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