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| jaatha-package | Fast estimation of demographic parameters |
| addFeature | Low level function for adding a new feature to a demographic Model |
| calculateJsfs | Calculates the JSFS for data imported with ape |
| callMs | Function to perform simulation using ms |
| 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 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-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.initialize | Initialization of a Jaatha estimation for population genetics |
| Jaatha.initialSearch | Search the parameter space for good starting positions |
| Jaatha.refinedSearch | Iterative search for the maximum composite likelihood parameters |
| Jaatha.setSeqgenExecutable | Set the path to the executable for seqgen |
| 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. |