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dMod (version 1.0.2)

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. The methods used in dMod were published in Kaschek et al, 2019, .

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Version

Install

install.packages('dMod')

Monthly Downloads

316

Version

1.0.2

License

GPL (>= 2)

Maintainer

Daniel Kaschek

Last Published

January 27th, 2021

Functions in dMod (1.0.2)

Id

An identity function which vanishes upon concatenation of fns
Pexpl

Parameter transformation
Y

Observation functions.
Xd

Model prediction function from data.frame
addReaction

Add reaction to reaction table
P

Generate a parameter transformation function
Xf

Model prediction function for ODE models without sensitivities.
Xs

Model prediction function for ODE models.
Pimpl

Parameter transformation (implicit)
as.objlist

Generate objective list from numeric vector
Xt

Generate a prediction function that returns times
attrs

Select attributes.
as.parvec.parframe

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

Profile uncertainty extraction
blockdiagSymb

Embed two matrices into one blockdiagonal matrix
combine

Combine several data.frames by rowbind
as.data.frame.eqnlist

Coerce equation list into a data frame
constraintL2

Soft L2 constraint on parameters
constraintExp2

Compute a differentiable box prior
as.data.frame.datalist

Coerce to a Data Frame
as.eqnvec

Coerce to an equation vector
getEquations

Extract the equations of an object
as.eventlist

Coerce to eventlist
controls

List, get and set controls for different functions
as.parframe.parlist

Coerce object to a parameter frame
fitErrorModel

Fit an error model
load.parlist

Construct fitlist from temporary files.
expand.grid.alt

Alternative version of expand.grid
getParameters

Extract the parameters of an object
getReactions

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

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

Access the covariates in the data
dot

Symbolic time derivative of equation vector given an equation list
coordTransform

Coordinate transformation for data frames
getFluxes

Generate list of fluxes from equation list
compare

Compare two objects and return differences
parfn

Parameter transformation function
loadDLL

Load shared object for a dMod object
objframe

Objective frame
objlist

Generate objective list
forcingsSymb

Return some useful forcing functions as strings
odemodel

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

Prediction frame
lsdMod

Print list of dMod objects in .GlobalEnv
plotPrediction

Plot a list of model predictions
plotPaths

Profile likelihood: plot of the parameter paths.
long2wide

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

Observation function
eqnlist

Generate eqnlist object
compile

Compile one or more prdfn, obsfn or parfn objects
getLocalDLLs

Determine loaded DLLs available in working directory
prdlist

Prediction list
datapointL2

L2 objective function for validation data point
datalist

Generate a datalist object
getObservables

Extract the observables of an object
define

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

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

Generate equation vector object
eventlist

Eventlist
format.eqnvec

Encode equation vector in format with sufficient spaces
lbind

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

Plot Fluxes given a list of flux Equations
normL2

L2 norm between data and model prediction
nullZ

Find integer-null space of matrix A
funC0

Evaluation of algebraic expressions defined by characters
getConditions

Extract the conditions of an object
plotProfile.parframe

Profile likelihood plot
plotPars.parframe

Plot parameter values for a fitlist
stat.parlist

Gather statistics of a fitlist
trust

Non-Linear Optimization
print.parvec

Pretty printing for a parameter vector
plotResiduals

Plot residuals for a fitlist
print0

Print object and its "default" attributes only.
unique.parframe

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

Calculate analytical steady states.
getDerivs

Extract the derivatives of an object
getCoefficients

Get coefficients from a character
repar

Reparameterization
summary.eqnvec

Summary of an equation vector
symmetryDetection

Search for symmetries in the loaded model
wrss

Compute the weighted residual sum of squares
write.eqnlist

Write equation list into a csv file
parframe

Generate a parameter frame
res

Compare data and model prediction by computing residuals
mname

Get modelname from single object (used internally)
match.fnargs

dMod match function arguments
wide2long.list

Translate wide output format (e.g. from ode) into long format
wide2long.matrix

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

Non-Linear Optimization, multi start
ggopen

Open last plot in external pdf viewer
priorL2

L2 objective function for prior value
prdfn

Prediction function
profile

Profile-likelihood (PL) computation
%.*%

Multiplication of objective functions with scalars
parvec

Parameter vector
+.objlist

Add two lists element by element
parlist

Parameter list
modelname

Get and set modelname
nll

Compute the negative log-likelihood
plot.datalist

Plot a list data points
msParframe

Reproducibly construct "random" parframes
plotValues.parframe

Plotting objective values of a collection of fits
+.datalist

Direct sum of datasets
predict.prdfn

Model Predictions
plot.parlist

Plot a parameter list.
+.objfn

Direct sum of objective functions
+.fn

Direct sum of functions
plotData.datalist

Plot a list data points
plotCombined

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

Print equation vector
progressBar

Progress bar
print.parfn

Pretty printing parameter transformations
print.eqnlist

Print or pander equation list
submatrix

Submatrix of a matrix returning ALWAYS a matrix
reduceReplicates

Reduce replicated measurements to mean and standard deviation
subset.eqnlist

subset of an equation list
theme_dMod

Standard plotting theme of dMod
scale_fill_dMod

Standard dMod color scheme
*.fn

Concatenation of functions
scale_color_dMod

Standard dMod color palette
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
rref

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

Elide character vector
resolveRecurrence

Place top elements into bottom elemens
strpad

Pad string to desired width