| Concatenation of functions | *.fn prodfn |
| Multiplication of objective functions with scalars | %.*% |
| Direct sum of datasets | +.datalist sumdatalist |
| Direct sum of functions | +.fn sumfn |
| Direct sum of objective functions | +.objfn sumobjfn |
| Add two lists element by element | +.objlist sumobjlist |
| Add reaction to reaction table | addReaction |
| Append an objective function to a basic dMod.frame | appendObj |
| Make a column "parframes" out of "fits" | appendParframes |
| Coerce to a Data Frame | as.data.frame.datalist as.data.frame.prdlist |
| Coerce equation list into a data frame | as.data.frame.eqnlist |
| Coerce to an equation vector | as.eqnvec as.eqnvec.character as.eqnvec.eqnlist |
| Coerce to eventlist | as.eventlist as.eventlist.data.frame as.eventlist.list |
| Generate objective list from numeric vector | as.objlist |
| Coerce object to a parameter frame | as.parframe as.parframe.parlist |
| Select a parameter vector from a parameter frame. | as.parvec.parframe |
| Select attributes. | attrs |
| Embed two matrices into one blockdiagonal matrix | blockdiagSymb |
| Run some checks on the prediction in normL2_indiv | check_and_sanitize_prediction |
| Load one row of a dMod.frame into the .GlobalEnv | checkout_hypothesis |
| Combine several data.frames by rowbind | combine |
| Compare two objects and return differences | compare compare.character compare.data.frame compare.eqnvec compare.list |
| Compile one or more prdfn, obsfn or parfn objects | compile |
| Profile uncertainty extraction | confint.parframe |
| Determine conserved quantites by finding the kernel of the stoichiometric matrix | conservedQuantities |
| Compute a differentiable box prior | constraintExp2 |
| Soft L2 constraint on parameters | constraintL2 |
| List, get and set controls for different functions | controls controls.fn controls.objfn controls<- controls<-.fn controls<-.objfn |
| Coordinate transformation for data frames | coordTransform |
| Access the covariates in the data | covariates covariates.data.frame covariates.datalist covariates.tbl_df |
| Open a unit test template. | createExample |
| Generate a datalist object | as.datalist as.datalist.data.frame as.datalist.list c.datalist datalist is.datalist names<-.datalist |
| L2 objective function for validation data point | datapointL2 |
| DatapointL2 without access to stored predictions | datapointL2_indiv |
| Define parameter transformations by 'define()', 'branch()' and 'insert()' | branch define insert |
| Detect number of free cores (on UNIX) | detectFreeCores |
| Run an any R function on a remote HPC system with SLURM | distributed_computing |
| Generate a dMod.frame | dMod.frame |
| Symbolic time derivative of equation vector given an equation list | dot |
| Generate eqnlist object | as.eqnlist as.eqnlist.data.frame eqnlist is.eqnlist |
| Generate equation vector object | eqnvec is.eqnvec |
| Eventlist | addEvent eventlist |
| Extract an example from a unit test file. | exmpextr |
| Alternative version of expand.grid | expand.grid.alt |
| Extract example from unit tests. | extractExamples |
| Fit an error model | fitErrorModel |
| Return some useful forcing functions as strings | forcingsSymb |
| Encode equation vector in format with sufficient spaces | format.eqnvec |
| Evaluation of algebraic expressions defined by characters | funC0 |
| Get coefficients from a character | getCoefficients |
| Extract the conditions of an object | getConditions getConditions.fn getConditions.list getConditions.tbl_df |
| Extract the derivatives of an object | getDerivs getDerivs.list getDerivs.objlist getDerivs.parvec getDerivs.prdframe getDerivs.prdlist |
| Get Symbols and Numeric constants from a character | getElements |
| Extract the equations of an object | getEquations getEquations.fn getEquations.odemodel getEquations.prdfn |
| Get Parameter mappings outer.estgrid - inner.estgrid | getEstGridParameterMapping |
| Generate list of fluxes from equation list | getFluxes |
| Determine loaded DLLs available in working directory | getLocalDLLs |
