adeverse / adephylo Goto Github PK

Exploratory analyses for the phylogenetic comparative method

R 66.19% C 33.81%

adephylo's Introduction

adephylo

Exploratory Analyses for the Phylogenetic Comparative Method

Please note! Since January 2024, this repository has belonged to the adeverse organization. To avoid confusion, we strongly recommend updating any existing local clones to point to the new repository URL. You can do this by using git remote on the command line:

git remote set-url origin [email protected]:adeverse/adephylo.git

git remote set-url origin https://github.com/adeverse/adephylo.git

Installing adephylo

To install the development version from github:

library(devtools)
install_github("adeverse/adephylo")

The stable version can be installed from CRAN using:

install.packages("adephylo")

Once installed, the package can be loaded using:

library("adephylo")

Development team

Authors/developers

adephylo is developed by:

Thibaut Jombart
Stéphane Dray
Anders Ellern Bilgrau

Maintainer

Aurélie Siberchicot

adephylo's People

Contributors

Stargazers

Watchers

Forkers

aebilgrau

adephylo's Issues

Add developers to project

Stephane Dray [email protected], Anders Ellern Bilgrau [email protected]

Use roxygen2 for documentation

We should be using roxygen2 to document the package.
Should be mandatory for new contributions, and we should try to migrate the rest of the doc.
See related thread #6

Add travis support

migrate old doc to roxygen2

might need to do this on a separate branch

abouheif.moran() plots (and output?) differ from earlier versions

I've been trying to interpret the output of the abouheif.moran() tests and one of the problems I'm running into is that the output seems to have changed between versions.

For example, the vignette from v.1.1-6 has the following output:adephylo-aboutest-v1.1-6.pdf. This figure shows a nice histogram showing the distribution of expected and observed values.

However, the current vignette (v1.1-10) shows the following figure:
adephylo-aboutest-v1.1-10.pdf. Just an observation and a block.

I'm wondering if this is related to the output of the Abouheif test which seems to have Infinite Std errors and either significant or non significant values (either 1.000 or 0.001):

tre <- read.tree(text=ungulates$tre)
x <- phylo4d(tre, ungulates$tab)

Found more than one class "phylo" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘treeio’

## Abouheif's tests for each trait
myTests <- abouheif.moran(x)
myTests

class: krandtest lightkrandtest 
Monte-Carlo tests
Call: as.krandtest(sim = matrix(res$result, ncol = nvar, byrow = TRUE), 
    obs = res$obs, alter = alter, names = test.names)

Number of tests:   4 

Adjustment method for multiple comparisons:   none 
Permutation number:   999 
  Test       Obs Std.Obs   Alter Pvalue
1 afbw 0.1653920    -Inf greater  1.000
2  mnw 0.3681410     Inf greater  0.001
3  fnw 0.3843272     Inf greater  0.001
4   ls 0.3002425     Inf greater  0.001

Have I misunderstood something, or is there a bug?

master: functional devel version, meant to be used by people, so it should be relatively safe. Please do not push changes preventing the package from being installed or breaking backward compatibility unless this has been agreed on, and avoid warnings at all cost - we need travis's green light.
newfeatures: used for pushing changes that still need testing/checking; warnings are fine, but avoid pushing changes preventing the package from installing

Experimental changes

For experimental changes, the best course of action is fork the project and make a pull request when your patch is ready.
Other (unused) branches

roxygen2: was used for migrating the doc of the package to roxygen2 (was manual before); not fully integrated, migration is only partial at this stage. This is an old branch.
gh-pages: would be used for a website on github pages; not used at the mom