%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
ABCSMC                  Performs and Approximate Bayesian Computation
                        as a Particle Filter
CRNN                    CRNN creates C code for a chemical reaction
                        neural network
KLD                     Kullback Leibler Divergence
[.experiments           Subset experiments with preserved class
[.simulation            Subset simulations with preserved class
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
base<-                  Convert to linear space
c_path                  Retrieve information about the model's C code
c_path<-                Add information about the model's C code
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
dCopulaPrior            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
defaultDistance         default distance function for one experiment
determinePrefix         Determine a prefix from a character vector str
                        of similar contents
exact_normal_kld        Multivariate Normal Distribution KLD
experiments             Extract Measured Data and Simulation Experiment
                        Instructions
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
gNormalPrior            gNormalPrior creates the gradient function of a
                        multivariate normal distribution with
                        independent components, in log-space
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
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
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
kinetic_law_matrix      Split Kinetic Law
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
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
name_method             Reverse look-up of method name from key
onlyCoefficients        Returns a list of reaction coefficients
onlyNames               Returns only the names in a reaction formula
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
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
replace_powers          replace_powers does string manipulation
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
tune_step_size          Find a good Step-Size for a given MCMC
                        Algorithm
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
unit_as_character       converts a unit data.frame into a printable
                        string
units_from_table        Get units from a data.frame column
uqsa_example            Load an example model for this package
values                  Find values in a data.frame that is derived
                        from a tsv file or similar
write_and_compile       Writes code to file and compiles
write_c_code            Write the C code to a file
yJacobian               Jacobian of string-math
