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 |
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.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.addSymmetricMigration | Adds symmetric migration between all populations |
dm.createDemographicModel | Create a basic demographic model |
dm.createThetaTauModel | Creates a standard "Theta/Tau" demopraphic model. |
dm.setMutationModel | Defines what mutation model is used for simulations |
dm.simSumStats | Simulates data according to a demographic model and calculates summary statistics form it |
getLogFile | Gets the current logging file |
getLogLevel | Gets the current logging level |
Jaatha-class | The "Jaatha" S4 class saves the basic parameters for a Jaatha estimation procedure |
Jaatha.defaultSumStats | These are the default summary statistics for Jaatha |
Jaatha.getLikelihoods | Gives the best estimates after a Jaatha search |
Jaatha.getStartingPoints | Print Start points |
Jaatha.initialize | Basic initialization of a Jaatha estimation |
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 |
setLogging | Function to activate/change logging |