Dynamic Modeling and Parameter Estimation in ODE Models

Documentation for package ‘dMod’ version 1.0.2

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A B C D E F G I J L M N O P R S T U W X Y misc

-- A --

addEvent	Eventlist
addReaction	Add reaction to reaction table
as.data.frame.datalist	Coerce to a Data Frame
as.data.frame.eqnlist	Coerce equation list into a data frame
as.data.frame.prdlist	Coerce to a Data Frame
as.datalist	Generate a datalist object
as.datalist.data.frame	Generate a datalist object
as.datalist.list	Generate a datalist object
as.eqnlist	Generate eqnlist object
as.eqnlist.data.frame	Generate eqnlist object
as.eqnvec	Coerce to an equation vector
as.eqnvec.character	Coerce to an equation vector
as.eqnvec.eqnlist	Coerce to an equation vector
as.eventlist	Coerce to eventlist
as.eventlist.data.frame	Coerce to eventlist
as.eventlist.list	Coerce to eventlist
as.objlist	Generate objective list from numeric vector
as.parframe	Coerce object to a parameter frame
as.parframe.parlist	Coerce object to a parameter frame
as.parlist	Parameter list
as.parvec	Parameter vector
as.parvec.numeric	Parameter vector
as.parvec.parframe	Select a parameter vector from a parameter frame.
as.prdlist	Prediction list
as.prdlist.list	Prediction list
attrs	Select attributes.

-- B --

blockdiagSymb	Embed two matrices into one blockdiagonal matrix
branch	Define parameter transformations by 'define()', 'branch()' and 'insert()'

-- C --

c.datalist	Generate a datalist object
c.parlist	Parameter list
c.parvec	Parameter vector
combine	Combine several data.frames by rowbind
compare	Compare two objects and return differences
compare.character	Compare two objects and return differences
compare.data.frame	Compare two objects and return differences
compare.eqnvec	Compare two objects and return differences
compare.list	Compare two objects and return differences
compile	Compile one or more prdfn, obsfn or parfn objects
confint.parframe	Profile uncertainty extraction
conservedQuantities	Determine conserved quantites by finding the kernel of the stoichiometric matrix
constraintExp2	Compute a differentiable box prior
constraintL2	Soft L2 constraint on parameters
controls	List, get and set controls for different functions
controls.fn	List, get and set controls for different functions
controls.objfn	List, get and set controls for different functions
controls<-	List, get and set controls for different functions
controls<-.fn	List, get and set controls for different functions
controls<-.objfn	List, get and set controls for different functions
coordTransform	Coordinate transformation for data frames
covariates	Access the covariates in the data
covariates.data.frame	Access the covariates in the data
covariates.datalist	Access the covariates in the data

-- D --

datalist	Generate a datalist object
datapointL2	L2 objective function for validation data point
define	Define parameter transformations by 'define()', 'branch()' and 'insert()'
dot	Symbolic time derivative of equation vector given an equation list

-- E --

eqnlist	Generate eqnlist object
eqnvec	Generate equation vector object
eventlist	Eventlist
expand.grid.alt	Alternative version of expand.grid

-- F --

fitErrorModel	Fit an error model
forcingsSymb	Return some useful forcing functions as strings
format.eqnvec	Encode equation vector in format with sufficient spaces
funC0	Evaluation of algebraic expressions defined by characters

-- G --

getCoefficients	Get coefficients from a character
getConditions	Extract the conditions of an object
getConditions.fn	Extract the conditions of an object
getConditions.list	Extract the conditions of an object
getDerivs	Extract the derivatives of an object
getDerivs.list	Extract the derivatives of an object
getDerivs.objlist	Extract the derivatives of an object
getDerivs.parvec	Extract the derivatives of an object
getDerivs.prdframe	Extract the derivatives of an object
getDerivs.prdlist	Extract the derivatives of an object
getEquations	Extract the equations of an object
getEquations.fn	Extract the equations of an object
getEquations.odemodel	Extract the equations of an object
getEquations.prdfn	Extract the equations of an object
getFluxes	Generate list of fluxes from equation list
getLocalDLLs	Determine loaded DLLs available in working directory
getObservables	Extract the observables of an object
getParameters	Extract the parameters of an object
getParameters.eqnlist	Extract the parameters of an object
getParameters.eventlist	Extract the parameters of an object
getParameters.fn	Extract the parameters of an object
getParameters.odemodel	Extract the parameters of an object
getParameters.parvec	Extract the parameters of an object
getParameters.prdframe	Extract the parameters of an object
getParameters.prdlist	Extract the parameters of an object
getReactions	Generate a table of reactions (data.frame) from an equation list
ggopen	Open last plot in external pdf viewer

-- I --

Id	An identity function which vanishes upon concatenation of fns
insert	Define parameter transformations by 'define()', 'branch()' and 'insert()'
is.datalist	Generate a datalist object
is.eqnlist	Generate eqnlist object
is.eqnvec	Generate equation vector object
is.parframe	Generate a parameter frame

