Man pages for dkaschek/dMod
Dynamic Modeling and Parameter Estimation in ODE Models
| addReaction | Add reaction to reaction table |
| addTrafoForPaths | transform parametersets from the profiles for path plotting |
| appendObj | Append an objective function to a basic dMod.frame |
| appendParframes | Make a column "parframes" out of "fits" |
| as.data.frame.dMod | 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 | 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 |
| check_and_sanitize_prediction | Run some checks on the prediction in normL2_indiv |
| checkout_hypothesis | Load one row of a dMod.frame into the .GlobalEnv |
| 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... |
| 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 |
| createExample | Open a unit test template. |
| datalist | Generate a datalist object |
| datapointL2 | L2 objective function for validation data point |
| datapointL2_indiv | DatapointL2 without access to stored predictions |
| define | Define parameter transformations by 'define()', 'branch()'... |
| detectFreeCores | Detect number of free cores (on UNIX) |
| distributed_computing | Run an any R function on a remote HPC system with SLURM |
| dMod.frame | Generate a dMod.frame |
| dot | Symbolic time derivative of equation vector given an equation... |
| eqnlist | Generate eqnlist object |
| eqnvec | Generate equation vector object |
| eventlist | Eventlist |
| exmpextr | Extract an example from a unit test file. |
| expand.grid.alt | Alternative version of expand.grid |
| extractExamples | Extract example from unit tests. |
| fitErrorModel | Fit an error model using maximum likelihood estimation |
| 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 |
| getElements | Get Symbols and Numeric constants from a character |
| getEquations | Extract the equations of an object |
| getEstGridParameterMapping | Get Parameter mappings outer.estgrid - inner.estgrid |
| getFluxes | Generate list of fluxes from equation list |
| getLinVars | Identify linear variables in an equation vector using sympy |
| getLocalDLLs | Determine loaded DLLs available in working directory |
| getObservables | Extract the observables of an object |
| getParameters | Extract the parameters of an object |
| getParameters.data.table | Title |
| getParametersToEstimate | Determine which parameters need sensitivities |
| getParGrids | Get est.grid and fixed.grid |
| getReactions | Generate a table of reactions (data.frame) from an equation... |
| getStepIndices | Get the indices of the n largest (not necessarily best) steps... |
| getSteps | Get the rows of the n largest steps of a parframe |
| ggopen | Open last plot in external pdf viewer |
| grapes-.-times-grapes | Multiplication of objective functions with scalars |
| gridlist | Collect grids in list |
| Id | An identity function which vanishes upon concatenation of fns |
| import_sbml | Import an SMBL model |
| indiv_addGlobalParsToGridlist | Add single-valued parameters to the pargrids |
| indiv_addLocalParsToGridList | Add individualized parameters to grids |
| init_empty_objlist | Create an objlist with zeros as entries |
| installJuliaForSteadyStates | Install the julia setup |
| jakstat | Time-course data for the JAK-STAT cell signaling pathway |
| lbind | Bind named list of data.frames into one data.frame |
| loadDLL | Load shared object for a dMod object |
| load.parlist | Construct fitlist from temporary files. |
| long2wide | Translate long to wide format (inverse of wide2long.matrix) |
| lsdMod | Print list of dMod objects in .GlobalEnv |
| make_pars | Extract pars, fixed and parnames from grids for a given... |
| 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 |
| mutatedMod.frame | A version of dplyr::mutate |
| nll | Compute the negative log-likelihood |
| nll_ALOQ | Non-linear log likelihood for the ALOQ part of the data |
| nll_BLOQ | Non-linear log likelihood for the BLOQ part of the data |
| normL2 | L2 norm between data and model prediction |
| normL2_indiv | Fast normL2 |
| nullZ | Find integer-null space of matrix A |
| objframe | Objective frame |
| objlist | Generate objective list |
| objtimes | Get vector of logarithmically spaced time points |
| obsfn | Observation function |
| odemodel | Generate the model objects for use in Xs (models with... |
| optimize | Optimize an Objective Function using Various Optimization... |
