pmc

:package: Phylogenetic Monte Carlo: Quantifying Uncertainty in Phylogenetic Methods (now on CRAN)

https://github.com/cboettig/pmc

Science Score: 49.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary

Keywords from Contributors

fish fishbase taxonomy

Last synced: 7 months ago · JSON representation

Repository

:package: Phylogenetic Monte Carlo: Quantifying Uncertainty in Phylogenetic Methods (now on CRAN)

Basic Info

Host: GitHub
Owner: cboettig
Language: R
Default Branch: master
Homepage: http://carlboettiger.info
Size: 248 KB

Statistics

Stars: 2
Watchers: 2
Forks: 1
Open Issues: 3
Releases: 1

Created almost 15 years ago · Last pushed over 2 years ago

Metadata Files

Readme Changelog Contributing Codemeta

README.Rmd

---
output:
  md_document:
    variant: markdown_github
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  cache = TRUE,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```



 
  [![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)
[![CRAN status](https://www.r-pkg.org/badges/version/pmc)](https://cran.r-project.org/package=pmc)
[![DOI](https://zenodo.org/badge/1822987.svg)](https://zenodo.org/badge/latestdoi/1822987)
  



This is a lightweight implementation of my `pmc` package focusing on what I think are the more common use cases (e.g. it will no longer support comparisons of a `geiger` model against an `ouch` model). Further, it does not cover many of the newer model fitting that have been implemented since `pmc` was first released. 

The goal of this release is mostly to provide compatibility with current versions of `geiger`.

## Getting started


Install the package:

```{r eval=FALSE}
library("devtools")
install_github("cboettig/pmc")
```

A trivial example with data simulated from the `lambda` model. 

```{r}
library("pmc")
library("geiger")
library("phytools")
phy <- sim.bdtree(n=10)
dat <- sim.char(rescale(phy, "lambda", .5), 1)[,1,]
out <- pmc(phy, dat, "BM", "lambda", nboot = 50)

```

Plot the results:

```{r}
dists <- data.frame(null = out$null, test = out$test)
library("ggplot2")
library("tidyr")
library("dplyr")
dists %>% 
  gather(dist, value) %>%
  ggplot(aes(value, fill = dist)) + 
  geom_density(alpha = 0.5) + 
  geom_vline(xintercept = out$lr)

```


## Citation

Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51.

Owner

Name: Carl Boettiger
Login: cboettig
Kind: user
Company: UC Berkeley

Website: http://carlboettiger.info
Repositories: 173
Profile: https://github.com/cboettig

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GitHub Events

Total

Last Year

Committers

Last synced: 8 months ago

All Time

Total Commits: 62
Total Committers: 4
Avg Commits per committer: 15.5
Development Distribution Score (DDS): 0.21

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Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Carl Boettiger	c**g@g**m	49
cboettig	r**o@e**m	7
Carl Boettiger	c**g@g**m	5
Seth Ariel Green	s**e@g**m	1

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Last synced: 7 months ago

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Total issues: 5
Total pull requests: 3
Average time to close issues: 2 minutes
Average time to close pull requests: about 2 months
Total issue authors: 2
Total pull request authors: 2
Average comments per issue: 0.6
Average comments per pull request: 0.67
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

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jackiebrown (1)

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Total packages: 1
Total downloads:
- cran 346 last-month
Total docker downloads: 43,390

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 11
Total maintainers: 1

cran.r-project.org: pmc

Phylogenetic Monte Carlo

Homepage: https://github.com/cboettig/pmc
Documentation: http://cran.r-project.org/web/packages/pmc/pmc.pdf
License: CC0
Latest release: 1.0.6
published over 2 years ago

Versions: 11
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 346 Last month
Docker Downloads: 43,390

Rankings

Dependent packages count: 18.7%

Forks count: 21.9%

Average: 27.2%

Stargazers count: 28.5%

Downloads: 31.2%

Dependent repos count: 35.5%

Maintainers (1)

cboettig@gmail.com

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

dplyr * imports
geiger * imports
ggplot2 * imports
ouch * imports
parallel * imports
tidyr * imports
covr * suggests
gridExtra * suggests
knitr * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

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Open Source Science

pmc

Science Score: 49.0%

Keywords from Contributors

Repository

Basic Info

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README.Rmd

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CodeMeta (codemeta.json)

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