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dMod (version 1.0.0)

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

294

Version

1.0.0

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

April 23rd, 2019

Functions in dMod (1.0.0)

Xd

Model prediction function from data.frame
controls

List, get and set controls for different functions
as.eqnvec

Coerce to an equation vector
getObservables

Extract the observables of an object
modelname

Get and set modelname
getLocalDLLs

Determine loaded DLLs available in working directory
msParframe

Reproducibly construct "random" parframes
as.eventlist

Coerce to eventlist
parfn

Parameter transformation function
parframe

Generate a parameter frame
as.data.frame.datalist

Coerce to a Data Frame
addReaction

Add reaction to reaction table
compare

Compare two objects and return differences
eqnlist

Generate eqnlist object
dot

Symbolic time derivative of equation vector given an equation list
compile

Compile one or more prdfn, obsfn or parfn objects
getConditions

Extract the conditions of an object
getDerivs

Extract the derivatives of an object
jakstat

Time-course data for the JAK-STAT cell signaling pathway
+.fn

Direct sum of functions
attrs

Select attributes.
Xf

Model prediction function for ODE models without sensitivities.
as.parvec.parframe

Select a parameter vector from a parameter frame.
confint.parframe

Profile uncertainty extraction
lbind

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

Coerce equation list into a data frame
obsfn

Observation function
odemodel

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

Parameter list
coordTransform

Coordinate transformation for data frames
+.objfn

Direct sum of objective functions
conservedQuantities

Determine conserved quantites by finding the kernel of the stoichiometric matrix
forcingsSymb

Return some useful forcing functions as strings
datapointL2

L2 objective function for validation data point
print.eqnvec

Print equation vector
parvec

Parameter vector
plotProfile.parframe

Profile likelihood plot
plotResiduals

Plot residuals for a fitlist
as.objlist

Generate objective list from numeric vector
covariates

Access the covariates in the data
priorL2

L2 objective function for prior value
print.parfn

Pretty printing parameter transformations
define

Define parameter transformations by define(), branch() and insert()
format.eqnvec

Encode equation vector in format with sufficient spaces
getParameters

Extract the parameters of an object
as.parframe.parlist

Coerce object to a parameter frame
getReactions

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

dMod match function arguments
profile

Profile-likelihood (PL) computation
progressBar

Progress bar
python_version_request

Check if rPython comes with the correct Python version
constraintExp2

Compute a differentiable box prior
constraintL2

Soft L2 constraint on parameters
steadyStates

Calculate analytical steady states.
eqnvec

Generate equation vector object
eventlist

Eventlist
long2wide

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

Elide character vector
lsdMod

Print list of dMod objects in .GlobalEnv
normL2

L2 norm between data and model prediction
python_version_rpython

Get the Python version to which rPython is linked
funC0

Evaluation of algebraic expressions defined by characters
mname

Get modelname from single object (used internally)
getCoefficients

Get coefficients from a character
ggopen

Open last plot in external pdf viewer
datalist

Generate a datalist object
python_version_sys

Check which Python versions are installed on the system
strpad

Pad string to desired width
expand.grid.alt

Alternative version of expand.grid
%.*%

Multiplication of objective functions with scalars
objframe

Objective frame
submatrix

Submatrix of a matrix returning ALWAYS a matrix
nullZ

Find integer-null space of matrix A
fitErrorModel

Fit an error model
getEquations

Extract the equations of an object
*.fn

Concatenation of functions
trust

Non-Linear Optimization
plotFluxes

Plot Fluxes given a list of flux Equations
objlist

Generate objective list
print.parvec

Pretty printing for a parameter vector
getFluxes

Generate list of fluxes from equation list
plot.datalist

Plot a list data points
print0

Print object and its "default" attributes only.
load.parlist

Construct fitlist from temporary files.
loadDLL

Load shared object for a dMod object
plot.parlist

Plot a parameter list.
symmetryDetection

Search for symmetries in the loaded model
+.objlist

Add two lists element by element
mstrust

Non-Linear Optimization, multi start
nll

Compute the negative log-likelihood
plotCombined

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

Plot a list data points
prdfn

Prediction function
plotValues.parframe

Plotting objective values of a collection of fits
plotPars.parframe

Plot parameter values for a fitlist
plotPaths

Profile likelihood: plot of the parameter paths.
predict.prdfn

Model Predictions
+.datalist

Direct sum of datasets
plotPrediction

Plot a list of model predictions
prdframe

Prediction frame
theme_dMod

Standard plotting theme of dMod
wide2long.matrix

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

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

Prediction list
reduceReplicates

Reduce replicated measurements to mean and standard deviation
print.eqnlist

Print or pander equation list
repar

Reparameterization
res

Compare data and model prediction by computing residuals
resolveRecurrence

Place top elements into bottom elemens
write.eqnlist

Write equation list into a csv file
subset.eqnlist

subset of an equation list
scale_fill_dMod

Standard dMod color scheme
summary.eqnvec

Summary of an equation vector
scale_color_dMod

Standard dMod color palette
stat.parlist

Gather statistics of a fitlist
wrss

Compute the weighted residual sum of squares
unique.parframe

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

Observation functions.
Pexpl

Parameter transformation
Pimpl

Parameter transformation (implicit)
Id

An identity function which vanishes upon concatenation of fns
Xs

Model prediction function for ODE models.
blockdiagSymb

Embed two matrices into one blockdiagonal matrix
P

Generate a parameter transformation function
Xt

Generate a prediction function that returns times
combine

Combine several data.frames by rowbind