Function reference • uqsa

User Functions

exported functions

ABCMCMC(): Performs and Approximate Bayesian Computation Sampling of Model Parameters

checkFitWithPreviousExperiments(): ABC acceptance of currently sampled values given old data (Prior)

checkModel(): checkModel tries to establish the simulation file for a given model

determinePrefix(): Determine a prefix from a character vector str of similar contents

dCopulaPrior(): copulaPrior creates a prior probability density function

dNormalPrior(): dNormalPrior creates the density function of a multivariate normal distribution with independent components

dUniformPrior(): dUniformPrior creates a uniform density function

defaultAcceptance(): default ABC acceptance probability function for one experiment

defaultDistance(): default distance function for one experiment

fitCopula(): Makes a Probability Density Estimate (from a sample)

generateCode(): Write C code

generateRCode(): Write R code

getMCMCPar(): Selects MCMC scheme specific setup parameters

gsa_binning(): Global Sensitivity Analysis

gsa_saltelli(): Outputs the global sensitivity scores SI and SIT, calculated by the Sobol-Homma-Saltelli method

saltelli_prior(): Outpts the random sample on which to perform the Sobol-Homma-Saltelli global sensitivity analysis

importReactionsSSA(): Functions to construct and run the stochastic simulation using GillespieSSA2 package

is.invertible(): checks whether a given matrix is a valid, invertible fisherInformation

log10ParMap(): LOG10 parameter mapping used by the MCMC module

log10ParMapJac(): LOG10 parameter mapping, jacobian

logParMap(): NATURAL LOG parameter mapping used by the MCMC module

logParMapJac(): NATURAL LOG parameter mapping, jacobian

makeGillespieModel(): makeGillespieModel interprets the provided SBtab file as a stochastic model

makeIndepCopula(): Copula Formulation for Uniform Prior Distributions

makeObjective(): creates Objective functions from ingredients

makeObjectiveSSA(): Function that creates the objective function

mcmc(): Markov Chain Monte Carlo

mcmcInit(): Initialize the Markov chain

mcmcUpdate(): This function proposes an MCMC candidate variable, and either accepts or rejects the candidate

parUpdate(): Updates Parameter Values

plotSimualtionsFromSBtab(): Simulate and plot Data and Simulation

preCalibration(): Determine a starting value for ABC's delta

replace_powers(): replace_powers

rCopulaPrior(): rCopulaPrior returns a function that generates random values from the copula model

rNormalPrior(): rNormalPrior returns a random vector generator

rUniformPrior(): rUniformPrior returns a random vector generator

sensitivity.graph(): plot the sensitivity matrix

showPosterior(): showPosterior makes a pairs plot for a sample

simulator.stoch(): Function that creates a closure that simulates a stochastic trajectory with the Gillespie algorithm given certain experimental conditions and a parameter vector, and computes the distance between the simulation and the experimental data

simstoch(): Simulate stochastic model

simulator.c(): This creates a closure that simulates the model

uqsa_example(): Load an example model for this package

`%otherwise%`: This function can be used to specify default values

smmala_move(): SMMALA move

smmala_move_density(): SMMALA transition kernel density

ggplotTimeSeries(): Plot time series simulations with experimental data

ggplotTimeSeriesStates(): Plot time series simulation with state variables

change_temperature(): Should 2 Markov chains exchange their temperatures

loadSample_mpi(): This function merges mpi-samples into one

mcmc_mpi(): The MPI version of the mcmc function

simc(): This creates a closure that simulates the model, similar to simulator.c

yacasMath(): yacasMath converts math to Ryacas compatible math

yJacobian(): Jacobian of string-math

SMMALA specific functions

helper functions

simfi(): This creates a closure that simulates the model, similar to simulator.c

simfiGaussianLogLikelihood(): SMMALA The default Extractor of the log-likelihood computed bu the simfi solver

simfiGaussianGradLogLikelihood(): SMMALA Extract the gradient of the log-likelihood from the simfi solver's return value

simfiGaussianFILL(): SMMALA Extract the approximate Fisher infomration from the simfi results

gsl_odeiv2_fi(): simulates an ode model with extra work

Experimental functions

for the stochastic solver (wip)

makeGillespieModel(): makeGillespieModel interprets the provided SBtab file as a stochastic model

ccc(): Concentration to Count Conversion

generateGillespieCode(): Generate C Code to solve a model stochastically

onlyCoefficients(): Returns a list of reaction coefficients

onlyNames(): Returns only the names in a reaction formula

parameterConversion(): Returns information about parameter conversion

stoichiometry(): This function returns a list of named stoichiometric vectors

scaleParameter(): Retruns a string that contains code to scale the parameter

Internal Functions

not exported functions

generateCodeFromFile(): Write C code

match.coefficients(): find the coefficients in a formula

match.names(): Find the variable names in a formula

observable.mean.in.bin(): The mean value of an observable value given a parameter bin

parameter.from.kinetic.law(): Attempt to find multiplicative reaction rate coefficients

parse.formula(): Splits a formula into a left and right side

parse.kinetic(): Find forward and backward component in a reaction kinetic

propensity(): propensity creates a propensity formula

sum.of.bin.variance(): Weighted Sum of Bin-specific variances

uqsa uqsa-package: uqsa: Uncertainty Quanitification and Global Sensitivity Analysis via ABC sampling

getDose(): Get the values of the input for a series of dose response experiments

plotTimeSeries(): Plot time series simulations with experimental data

Rmpi_swap_temperatures(): Communicate with other ranks and swap beta

fisherInformationFromGSA(): Calculate Global Fisher Information

fisherInformationFunc(): Fisher Information from Sensitivity

gatherSample(): gatherSample collects all sample points, from all files, with the given temperature

gradLogLikelihoodFunc(): Default log-likelihood function, gradient

gradLog_NormalPrior(): Gradient of the logarithm of a normal prior

`%has%`: checks whether a variable has the named attributes

loadODE(): Load an ODE model from a file

loadSubSample_mpi(): This function merges mpi-samples into one

logLikelihoodFunc(): Default log-likelihood function

parameters_from_expressions_func(): Function that creates a function that reads the SBtab expression table and computes the expressions (which are functions of parameters) given the parameters passed in input

pbdMPI_bcast_reduce_temperatures(): Broadcast to other ranks and swap temperatures with any of them

pbdMPI_swap_temperatures(): Communicate with other ranks and swap beta

sampleWithNoise(): (for testing) A non-Copula sampling function as fallback

simcf(): This creates a closure that simulates the model, similar to simulator.c

swap_points_locally(): Swap the end-points of two Markov chains

writeCFunction(): Write C Function

ggplotDoseResponse(): Plot dose response simulations with experimental data

plotTimeSeriesBase(): plot function for experiments