Dynamic Modeling and Parameter Estimation in ODE Models
Model Predictions
Print or pander equation list
Print equation vector
Pretty printing parameter transformations
Pretty printing for a parameter vector
Print object and its "default" attributes only.
L2 objective function for prior value
Profile-likelihood (PL) computation
Progress bar
Reduce replicated measurements to mean and standard deviation
Direct sum of objective functions
Add two lists element by element
Prediction function
Reparameterization
Compare data and model prediction by computing residuals
Place top elements into bottom elemens
Transform matrix A into reduced row echelon form this function is writ...
Standard dMod color palette
Standard dMod color scheme
Gather statistics of a fitlist
Calculate analytical steady states.
Elide character vector
Pad string to desired width
Submatrix of a matrix returning ALWAYS a matrix
subset of an equation list
Add reaction to reaction table
Coerce to a Data Frame
Coerce equation list into a data frame
Coerce to an equation vector
Coerce to eventlist
Generate objective list from numeric vector
Coerce object to a parameter frame
Select a parameter vector from a parameter frame.
Select attributes.
Embed two matrices into one blockdiagonal matrix
Combine several data.frames by rowbind
Compare two objects and return differences
Compile one or more prdfn, obsfn or parfn objects
Profile uncertainty extraction
Determine conserved quantites by finding the kernel of the stoichiomet...
Compute a differentiable box prior
Soft L2 constraint on parameters
List, get and set controls for different functions
Coordinate transformation for data frames
Access the covariates in the data
Generate a datalist object
L2 objective function for validation data point
Define parameter transformations by define(), branch() and `insert...
Summary of an equation vector
Symbolic time derivative of equation vector given an equation list
Generate eqnlist object
Generate equation vector object
Eventlist
Alternative version of expand.grid
Fit an error model
Return some useful forcing functions as strings
Encode equation vector in format with sufficient spaces
Evaluation of algebraic expressions defined by characters
Get coefficients from a character
Extract the conditions of an object
Extract the derivatives of an object
Extract the equations of an object
Generate list of fluxes from equation list
Determine loaded DLLs available in working directory
Extract the observables of an object
Extract the parameters of an object
Generate a table of reactions (data.frame) from an equation list
Open last plot in external pdf viewer
Multiplication of objective functions with scalars
An identity function which vanishes upon concatenation of fns
Time-course data for the JAK-STAT cell signaling pathway
Bind named list of data.frames into one data.frame
Construct fitlist from temporary files.
Load shared object for a dMod object
Translate long to wide format (inverse of wide2long.matrix)
Print list of dMod objects in .GlobalEnv
dMod match function arguments
Get modelname from single object (used internally)
Get and set modelname
Reproducibly construct "random" parframes
Non-Linear Optimization, multi start
Compute the negative log-likelihood
L2 norm between data and model prediction
Find integer-null space of matrix A
Objective frame
Generate objective list
Prediction frame
Observation function
Generate the model objects for use in Xs (models with sensitivities)
Generate a parameter transformation function
Parameter transformation function
Prediction list
Generate a parameter frame
Parameter list
Parameter vector
Parameter transformation
Parameter transformation (implicit)
Plot a list data points
Plot a parameter list.
Plot a list of model predictions and a list of data points in a combin...
Plot a list data points
Plot Fluxes given a list of flux Equations
Plot parameter values for a fitlist
Profile likelihood: plot of the parameter paths.
Plot a list of model predictions
Profile likelihood plot
Plot residuals for a fitlist
Plotting objective values of a collection of fits
Direct sum of datasets
Direct sum of functions
Search for symmetries in the loaded model
Standard plotting theme of dMod
Concatenation of functions
Non-Linear Optimization
Extract those lines of a parameter frame with unique elements in the v...
Translate wide output format (e.g. from ode) into long format
Translate wide output format (e.g. from ode) into long format
Translate wide output format (e.g. from ode) into long format
Translate wide output format (e.g. from ode) into long format
Write equation list into a csv file
Compute the weighted residual sum of squares
Model prediction function from data.frame
Model prediction function for ODE models without sensitivities.
Model prediction function for ODE models.
Generate a prediction function that returns times
Observation functions.
The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives. The methods used in dMod were published in Kaschek et al, 2019, <doi:10.18637/jss.v088.i10>.