| Extract the observables of an object | getObservables getObservables.tbl_df |
| Extract the parameters of an object | getParameters getParameters.eqnlist getParameters.eventlist getParameters.fn getParameters.odemodel getParameters.parvec getParameters.prdframe getParameters.prdlist |
| Title | getParameters.data.table |
| Determine which parameters need sensitivities | getParametersToEstimate |
| Get est.grid and fixed.grid | getParGrids |
| Generate a table of reactions (data.frame) from an equation list | getReactions |
| Get the indices of the n largest (not necessarily best) steps of a parframe | getStepIndices |
| Get the rows of the n largest steps of a parframe | getSteps |
| Open last plot in external pdf viewer | ggopen |
| Collect grids in list | gridlist |
| An identity function which vanishes upon concatenation of fns | Id |
| Import an SMBL model | import_sbml |
| Add single-valued parameters to the pargrids | indiv_addGlobalParsToGridlist |
| Add individualized parameters to grids | indiv_addLocalParsToGridList |
| Create an objlist with zeros as entries | init_empty_objlist |
| Install the julia setup | installJuliaForSteadyStates |
| Time-course data for the JAK-STAT cell signaling pathway | jakstat |
| Bind named list of data.frames into one data.frame | lbind |
| Construct fitlist from temporary files. | load.parlist |
| Load shared object for a dMod object | loadDLL |
| Translate long to wide format (inverse of wide2long.matrix) | long2wide |
| Print list of dMod objects in .GlobalEnv | lsdMod |
| Extract pars, fixed and parnames from grids for a given condition | make_pars |
| dMod match function arguments | match.fnargs |
| Get modelname from single object (used internally) | mname mname.character mname.fn mname.NULL mname.objfn |
| Get and set modelname | modelname modelname<- modelname<-.fn modelname<-.objfn |
| Reproducibly construct "random" parframes | msParframe |
| Non-Linear Optimization, multi start | mstrust |
| A version of dplyr::mutate | mutatedMod.frame |
| Compute the negative log-likelihood | nll |
| Non-linear log likelihood for the ALOQ part of the data | nll_ALOQ |
| Non-linear log likelihood for the BLOQ part of the data | nll_BLOQ |
| L2 norm between data and model prediction | normL2 |
| Fast normL2 | normL2_indiv |
| Find integer-null space of matrix A | nullZ |
| Objective frame | objframe |
| Generate objective list | objlist |
| Get vector of logarithmically spaced time points | objtimes |
| Observation function | obsfn |
| Generate the model objects for use in Xs (models with sensitivities) | odemodel |
| Get default arguments for integrators | optionsLSODA optionsLSODE optionsLSODES |
| Generate a parameter transformation function | P |
| Title | P_indiv |
| Parameter transformation function | parfn |
| Generate a parameter frame | is.parframe parframe subset.parframe [.parframe |
| Parameter list | as.parlist c.parlist parlist summary.parlist |
| Parameter vector | as.parvec as.parvec.numeric c.parvec parvec [.parvec |
| Parameter transformation | Pexpl |
| Parameter transformation (implicit) | Pimpl |
| Plot a list data points | plot.datalist |
| Plot a parameter list. | plot.parlist |
| Plot an array of trajectories along the profile of a parameter | plotArray |
| Plot a list of model predictions and a list of data points in a combined plot | plot.prdframe plot.prdlist plotCombined plotCombined.prdlist plotCombined.tbl_df |
| Plot a list data points | plotData plotData.data.frame plotData.datalist plotData.tbl_df |
| Plot Fluxes given a list of flux Equations | plotFluxes |
| Plot parameter values for a fitlist | plotPars plotPars.parframe plotPars.tbl_df |
| Profile likelihood: plot of the parameter paths. | plotPaths plotPaths.tbl_df |
| Profile likelihood: plot all parameter paths belonging to one profile in one plot | plotPathsMulti |
| Plot a list of model predictions | plotPrediction plotPrediction.prdlist plotPrediction.tbl_df |
| Profile likelihood plot | plotProfile plotProfile.list plotProfile.parframe plotProfile.tbl_df |
