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dMod (version 1.0.1)

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

245

Version

1.0.1

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

February 10th, 2020

Functions in dMod (1.0.1)

Xd

Model prediction function from data.frame
Xf

Model prediction function for ODE models without sensitivities.
as.data.frame.datalist

Coerce to a Data Frame
Y

Observation functions.
as.data.frame.eqnlist

Coerce equation list into a data frame
Xs

Model prediction function for ODE models.
Xt

Generate a prediction function that returns times
covariates

Access the covariates in the data
datalist

Generate a datalist object
Pimpl

Parameter transformation (implicit)
Pexpl

Parameter transformation
addReaction

Add reaction to reaction table
as.parvec.parframe

Select a parameter vector from a parameter frame.
forcingsSymb

Return some useful forcing functions as strings
Id

An identity function which vanishes upon concatenation of fns
blockdiagSymb

Embed two matrices into one blockdiagonal matrix
format.eqnvec

Encode equation vector in format with sufficient spaces
attrs

Select attributes.
P

Generate a parameter transformation function
as.parframe.parlist

Coerce object to a parameter frame
expand.grid.alt

Alternative version of expand.grid
as.objlist

Generate objective list from numeric vector
conservedQuantities

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

Combine several data.frames by rowbind
constraintExp2

Compute a differentiable box prior
confint.parframe

Profile uncertainty extraction
constraintL2

Soft L2 constraint on parameters
eqnvec

Generate equation vector object
getLocalDLLs

Determine loaded DLLs available in working directory
getObservables

Extract the observables of an object
loadDLL

Load shared object for a dMod object
load.parlist

Construct fitlist from temporary files.
modelname

Get and set modelname
compare

Compare two objects and return differences
getParameters

Extract the parameters of an object
getReactions

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

Fit an error model
parfn

Parameter transformation function
msParframe

Reproducibly construct "random" parframes
parframe

Generate a parameter frame
compile

Compile one or more prdfn, obsfn or parfn objects
as.eqnvec

Coerce to an equation vector
dot

Symbolic time derivative of equation vector given an equation list
as.eventlist

Coerce to eventlist
controls

List, get and set controls for different functions
coordTransform

Coordinate transformation for data frames
getConditions

Extract the conditions of an object
eventlist

Eventlist
+.fn

Direct sum of functions
+.objfn

Direct sum of objective functions
datapointL2

L2 objective function for validation data point
getDerivs

Extract the derivatives of an object
print.parfn

Pretty printing parameter transformations
print.eqnvec

Print equation vector
ggopen

Open last plot in external pdf viewer
rref

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

Multiplication of objective functions with scalars
match.fnargs

dMod match function arguments
define

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

Standard dMod color palette
eqnlist

Generate eqnlist object
getCoefficients

Get coefficients from a character
funC0

Evaluation of algebraic expressions defined by characters
lsdMod

Print list of dMod objects in .GlobalEnv
long2wide

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

Observation function
odemodel

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

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

Summary of an equation vector
subset.eqnlist

subset of an equation list
*.fn

Concatenation of functions
plotData.datalist

Plot a list data points
mstrust

Non-Linear Optimization, multi start
mname

Get modelname from single object (used internally)
plotProfile.parframe

Profile likelihood plot
objframe

Objective frame
plotValues.parframe

Plotting objective values of a collection of fits
plotFluxes

Plot Fluxes given a list of flux Equations
objlist

Generate objective list
plotPars.parframe

Plot parameter values for a fitlist
plotResiduals

Plot residuals for a fitlist
+.datalist

Direct sum of datasets
trust

Non-Linear Optimization
getFluxes

Generate list of fluxes from equation list
getEquations

Extract the equations of an object
jakstat

Time-course data for the JAK-STAT cell signaling pathway
normL2

L2 norm between data and model prediction
lbind

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

Prediction frame
prdlist

Prediction list
nll

Compute the negative log-likelihood
parlist

Parameter list
nullZ

Find integer-null space of matrix A
parvec

Parameter vector
print.eqnlist

Print or pander equation list
predict.prdfn

Model Predictions
+.objlist

Add two lists element by element
prdfn

Prediction function
progressBar

Progress bar
python_version_request

Check if rPython comes with the correct Python version
print.parvec

Pretty printing for a parameter vector
theme_dMod

Standard plotting theme of dMod
plot.datalist

Plot a list data points
plot.parlist

Plot a parameter list.
symmetryDetection

Search for symmetries in the loaded model
res

Compare data and model prediction by computing residuals
reduceReplicates

Reduce replicated measurements to mean and standard deviation
print0

Print object and its "default" attributes only.
plotPaths

Profile likelihood: plot of the parameter paths.
wide2long.data.frame

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

Plot a list of model predictions
wide2long.list

Translate wide output format (e.g. from ode) into long format
priorL2

L2 objective function for prior value
profile

Profile-likelihood (PL) computation
python_version_rpython

Get the Python version to which rPython is linked
unique.parframe

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

Standard dMod color scheme
stat.parlist

Gather statistics of a fitlist
wide2long

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

Check which Python versions are installed on the system
resolveRecurrence

Place top elements into bottom elemens
steadyStates

Calculate analytical steady states.
wrss

Compute the weighted residual sum of squares
strelide

Elide character vector
repar

Reparameterization
strpad

Pad string to desired width
submatrix

Submatrix of a matrix returning ALWAYS a matrix
wide2long.matrix

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

Write equation list into a csv file