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