-- J --

jakstat

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

-- L --

lbind	Bind named list of data.frames into one data.frame
load.parlist	Construct fitlist from temporary files.
loadDLL	Load shared object for a dMod object
long2wide	Translate long to wide format (inverse of wide2long.matrix)
lsdMod	Print list of dMod objects in .GlobalEnv

-- M --

match.fnargs	dMod match function arguments
mname	Get modelname from single object (used internally)
mname.character	Get modelname from single object (used internally)
mname.fn	Get modelname from single object (used internally)
mname.NULL	Get modelname from single object (used internally)
mname.objfn	Get modelname from single object (used internally)
modelname	Get and set modelname
modelname<-	Get and set modelname
modelname<-.fn	Get and set modelname
modelname<-.objfn	Get and set modelname
msParframe	Reproducibly construct "random" parframes
mstrust	Non-Linear Optimization, multi start

-- N --

names<-.datalist	Generate a datalist object
nll	Compute the negative log-likelihood
normL2	L2 norm between data and model prediction
nullZ	Find integer-null space of matrix A

-- O --

objframe	Objective frame
objlist	Generate objective list
obsfn	Observation function
odemodel	Generate the model objects for use in Xs (models with sensitivities)

-- P --

P	Generate a parameter transformation function
parfn	Parameter transformation function
parframe	Generate a parameter frame
parlist	Parameter list
parvec	Parameter vector
Pexpl	Parameter transformation
Pimpl	Parameter transformation (implicit)
plot.datalist	Plot a list data points
plot.parlist	Plot a parameter list.
plot.prdframe	Plot a list of model predictions and a list of data points in a combined plot
plot.prdlist	Plot a list of model predictions and a list of data points in a combined plot
plotCombined	Plot a list of model predictions and a list of data points in a combined plot
plotCombined.prdlist	Plot a list of model predictions and a list of data points in a combined plot
plotData	Plot a list data points
plotData.data.frame	Plot a list data points
plotData.datalist	Plot a list data points
plotFluxes	Plot Fluxes given a list of flux Equations
plotPars	Plot parameter values for a fitlist
plotPars.parframe	Plot parameter values for a fitlist
plotPaths	Profile likelihood: plot of the parameter paths.
plotPrediction	Plot a list of model predictions
plotPrediction.prdlist	Plot a list of model predictions
plotProfile	Profile likelihood plot
plotProfile.list	Profile likelihood plot
plotProfile.parframe	Profile likelihood plot
plotResiduals	Plot residuals for a fitlist
plotValues	Plotting objective values of a collection of fits
plotValues.parframe	Plotting objective values of a collection of fits
prdfn	Prediction function
prdframe	Prediction frame
prdlist	Prediction list
predict.prdfn	Model Predictions
print.eqnlist	Print or pander equation list
print.eqnvec	Print equation vector
print.parfn	Pretty printing parameter transformations
print.parvec	Pretty printing for a parameter vector
print0	Print object and its "default" attributes only.
priorL2	L2 objective function for prior value
prodfn	Concatenation of functions
profile	Profile-likelihood (PL) computation
progressBar	Progress bar

-- R --

reduceReplicates	Reduce replicated measurements to mean and standard deviation
repar	Reparameterization
res	Compare data and model prediction by computing residuals
resolveRecurrence	Place top elements into bottom elemens
rref	Transform matrix A into reduced row echelon form this function is written along the lines of the rref-matlab function.

-- S --

scale_color_dMod	Standard dMod color palette
scale_fill_dMod	Standard dMod color scheme
stat.parlist	Gather statistics of a fitlist
steadyStates	Calculate analytical steady states.
strelide	Elide character vector
strpad	Pad string to desired width
submatrix	Submatrix of a matrix returning ALWAYS a matrix
subset.eqnlist	subset of an equation list
subset.parframe	Generate a parameter frame
sumdatalist	Direct sum of datasets
sumfn	Direct sum of functions
summary.eqnvec	Summary of an equation vector
summary.parlist	Parameter list
sumobjfn	Direct sum of objective functions
sumobjlist	Add two lists element by element
symmetryDetection	Search for symmetries in the loaded model

-- T --

theme_dMod	Standard plotting theme of dMod
trust	Non-Linear Optimization
trustL1	Non-Linear Optimization

-- U --

unique.parframe

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

-- W --

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
wide2long.matrix	Translate wide output format (e.g. from ode) into long format
write.eqnlist	Write equation list into a csv file
wrss	Compute the weighted residual sum of squares

-- X --

Xd	Model prediction function from data.frame
Xf	Model prediction function for ODE models without sensitivities.
Xs	Model prediction function for ODE models.
Xt	Generate a prediction function that returns times

-- Y --

Y	Observation functions.

-- misc --

%.*%	Multiplication of objective functions with scalars
*.fn	Concatenation of functions
+.datalist	Direct sum of datasets
+.fn	Direct sum of functions
+.objfn	Direct sum of objective functions
+.objlist	Add two lists element by element
[.parframe	Generate a parameter frame
[.parvec	Parameter vector