This package enables users to access MongoDB by running queries
and returning their results in R data frames. Usually, data in MongoDB is
only available in the form of a JSON document. jSonarR uses data
processing and conversion capabilities in the jSonar Analytics Platform
and the JSON Studio Gateway (http://www.jsonstudio.com), to convert it to
a tabular format which is easy to use with existing R packages.

Jaatha - A Fast Parameter Estimation Method for Evolutionary
Biology
Lisha Mathew, Paul R. Staab and Dirk Metzler
Jaatha is a composite likelihood method for inferring
evolutionary parameters using genetic data. Given a model of
the evolutionary history of two biological populations as well
as SNP data from multiple individuals from each population, it
estimates model parameters like the time of separation of both
species.
methods, foreach, phyclust (>= 0.1-14), ape, Rcpp
'aaa_SimProgram.R' 'Block.R' 'DataProcessor.R'
'DemographicModel.R' 'helper_functions.R' 'Jaatha.R'
'ModelFitting.R' 'parallelization.R' 'read_fasta.R'
'sim_program_ms.R' 'sim_program_seqgen.R' 'Simulator.R'
'summary_statistics.R'

A Fast Parameter Estimation Method for Evolutionary Biology

Jaatha is a composite likelihood method for inferring evolutionary
parameters using genetic data. Given a model of the evolutionary history of
two biological populations as well as SNP data from multiple individuals
from each population, it estimates model parameters like the time of
separation of both species.
'aaa_SimProgram.R' 'Block.R' 'calc_likelihood.R'
'DemographicModel.R' 'glm_fitting.R' 'helper_functions.R'
'initial_search.R' 'Jaatha.R' 'parallelization.R'
'read_fasta.R' 'refined_search.R' 'sim_program_ms.R'
'sim_program_seqgen.R' 'simulate_dm.R'
'simulate_within_block.R' 'summary_statistics.R'

foreach (>= 1.2.0-1), phyclust (>= 0.1-14), parallel
'aaa_SimProgram.R' 'Block.R' 'confidence_intervals.R'
'DemographicModel.R' 'estimate_log_likelihood.R'
'find_best_par_in_block.R' 'fit_glm.R' 'helper_functions.R'
'initial_search.R' 'Jaatha.R' 'normalize.R' 'parallelization.R'
'read_fasta.R' 'refined_search.R' 'run_simulations.R'
'sim_program_ms.R' 'sim_program_seqgen.R'
'simulate_within_block.R' 'summary_statistics.R'
'sim_likelihood.R'