Jaatha-class            The "Jaatha" S4 class saves the basic
                        parameters for a Jaatha estimation procedure
Jaatha.confidenceIntervals
                        Function for calculating bootstrap confidence
                        intervals for jaatha estimates.
Jaatha.getCIsFromLogs   Function for calculating bootstrap confidence
                        intervals from logs of a previous run of
                        Jaatha.confidenceIntervals.
Jaatha.getLikelihoods   Gives the best estimates after a Jaatha search
Jaatha.getStartingPoints
                        Print Start points
Jaatha.initialSearch    Search the parameter space for good starting
                        positions
Jaatha.initialize       Initialization of a Jaatha estimation for
                        population genetics
Jaatha.refinedSearch    Iterative search for the maximum composite
                        likelihood parameters
Jaatha.setSeqgenExecutable
                        Set the path to the executable for seqgen
addFeature              Low level function for adding a new feature to
                        a demographic Model
calcJsfs                Calculate the JSFS from a list of segregating
                        sites statistics
calculateJsfs           Calculates the JSFS for data imported with ape
checkType               Checks if a variable is of a given type and
                        calls stop() on type mismatch
convertSimResultsToDataFrame
                        Converts simulation results into a data frame
                        that is usable for fitting a glm.
denormalize             Convert parameters from Jaatha's internal scale
                        into their natural scale
dm.addGrowth            Adds an growth or decline of the population
                        size of one population to a model.
dm.addMigration         Add migration/gene flow between two populations
                        to a demographic model
dm.addMutation          Adds mutations to a demographic model
dm.addMutationRateHeterogenity
                        Allows the mutation rate on different sites
                        within one locus to vary according to a Gamma
                        Distribution.
dm.addOutgroup          Adds an outgroup to a demographic model
dm.addParameter         Create a parameter that can be used for one or
                        more features
dm.addRecombination     Adds recombination events to a demographic
                        model
dm.addSampleSize        Sets how many individuals from each population
                        are sampled at time 0.
dm.addSizeChange        Adds an instantaneous change of the population
                        size of one population to a model.
dm.addSpeciationEvent   Adds a speciation event to a demographic model
dm.addSummaryStatistic
                        Adds a summary statistic to the model.
dm.addSymmetricMigration
                        Adds symmetric migration between all
                        populations
dm.createDemographicModel
                        Create a basic demographic model
dm.createThetaTauModel
                        Creates a standard "Theta/Tau" demopraphic
                        model.
dm.getGroups            Returns the groups currently in the model
dm.getLociLength        Gets how long the loci in a group are
dm.getLociNumber        Gets how many loci belong to a group of loci
dm.setLociLength        Defines the sequence length of each loci in a
                        group of loci
dm.setLociNumber        Defines how many identical loci belong to a
                        group of loci
dm.setMutationModel     Defines what mutation model is used for
                        simulations
dm.simSumStats          Simulates data according to a demographic model
estimateLogLikelihood   Estimates the likelihood for a parameter
                        combination
findBestParInBlock      Functions that uses the fitted GLMs to estimate
                        the parameters that have the highest
                        likelihood.
fitGlm                  Fits a Generalized Linear Model within a block.
fitGlmPoiTransformed    Fits a GLM for a summary statistics of type
                        "poisson.transformed" and "poisson.independent"
fitPoiSmoothed          Fits a GLM for a summary statistics of type
                        "poisson.smoothed"
jaatha-package          Fast estimation of demographic parameters
normalize               Convert parameters from the natural scale into
                        Jaatha's internal scale
runSimulations          The function that actually executes the
                        simulations from within Jaatha.
setCores                Function to set the number of cores that Jaatha
                        uses for simulations
simulateWithinBlock     This function executes simulations for a number
                        of random parameter values inside a block.