| Profile likelihood: plot profiles along with their parameter paths | plotProfilesAndPaths |
| Plot residuals for a fitlist | plotResiduals |
| Plotting objective values of a collection of fits | plotValues plotValues.parframe plotValues.tbl_df |
| Title | PRD_indiv |
| Prediction function | prdfn |
| Prediction frame | prdframe |
| Prediction list | as.prdlist as.prdlist.list prdlist |
| Model Predictions | predict.prdfn |
| Get a vector of linearly spaced time points for prediction | predtimes |
| Print or pander equation list | print.eqnlist |
| Print equation vector | print.eqnvec |
| Pretty printing parameter transformations | print.parfn |
| Pretty printing for a parameter vector | print.parvec |
| Print object and its "default" attributes only. | print0 |
| L2 objective function for prior value | priorL2 |
| Profile-likelihood (PL) computation | profile |
| Generate parameter list for distributed profile calculation | profile_pars_per_node |
| Progress bar | progressBar |
| Check if rPython comes with the correct Python version | python_version_request |
| Get the Python version to which rPython is linked | python_version_rpython |
| Check which Python versions are installed on the system | python_version_sys |
| Reduce replicated measurements to mean and standard deviation | reduceReplicates |
| Method for files (character) | reduceReplicates.character |
| Method for data frames | reduceReplicates.data.frame |
| Update attr(prediction, "deriv") to correct par.grid.outer names | renameDerivPars |
| Rename the gradient and hessian of an objlist | renameDerivParsInObjlist |
| Reparameterization | repar |
| Named repititions | repWithNames |
| Compare data and model prediction by computing residuals | res |
| Place top elements into bottom elemens | resolveRecurrence |
| Transform matrix A into reduced row echelon form this function is written along the lines of the rref-matlab function. | rref |
| Run an R expression in the background (only on UNIX) | runbg |
| Run an R expression on the bwForCluster | runbg_bwfor |
| Run an R expression on the bwForCluster via sshpass and slurm | runbg_bwfor_slurm |
| Run an R expression on the bwForCluster via sshpass | runbg_bwfor_sshpass |
| Remote install dMod to a ssh-reachable host | runbgInstall |
| Save the necessary objects for dModtoShiny with the correct names | saveShiny |
| SaveShiny for dMod.frames | saveShiny_dMod.frame |
| Standard dMod color palette | scale_color_dMod |
| Standard dMod color scheme | scale_fill_dMod |
| Scale dependent flux sensitivity Analysis | scaledependent |
| Scale invariant flux sensitivity Analysis | scaleinvariant |
| Gather statistics of a fitlist | stat.parlist |
| Calculate analytical steady states. | steadyStates |
| Calculated the steady states of a given model | steadyStateToolJulia |
| Elide character vector | strelide |
| Pad string to desired width | strpad |
| Submatrix of a matrix returning ALWAYS a matrix | submatrix |
| subset of an equation list | subset.eqnlist |
| Sum redundant columns | sumDuplicatedParsInDeriv |
| Remove redundant outer names | sumDuplicatedParsInObjlist |
| Summary of an equation vector | summary.eqnvec |
| Search for symmetries in the loaded model | symmetryDetection |
| Standard plotting theme of dMod | theme_dMod |
| DatapointL2 without env access | timepointL2_indiv |
| Non-Linear Optimization | trust trustL1 |
| Extract those lines of a parameter frame with unique elements in the value column | unique.parframe |
| Get variance-covariance matrix from trust result | vcov |
| Translate wide output format (e.g. from ode) into long format | 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 |
| Write equation list into a csv file | write.eqnlist |
| Model prediction function from data.frame | Xd |
| Model prediction function for ODE models without sensitivities. | Xf |
| Model prediction function for ODE models. | Xs |
| Generate a prediction function that returns times | Xt |
| Observation functions. | Y |
