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dMod (version 0.4)

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

0.4

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

September 8th, 2017

Functions in dMod (0.4)

Parameter transformation (implicit)

Model prediction function from data.frame

Add reaction to reaction table

as.data.frame.datalist

Coerce to a Data Frame

Model prediction function for ODE models without sensitivities.

Model prediction function for ODE models.

Generate a parameter transformation function

Parameter transformation

Generate a prediction function that returns times

Observation functions.

Compare two objects and return differences

Compile one or more prdfn, obsfn or parfn objects

List, get and set controls for different functions

Coordinate transformation for data frames

Generate objective list from numeric vector

Coerce object to a parameter frame

Generate a datalist object

L2 objective function for validation data point

Evaluation of algebraic expressions defined by characters

as.data.frame.eqnlist

Coerce equation list into a data frame

Coerce to an equation vector

confint.parframe

Profile uncertainty extraction

conservedQuantities

Determine conserved quantites by finding the kernel of the stoichiometric matrix

Embed two matrices into one blockdiagonal matrix

Combine several data.frames by rowbind

Compute a differentiable box prior

expand.grid.alt

Alternative version of expand.grid

Fit an error model

Open last plot in external pdf viewer

Multiplication of objective functions with scalars

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

Print list of dMod objects in .GlobalEnv

Plot a parameter list.

getCoefficients

Get coefficients from a character

Generate list of fluxes from equation list

Determine loaded DLLs available in working directory

Get modelname from single object (used internally)

Get and set modelname

Soft L2 constraint on parameters

Return some useful forcing functions as strings

Construct fitlist from temporary files.

Load shared object for a dMod object

as.parvec.parframe

Select a parameter vector from a parameter frame.

Select attributes.

detectFreeCores

Detect number of free cores (on UNIX)

Symbolic time derivative of equation vector given an equation list

Encode equation vector in format with sufficient spaces

Extract the conditions of an object

Extract the derivatives of an object

Extract the parameters of an object

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

Compute the negative log-likelihood

L2 norm between data and model prediction

Generate objective list

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

Parameter transformation function

Direct sum of datasets

Direct sum of functions

Print or pander equation list

Generate sample for multi-start fit

Non-Linear Optimization, multi start

Generate a paramter frame

Print equation vector

python.version.sys

Check which Python versions are installed on the system

reduceReplicates

Reduce replicated measurements to mean and standard deviation

Plot a list data points

Plot Fluxes given a list of flux Equations

Prediction function

Prediction frame

Print object and its "default" attributes only.

L2 objective function for prior value

Compare data and model prediction by computing residuals

resolveRecurrence

Place top elements into bottom elemens

Non-Linear Optimization

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

Remote install dMod to a ssh-reachable host

Run an R expression on the bwForCluster

Summary of an equation vector

symmetryDetection

Search for symmetries in the loaded model

wide2long.data.frame

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

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

Plot parameter values for a fitlist

Profile likelihood: plot of the parameter paths.

Pretty printing parameter transformations

Pretty printing for a parameter vector

Generate eqnlist object

Generate equation vector object

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

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

Find integer-null space of matrix A

Observation function

Plot residuals for a fitlist

Plotting objective values of a collection of fits

Prediction list

Model Predictions

Objective frame

Parameter vector

Plot a list data points

Plot a list of model predictions

Profile-likelihood (PL) computation

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

Profile likelihood plot

Direct sum of objective functions

Add two lists element by element

Named repititions

Reparameterization

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

Submatrix of a matrix returning ALWAYS a matrix

subset of an equation list

Compute the weighted residual sum of squares

python.version.request

Check if rPython comes with the correct Python version

python.version.rpython

Get the Python version to which rPython is linked

Gather statistics of a fitlist

Calculate analytical steady states

Standard plotting theme of dMod

Concatenation of functions

wide2long.matrix

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

Write equation list into a csv file

scale_color_dMod

Standard dMod color palette

scale_fill_dMod

Standard dMod color scheme

Elide character vector

Pad string to desired width

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