R: Dynamic Modeling and Parameter Estimation in ODE Models

# Dynamic Modeling and Parameter Estimation in ODE Models

## Documentation for package ‘dMod’ version 1.0.2

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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