Man pages for dkaschek/dMod
Dynamic Modeling and Parameter Estimation in ODE Models

addReactionAdd reaction to reaction table
as.data.frame.dModCoerce to a Data Frame
as.data.frame.eqnlistCoerce equation list into a data frame
as.eqnvecCoerce to an equation vector
as.objlistGenerate objective list from numeric vector
as.parframeCoerce object to a parameter frame
as.parvec.parframeSelect a parameter vector from a parameter frame.
attrsSelect attributes.
blockdiagSymbEmbed two matrices into one blockdiagonal matrix
combineCombine several data.frames by rowbind
compareCompare two objects and return differences
compileCompile one or more prdfn, obsfn or parfn objects
confint.parframeProfile uncertainty extraction
conservedQuantitiesDetermine conserved quantites by finding the kernel of the...
constraintExp2Compute a differentiable box prior
constraintL2Soft L2 constraint on parameters
controlsList, get and set controls for different functions
coordTransformCoordinate transformation for data frames
datalistGenerate a datalist object
datapointL2L2 objective function for validation data point
detectFreeCoresDetect number of free cores (on UNIX)
dotSymbolic time derivative of equation vector given an equation...
eqnlistGenerate eqnlist object
eqnvecGenerate equation vector object
expand.grid.altAlternative version of expand.grid
fitErrorModelFit an error model
forcingsSymbReturn some useful forcing functions as strings
format.eqnvecEncode equation vector in format with sufficient spaces
funC0Evaluation of algebraic expressions defined by characters
getCoefficientsGet coefficients from a character
getConditionsExtract the conditions of an object
getDerivsExtract the derivatives of an object
getFluxesGenerate list of fluxes from equation list
getLocalDLLsDetermine loaded DLLs available in working directory
getParametersExtract the parameters of an object
getReactionsGenerate a table of reactions (data.frame) from an equation...
ggopenOpen last plot in external pdf viewer
grapes-.-times-grapesMultiplication of objective functions with scalars
jakstatTime-course data for the JAK-STAT cell signaling pathway
lbindBind named list of data.frames into one data.frame
loadDLLLoad shared object for a dMod object
load.parlistConstruct fitlist from temporary files.
long2wideTranslate long to wide format (inverse of wide2long.matrix)
lsdModPrint list of dMod objects in .GlobalEnv
mnameGet modelname from single object (used internally)
modelnameGet and set modelname
mssampleGenerate sample for multi-start fit
mstrustNon-Linear Optimization, multi start
nllCompute the negative log-likelihood
normL2L2 norm between data and model prediction
nullZFind integer-null space of matrix A
objframeObjective frame
objlistGenerate objective list
obsfnObservation function
odemodelGenerate the model objects for use in Xs (models with...
PGenerate a parameter transformation function
parfnParameter transformation function
parframeGenerate a paramter frame
parlistParameter list
parvecParameter vector
PexplParameter transformation
PimplParameter transformation (implicit)
plotCombinedPlot a list of model predictions and a list of data points in...
plotDataPlot a list data points
plot.datalistPlot a list data points
plotFluxesPlot Fluxes given a list of flux Equations
plot.parlistPlot a parameter list.
plotParsPlot parameter values for a fitlist
plotPathsProfile likelihood: plot of the parameter paths.
plotPredictionPlot a list of model predictions
plotProfileProfile likelihood plot
plotResidualsPlot residuals for a fitlist
plotValuesPlotting objective values of a collection of fits
plus-.datalistDirect sum of datasets
plus-.fnDirect sum of functions
plus-.objfnDirect sum of objective functions
plus-.objlistAdd two lists element by element
prdfnPrediction function
prdframePrediction frame
prdlistPrediction list
predict.prdfnModel Predictions
print0Print object and its "default" attributes only.
print.eqnlistPrint or pander equation list
print.eqnvecPrint equation vector
print.parfnPretty printing parameter transformations
print.parvecPretty printing for a parameter vector
priorL2L2 objective function for prior value
profileProfile-likelihood (PL) computation
progressBarProgress bar
python.version.requestCheck if rPython comes with the correct Python version
python.version.rpythonGet the Python version to which rPython is linked
python.version.sysCheck which Python versions are installed on the system
reduceReplicatesReduce replicated measurements to mean and standard deviation
reparReparameterization
repWithNamesNamed repititions
resCompare data and model prediction by computing residuals
resolveRecurrencePlace top elements into bottom elemens
rrefTransform matrix A into reduced row echelon form this...
runbgRun an R expression in the background (only on UNIX)
runbg_bwforRun an R expression on the bwForCluster
runbgInstallRemote install dMod to a ssh-reachable host
scale_color_dModStandard dMod color palette
scale_fill_dModStandard dMod color scheme
stat.parlistGather statistics of a fitlist
steadyStatesCalculate analytical steady states
strelideElide character vector
strpadPad string to desired width
submatrixSubmatrix of a matrix returning ALWAYS a matrix
subset.eqnlistsubset of an equation list
summary.eqnvecSummary of an equation vector
symmetryDetectionSearch for symmetries in the loaded model
theme_dModStandard plotting theme of dMod
times-.fnConcatenation of functions
trustNon-Linear Optimization
wide2longTranslate wide output format (e.g. from ode) into long format
wide2long.data.frameTranslate wide output format (e.g. from ode) into long format
wide2long.listTranslate wide output format (e.g. from ode) into long format
wide2long.matrixTranslate wide output format (e.g. from ode) into long format
write.eqnlistWrite equation list into a csv file
wrssCompute the weighted residual sum of squares
XdModel prediction function from data.frame
XfModel prediction function for ODE models without...
XsModel prediction function for ODE models.
XtGenerate a prediction function that returns times
YObservation functions.
dkaschek/dMod documentation built on Dec. 9, 2017, 12:26 a.m.