| optionsLSODES | Get default arguments for integrators |
| 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) |
| P_indiv | Title |
| plotArray | Plot an array of trajectories along the profile of a... |
| plotCombined | Plot a list of model predictions and a list of data points in... |
| plotData | Plot a list data points |
| plot.datalist | Plot a list data points |
| plotFluxes | Plot Fluxes given a list of flux Equations |
| plot.parlist | Plot a parameter list. |
| plotPars | Plot parameter values for a fitlist |
| plotPaths | Profile likelihood: plot of the parameter paths. |
| plotPathsMulti | Profile likelihood: plot all parameter paths belonging to one... |
| plotPrediction | Plot a list of model predictions |
| plotProfile | Profile likelihood plot |
| plotProfilesAndPaths | Profile likelihood: plot profiles along with their parameter... |
| plotResiduals | Plot residuals for a fitlist |
| plotValues | Plotting objective values of a collection of fits |
| plus-.datalist | Direct sum of datasets |
| plus-.fn | Direct sum of functions |
| plus-.objfn | Direct sum of objective functions |
| plus-.objlist | Add two lists element by element |
| prdfn | Prediction function |
| prdframe | Prediction frame |
| PRD_indiv | Title |
| prdlist | Prediction list |
| predict.prdfn | Model Predictions |
| predtimes | Get a vector of linearly spaced time points for prediction |
| print0 | Print object and its "default" attributes only. |
| 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 |
| priorL2 | L2 objective function for prior value |
| profile | Profile-likelihood (PL) computation |
| profile_pars_per_node | Generate parameter list for distributed profile calculation |
| progressBar | Progress bar |
| python_version_request | Check if rPython comes with the correct Python version |
| python_version_rpython | Get the Python version to which rPython is linked |
| python_version_sys | Check which Python versions are installed on the system |
| reduceReplicates | Reduce replicated measurements to mean and standard deviation |
| reduceReplicates.character | Method for files (character) |
| reduceReplicates.data.frame | Method for data frames |
| renameDerivPars | Update attr(prediction, "deriv") to correct par.grid.outer... |
| renameDerivParsInObjlist | Rename the gradient and hessian of an objlist |
| repar | Reparameterization |
| repWithNames | Named repititions |
| 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... |
| runbg | Run an R expression in the background (only on UNIX) |
| runbg_bwfor | Run an R expression on the bwForCluster |
| runbg_bwfor_slurm | Run an R expression on the bwForCluster via sshpass and slurm |
| runbg_bwfor_sshpass | Run an R expression on the bwForCluster via sshpass |
| runbgInstall | Remote install dMod to a ssh-reachable host |
| saveShiny | Save the necessary objects for dModtoShiny with the correct... |
| saveShiny_dMod.frame | SaveShiny for dMod.frames |
| scale_color_dMod | Standard dMod color palette |
| scaledependent | Scale dependent flux sensitivity Analysis |
| scale_fill_dMod | Standard dMod color scheme |
| scaleinvariant | Scale invariant flux sensitivity Analysis |
| stat.parlist | Gather statistics of a fitlist |
| steadyStates | Calculate analytical steady states. |
| steadyStateToolJulia | Calculated the steady states of a given model |
| 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 |
| sumDuplicatedParsInDeriv | Sum redundant columns |
| sumDuplicatedParsInObjlist | Remove redundant outer names |
| summary.eqnvec | Summary of an equation vector |
| symmetryDetection | Search for symmetries in the loaded model |
| theme_dMod | Standard plotting theme of dMod |
| timepointL2_indiv | DatapointL2 without env access |
| times-.fn | Concatenation of functions |
| trust | Non-Linear Optimization |
| unique.parframe | Extract those lines of a parameter frame with unique elements... |
| vcov | Get variance-covariance matrix from trust result |
| 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 |
| x2logx | Log-transform variables in an equation vector using SymPy |
| Xd | Model prediction function from data.frame |
| Xf | Model prediction function for ODE models without... |
| Xs | Model prediction function for ODE models. |
| Xt | Generate a prediction function that returns times |
| Y | Observation functions. |
