Uncertainty Quantification and Global Sensitivity Analysis

Documentation for package ‘uqsa’ version 0.8.0

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A B C D E F G H K L M N O P R S T U V W Y misc

-- A --

ABCSMC	Performs and Approximate Bayesian Computation as a Particle Filter
abc_mcmc	Performs and Approximate Bayesian Computation Sampling of Model Parameters
as_cme	Interprets the provided model as a stochastic model
as_ode	Interpret a model as an ODE

-- B --

base<-

Convert to linear space

-- C --

change_temperature	Should 2 Markov chains exchange their temperatures
clear_yacas_environment	Clear Yacas variables
column	Get j-th column with names
conservation_law_analysis	Reduce the size of the system
CRNN	CRNN creates C code for a chemical reaction neural network
c_path	Retrieve information about the model's C code
c_path<-	Add information about the model's C code

-- D --

dCopulaPrior	Creates a prior probability density function
defaultDistance	default distance function for one experiment
determinePrefix	Determine a prefix from a character vector str of similar contents
dNormalPrior	dNormalPrior creates the density function of a multivariate normal distribution with independent components
dUniformPrior	dUniformPrior creates a uniform density function

-- E --

exact_normal_kld	Multivariate Normal Distribution KLD
experiments	Extract Measured Data and Simulation Experiment Instructions

-- F --

fi	Default gradient-Log-likelihood Function
fitCopula	Makes a Probability Density Estimate (from a sample)
formulae	Find a column that contains some kind of mathematic expression in a data.frame

-- G --

gatherReplicas	Collect statistical Replicas
gatherSample	gatherSample collects all sample points, from all files, with the given temperature
generate_code	Construct Code
gllf	Default gradient-log-likelihood Function
gNormalPrior	gNormalPrior creates the gradient function of a multivariate normal distribution with independent components, in log-space
grapes-at-grapes	Fetch an Attribute
gsa_binning	Global Sensitivity Analysis
gsa_saltelli	Outputs the global sensitivity scores SI and SIT, calculated by the Sobol-Homma-Saltelli method
gsl_odeiv2_CRNN	simulates a CRNN ode model with extra work
gsl_odeiv2_fi	simulates an ode model with extra work

-- H --

highCor	highCor returns ordered index-pairs of high to low correlation
high_level_metropolis	High Level Metropolis function
high_level_smmala	High Level SMMALA function

-- K --

kinetic_law_matrix	Split Kinetic Law
KLD	Kullback Leibler Divergence

-- L --

linear_scale	Interprets a character vector as names of logarithms
ll	Default Log-likelihood Function
loadSample_mpi	This function merges mpi-samples into one
log10ParMap	LOG10 parameter mapping used by the MCMC module
log10ParMapJac	LOG10 parameter mapping, jacobian
log2ParMap	LOG2 parameter mapping used by the MCMC module
log2ParMapJac	LOG2 parameter mapping, jacobian
logLikelihoodFunc	Default log-likelihood function
logParMap	NATURAL LOG parameter mapping used by the MCMC module
logParMapJac	NATURAL LOG parameter mapping, jacobian

-- M --

makeObjective	creates Objective functions from ingredients
mcmc	Markov Chain Monte Carlo
mcmc_init	Initialize the Markov chain
mcmc_mpi	The MPI version of the mcmc function
method	Find Integer
metropolis_update	Metropolis Update is an MCMC update function
model_from_tsv	model_from_tsv loads the content from a series of tsv files
modify<-	Modifies a value

-- N --

name_method

Reverse look-up of method name from key

-- O --

onlyCoefficients	Returns a list of reaction coefficients
onlyNames	Returns only the names in a reaction formula

-- P --

parse_concise	Read Concise Error Notation
pcDist	plots a sample in parallel coordinates
plot.experiments	plot function for experiments
print.cme	Print a Summary about the CME model
print.experiments	prints the simulation experiments
print.mcmcVariable	print information about the mcmc variable
print.ode	Print a summary about the ode
print.simulation	prints the simulation results
print.unit_of_measurement	Prints an interpretation string of a unit

-- R --

rCopulaPrior	rCopulaPrior returns a function that generates random values from the copula model
replace_powers	replace_powers does string manipulation
rNormalPrior	rNormalPrior returns a random vector generator
rUniformPrior	rUniformPrior returns a random vector generator

-- S --

saltelli_prior	Sample for the Sobol-Homma-Saltelli Global Sensitivity Analysis
scrnn	scrnn returns a closure around gsl_odeiv2_CRNN()
sensitivity.graph	plot the sensitivity matrix
shlib	Compile C code to shared library
showPosterior	showPosterior makes a pairs plot for a sample
simfi	This creates a closure that simulates the model, similar to simulator.c
simple.unit	Simple unit from string
simstoch	Simulate stochastic model
simulator.c	This creates a closure that simulates the model
small	This function reduces the sample to its effective size
smmala_update	SMMALA Update is an MCMC update function
so_path	Retrieve information about compiled code
so_path<-	Add information about compiled code
standard_error_matrix	Standard Error Matrix from an errors object
stoichiometric_matrix	The stoichiometric matrix of a reaction network
stoichiometry	This function returns a list of named stoichiometric vectors

-- T --

tune_step_size

Find a good Step-Size for a given MCMC Algorithm

-- U --

uncertainty	Find the uncertainty of values in a data.frame that is derived from a tsv file or similar
unit.from.string	Unit Interpreter
unit.id	Converts a unit to a string that works as an identifier
units_from_table	Get units from a data.frame column
unit_as_character	converts a unit data.frame into a printable string
uqsa_example	Load an example model for this package

-- V --

values

Find values in a data.frame that is derived from a tsv file or similar

-- W --

write_and_compile	Writes code to file and compiles
write_c_code	Write the C code to a file

-- Y --

yJacobian

Jacobian of string-math

-- misc --

%@%	Fetch an Attribute
%as%	%as% is a binary operator on strings with units in them
%has%	checks whether a variable has the named attributes
%otherwise%	This function can be used to specify default values
[.experiments	Subset experiments with preserved class
[.simulation	Subset simulations with preserved class