matrix

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

Write equation list into a csv file

python.version.sys

Check which Python versions are installed on the system

quasiSteadyStates

Reduce the ODE system by means of a quasi steady-state assumption

Pad string to desired width

Submatrix of a matrix returning ALWAYS a matrix

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

Prediction list

Prediction frame

Add two lists element by element

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

Prediction function

reduceReplicates

Reduce replicated measurements to mean and standard deviation

Named repititions

symmetryDetection

Search for symmetries in the loaded model

Model prediction function for ODE models without sensitivities.

Standard plotting theme of dMod

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

Remote install dMod to a ssh-reachable host

Pretty printing parameter transformations

Model prediction function for ODE models.

Pretty printing for a parameter vector

Profile-likelihood (PL) computation

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

Compute the weighted residual sum of squares

scale_color_dMod

Standard dMod color palette

Concatenation of functions

wide2long.data.frame

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

L2 objective function for prior value

Print object and its "default" attributes only.

Model prediction function from data.frame

python.version.rpython

Get the Python version to which rPython is linked

python.version.request

Check if rPython comes with the correct Python version

scale_fill_dMod

Standard dMod color scheme

Summary of an equation vector

subset of an equation list

Gather statistics of a fitlist

Generate a prediction function that returns times

Observation functions.