Package: jaatha 3.2.5
Dirk Metzler
jaatha: Simulation-Based Maximum Likelihood Parameter Estimation
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 (Naduvilezhath et al., 2011 <doi:10.1111/j.1365-294X.2011.05131.x>, Mathew et al., 2013 <doi:10.1002/ece3.722>). It has optional support for conducting coalescent simulation using the 'coala' package.
Authors:
jaatha_3.2.5.tar.gz
jaatha_3.2.5.zip(r-4.5)jaatha_3.2.5.zip(r-4.4)jaatha_3.2.5.zip(r-4.3)
jaatha_3.2.5.tgz(r-4.4-any)jaatha_3.2.5.tgz(r-4.3-any)
jaatha_3.2.5.tar.gz(r-4.5-noble)jaatha_3.2.5.tar.gz(r-4.4-noble)
jaatha_3.2.5.tgz(r-4.4-emscripten)jaatha_3.2.5.tgz(r-4.3-emscripten)
jaatha.pdf |jaatha.html✨
jaatha/json (API)
NEWS
| # Install 'jaatha' in R: |
| install.packages('jaatha', repos = c('https://statgenlmu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/statgenlmu/jaatha/issues
Last updated 10 months agofrom:805633be96. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 12 2024 |
| R-4.5-win | OK | Oct 12 2024 |
| R-4.5-linux | OK | Oct 12 2024 |
| R-4.4-win | OK | Oct 12 2024 |
| R-4.4-mac | OK | Oct 12 2024 |
| R-4.3-win | OK | Oct 12 2024 |
| R-4.3-mac | OK | Oct 12 2024 |
Exports:boot_jaathacoarsen_jsfscreate_jaatha_datacreate_jaatha_modelcreate_jaatha_model.coalmodelcreate_jaatha_model.functioncreate_jaatha_statestimate_llhjaatha
Dependencies:assertthatR6
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Parametric Bootstrapping of Jaatha Estimates | boot_jaatha |
| Divides the joint site frequency spectrum (jsfs) into blocks and returns the sum of the jsfs entries for each block. | coarsen_jsfs |
| Prepare the observed data for Jaatha | create_jaatha_data create_jaatha_data.default |
| Specify a Model for a Jaatha Analysis | create_jaatha_model |
| Use a coala model in Jaatha | create_jaatha_model.coalmodel |
| Specify a jaatha model using a simulation function | create_jaatha_model.function |
| Create a summary statistic for Jaatha | create_jaatha_stat |
| Estimate the Log-Likelihood for a given parameter combination | estimate_llh |
| Simulation based maximum likelihood estimation | jaatha |
