jaatha: Simulation-Based Maximum Likelihood Parameter Estimation
Version 3.2.0

An estimation method that can use computer simulations to approximate maximum-likelihood estimates even when the likelihood function can not be evaluated directly. It can be applied whenever it is feasible to conduct many simulations, but works best when the data is approximately Poisson distributed. It was originally designed for demographic inference in evolutionary biology. It has optional support for conducting coalescent simulation using the 'coala' package.

AuthorPaul Staab [aut, cre], Lisha Mathew [aut], Dirk Metzler [aut, ths]
Date of publication2016-05-13 22:54:03
MaintainerPaul Staab <develop@paulstaab.de>
LicenseGPL (>= 3)
Version3.2.0
URL https://github.com/statgenlmu/jaatha
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("jaatha")

Getting started

README.md
Demographic Inference with Jaatha
Introduction to Jaatha

Popular man pages

boot_jaatha: Parametric Bootstrapping of Jaatha Estimates
coarsen_jsfs: Divides the joint site frequency spectrum (jsfs) into blocks...
create_jaatha_data: Prepare the observed data for Jaatha
create_jaatha_model: Specify a Model for a Jaatha Analysis
create_jaatha_stat: Create a summary statistic for Jaatha
get_start_pos: Determine good starting postions
jaatha: Simulation based maximum likelihood estimation
See all...

All man pages Function index File listing

Man pages

boot_jaatha: Parametric Bootstrapping of Jaatha Estimates
coarsen_jsfs: Divides the joint site frequency spectrum (jsfs) into blocks...
create_jaatha_data: Prepare the observed data for Jaatha
create_jaatha_model: Specify a Model for a Jaatha Analysis
create_jaatha_model.coalmodel: Use a coala model in Jaatha
create_jaatha_model.function: Specify a jaatha model using a simulation function
create_jaatha_stat: Create a summary statistic for Jaatha
estimate_llh: Estimate the Log-Likelihood for a given parameter combination
get_start_pos: Determine good starting postions
jaatha: Simulation based maximum likelihood estimation

Functions

approximate_llh Source code
approximate_llh.default Source code
approximate_llh.jaatha_model Source code
approximate_llh.jaatha_stat_basic Source code
boot_jaatha Man page Source code
calc_folded_jsfs_sums Source code
calc_poisson_llh Source code
coarsen_jsfs Man page Source code
convert_coala_sumstats Source code
create_block Source code
create_initial_blocks Source code
create_jaatha_data Man page Source code
create_jaatha_data.default Man page Source code
create_jaatha_model Man page Source code
create_jaatha_model.coalmodel Man page Source code
create_jaatha_model.default Source code
create_jaatha_model.function Man page Source code
create_jaatha_stat Man page Source code
create_test_data Source code
create_test_model Source code
determine_bpp Source code
do_initial_search Source code
do_zoom_in_search Source code
estimate_llh Man page Source code
estimate_local_ml Source code
fit_glm Source code
fit_glm.default Source code
fit_glm.jaatha_model Source code
fit_glm.jaatha_stat_basic Source code
get_start_pos Man page Source code
is_jaatha_data Source code
is_jaatha_model Source code
is_jaatha_result Source code
is_par_ranges Source code
is_single_logical Source code
is_single_numeric Source code
jaatha Man page Source code
multi_index_range Source code
optimize_llh Source code
print.jaatha_result Source code
require_package Source code
sample_seed Source code
stat_identity Source code
stat_sum Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/jaatha-intro.Rmd
inst/doc/jaatha-intro.R
inst/doc/jaatha-evolution.html
inst/doc/jaatha-intro.html
inst/doc/jaatha-evolution.R
inst/doc/jaatha-evolution.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-block.R
tests/testthat/test-fit-glm.R
tests/testthat/test-jaatha-log.R
tests/testthat/test-initialization.R
tests/testthat/test-likelihood.R
tests/testthat/test-tools.R
tests/testthat/test-sim-cache.R
tests/testthat/test-stat-cubes.R
tests/testthat/test-jaatha-data.R
tests/testthat/test-jaatha-model.R
tests/testthat/test-zzz-bootstrapping.R
tests/testthat/test-coala-interface.R
tests/testthat/test-jaatha-function.R
tests/testthat/test-par-ranges.R
NAMESPACE
NEWS.md
R
R/jaatha_model.R
R/initialization.R
R/jaatha_data.R
R/boot_jaatha.R
R/jaatha.R
R/simulation_cache.R
R/stat_cube.R
R/block.R
R/coala_interface.R
R/fit_glm.R
R/jaatha_log.R
R/tools.R
R/par_ranges.R
R/likelihood.R
R/stat_basic.R
vignettes
vignettes/jaatha-intro.Rmd
vignettes/jaatha-evolution.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/create_jaatha_model.Rd
man/create_jaatha_model.function.Rd
man/create_jaatha_stat.Rd
man/create_jaatha_data.Rd
man/jaatha.Rd
man/coarsen_jsfs.Rd
man/create_jaatha_model.coalmodel.Rd
man/get_start_pos.Rd
man/estimate_llh.Rd
man/boot_jaatha.Rd
jaatha documentation built on May 19, 2017, 11:37 p.m.

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