{"Package":"pmc","Version":"1.0.6","Title":"Phylogenetic Monte Carlo","Description":"Monte Carlo based model choice for applied phylogenetics of\ncontinuous traits. Method described in Carl Boettiger, Graham Coop,\nPeter Ralph (2012) Is your phylogeny informative? Measuring\nthe power of comparative methods, Evolution 66 (7)\n2240-51. .","Authors@R":"person('Carl', 'Boettiger', email='cboettig@gmail.com', role =c('aut', 'cre'))","URL":"https://github.com/cboettig/pmc","BugReports":"https://github.com/cboettig/pmc/issues","License":"CC0","LazyData":"true","VignetteBuilder":"knitr","Suggests":"covr, gridExtra, knitr, testthat, rmarkdown","Imports":"dplyr, geiger (>= 2.0.11), ggplot2, parallel, ouch, tidyr,\nphytools (>= 1.5-1)","RoxygenNote":"7.2.3","Encoding":"UTF-8","NeedsCompilation":"no","Packaged":"2023-10-02 22:38:10 UTC; cboettig","Author":"Carl Boettiger [aut, cre]","Maintainer":"Carl Boettiger ","Repository":"CRAN","Date/Publication":"2023-10-03 01:00:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/pmc_1.0.6.tar.gz","jsonAuthors":[{"name":"Carl Boettiger","email":"cboettig@gmail.com","maintainer":true}],"readme":"\n\n\n\n[![R-CMD-check](https://github.com/cboettig/pmc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cboettig/pmc/actions/workflows/R-CMD-check.yaml)\n[![CRAN\nstatus](https://www.r-pkg.org/badges/version/pmc)](https://cran.r-project.org/package=pmc)\n[![DOI](https://zenodo.org/badge/1822987.svg)](https://zenodo.org/badge/latestdoi/1822987)\n\n\nThis is a lightweight implementation of my `pmc` package focusing on\nwhat I think are the more common use cases (e.g. it will no longer\nsupport comparisons of a `geiger` model against an `ouch` model).\nFurther, it does not cover many of the newer model fitting that have\nbeen implemented since `pmc` was first released.\n\nThe goal of this release is mostly to provide compatibility with current\nversions of `geiger`.\n\n## Getting started\n\nInstall the package:\n\n``` r\nlibrary(\"devtools\")\ninstall_github(\"cboettig/pmc\")\n```\n\nA trivial example with data simulated from the `lambda` model.\n\n``` r\nlibrary(\"pmc\")\nlibrary(\"geiger\")\n#> Loading required package: ape\n#> Loading required package: phytools\n#> Loading required package: maps\nlibrary(\"phytools\")\nphy <- sim.bdtree(n=10)\ndat <- sim.char(rescale(phy, \"lambda\", .5), 1)[,1,]\nout <- pmc(phy, dat, \"BM\", \"lambda\", nboot = 50)\n#> Warning in geiger::fitContinuous(phy = tree, dat = data, model = model, : \n#> Parameter estimates appear at bounds:\n#> lambda\n```\n\nPlot the results:\n\n``` r\ndists <- data.frame(null = out$null, test = out$test)\nlibrary(\"ggplot2\")\nlibrary(\"tidyr\")\nlibrary(\"dplyr\")\n#> \n#> Attaching package: 'dplyr'\n#> The following object is masked from 'package:ape':\n#> \n#> where\n#> The following objects are masked from 'package:stats':\n#> \n#> filter, lag\n#> The following objects are masked from 'package:base':\n#> \n#> intersect, setdiff, setequal, union\ndists %>% \n gather(dist, value) %>%\n ggplot(aes(value, fill = dist)) + \n geom_density(alpha = 0.5) + \n geom_vline(xintercept = out$lr)\n```\n\n![](man/figures/README-unnamed-chunk-3-1.png)\n\n## Citation\n\nCarl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny\ninformative? Measuring the power of comparative methods, Evolution 66\n(7) 2240-51. ","jobInfo":{"package":"pmc","version":"1.0.6","parsingStatus":"success","parserVersion":2,"parsedAt":"2023-10-03T03:29:48+0000"}}

Description

Arguments