jaatha: Simulation-Based Maximum Likelihood Parameter Estimation

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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.

Author
Paul Staab [aut, cre], Lisha Mathew [aut], Dirk Metzler [aut, ths]
Date of publication
2016-05-13 22:54:03
Maintainer
Paul Staab <develop@paulstaab.de>
License
GPL (>= 3)
Version
3.2.0
URLs

View on CRAN

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

Files in this package

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