ALIEN: The aim of the package is to predict All Links In Ecological Networks

Incoming content

Methods

Predictions

• Direct matching centrality
• Indirect matching centrality (latent ~ traits)
• 4th corner (Brown et al. MEE 2014)
• Niche binary
• Niche probabilistic
• KNN

To be implemented

• Ives' phylo (2006, Amnat see package picante) (GB)

Installation

install.packages("remotes")
remotes::install_github("TheoreticalEcosystemEcology/alien")

Generate package metadata

To build the metadata files (i.e. NAMESPACE, DESCRIPTION), devtools must be installed, then follow the three following steps (assuming your working diretory is the folder containing this package):

## Load your current version of the package
devtools::load_all()

## Create man pages
devtools::document()

## Testing the code with testthat package
devtools::test()

Contribute to this package

Development pratices

• the master branch is protected -- code can only arrive in it after a pull request, that has to be reviewed and approved by Steve
• everyone work on branches in this repo
• git fetch / git pull before you do anything else
• new branches must be made from master -- if not, you are responsible for rebasing
• good commit messages are 72 chars on the first line and explain what has been done in the imperative tone. A good rule of thumb is that if you say "If merged, this commit will" before the commit message, it should be a sentence. A good commit message is: add informations about development practices. A bad commit message is CONTRIBUTING changes
• if the branching complexity of your function is > 3 (number of nested for / if / while), rewrite

Styleguide

• function names are explicit and with CamelCased verbs, e.g. SimulatesNicheModel.
• objects are declared with lowercase, underscores and small caps, e.g. trophic_level
• namespaces with :: (e.g reshape2::acast)
• Packages dependancies are declared in the DESCRIPTION (import section)
• all roxygen2 flags (e.g. @param etc.) are to be set up.
• R extension file has to be written in capital letter (e.g fitBayesReg.R)

Have a look at http://adv-r.had.co.nz/Style.html

For further details on namespaces: http://r-pkgs.had.co.nz/namespace.html

License

Copyright (c) 2016-2020 IELab research group

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.