%.*%                    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
Id                      An identity function which vanishes upon
                        concatenation of fns
P                       Generate a parameter transformation function
Pexpl                   Parameter transformation
Pimpl                   Parameter transformation (implicit)
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                       Observation functions.
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.eqnvec               Coerce to an equation vector
as.eventlist            Coerce to eventlist
as.objlist              Generate objective list from numeric vector
as.parframe.parlist     Coerce object to a parameter frame
as.parvec.parframe      Select a parameter vector from a parameter
                        frame.
attrs                   Select attributes.
blockdiagSymb           Embed two matrices into one blockdiagonal
                        matrix
combine                 Combine several data.frames by rowbind
compare                 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
coordTransform          Coordinate transformation for data frames
covariates              Access the covariates in the data
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
eqnlist                 Generate eqnlist object
eqnvec                  Generate equation vector object
eventlist               Eventlist
expand.grid.alt         Alternative version of expand.grid
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
getCoefficients         Get coefficients from a character
getConditions           Extract the conditions of an object
getDerivs               Extract the derivatives of an object
getEquations            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
getReactions            Generate a table of reactions (data.frame) from
                        an equation list
ggopen                  Open last plot in external pdf viewer
jakstat                 Time-course data for the JAK-STAT cell
                        signaling pathway
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
match.fnargs            dMod match function arguments
mname                   Get modelname from single object (used
                        internally)
modelname               Get and set modelname
msParframe              Reproducibly construct "random" parframes
mstrust                 Non-Linear Optimization, multi start
nll                     Compute the negative log-likelihood
normL2                  L2 norm between data and model prediction
nullZ                   Find integer-null space of matrix A
objframe                Objective frame
objlist                 Generate objective list
obsfn                   Observation function
odemodel                Generate the model objects for use in Xs
                        (models with sensitivities)
parfn                   Parameter transformation function
parframe                Generate a parameter frame
parlist                 Parameter list
parvec                  Parameter vector
plot.datalist           Plot a list data points
plot.parlist            Plot a parameter list.
plotCombined            Plot a list of model predictions and a list of
                        data points in a combined plot
plotData.datalist       Plot a list data points
plotFluxes              Plot Fluxes given a list of flux Equations
plotPars.parframe       Plot parameter values for a fitlist
plotPaths               Profile likelihood: plot of the parameter
                        paths.
plotPrediction          Plot a list of model predictions
plotProfile.parframe    Profile likelihood plot
plotResiduals           Plot residuals for a fitlist
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
profile                 Profile-likelihood (PL) computation
progressBar             Progress bar
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.
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
summary.eqnvec          Summary of an equation vector
symmetryDetection       Search for symmetries in the loaded model
theme_dMod              Standard plotting theme of dMod
trust                   Non-Linear Optimization
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
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
