phenotypespace

Quantyfing phenotypic spaces

https://github.com/marce10/phenotypespace

Science Score: 44.0%

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Keywords

phenotype quantitative-metrics rpackage

Last synced: 6 months ago · JSON representation ·

Repository

Quantyfing phenotypic spaces

Basic Info

Host: GitHub
Owner: maRce10
Language: R
Default Branch: master
Homepage: https://marce10.github.io/PhenotypeSpace/
Size: 16.7 MB

Statistics

Stars: 1
Watchers: 2
Forks: 0
Open Issues: 10
Releases: 0

Topics

phenotype quantitative-metrics rpackage

Created about 4 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Citation

README.Rmd

---
title: "PhenotypeSpace: quantifying phenotypic trait spaces"
output: github_document
editor_options: 
  chunk_output_type: console
---




[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![Dependencies](https://tinyverse.netlify.com/badge/PhenotypeSpace)](https://cran.r-project.org/package=PhenotypeSpace) [![Project Status: Active  The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Licence](https://img.shields.io/badge/https://img.shields.io/badge/licence-GPL--2-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) [![minimal R version](https://img.shields.io/badge/R%3E%3D-`r strsplit(gsub("depends: R \\(|\\)", "", grep("^DEPENDS", ignore.case = TRUE, readLines(con = "./DESCRIPTION"), value = TRUE), ignore.case = TRUE), ",")[[1]][1]`-6666ff.svg)](https://cran.r-project.org/) [![packageversion](https://img.shields.io/badge/Package%20version-`r gsub("version: |version:", "", grep("^version", ignore.case = TRUE, readLines(con = "./DESCRIPTION"), value = TRUE), ignore.case = TRUE)`-orange.svg?style=flat-square)](commits/develop) [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](/commits/master) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/PhenotypeSpace)](https://cran.r-project.org/package=PhenotypeSpace)
[![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/PhenotypeSpace)](https://cranlogs.r-pkg.org/badges/grand-total/PhenotypeSpace)




[PhenotypeSpace](https://github.com/maRce10/PhenotypeSpace) is intended to facilitate the quantification of phenotypic space features.

The package offers functions for:

   - Estimate absolute values of phenotypic spaces
   - Compare trait spaces across groups
   - Modify output formats to facilitate statistical analysis
   
All functions allow the parallelization of tasks, which distributes the tasks among several processors to improve computational efficiency. 


To install the latest developmental version from [github](https://github.com/) you will need the R package [remotes](https://cran.r-project.org/package=remotes):

```{r, eval = FALSE}
remotes::install_github("maRce10/PhenotypeSpace")

#load package
library(PhenotypeSpace)

```

Please cite [PhenotypeSpace](https://github.com/maRce10/PhenotypeSpace) as follows:

Araya-Salas, M., & K. Odom. 2022. PhenotypeSpace: and R package to quantify and compare phenotypic trait spaces. R package version 0.1.0.

Owner

Name: Marcelo Araya-Salas
Login: maRce10
Kind: user
Location: Costa Rica
Company: Universidad de Costa Rica

Website: https://marceloarayasalas.weebly.com/
Twitter: M_Araya_Salas
Repositories: 58
Profile: https://github.com/maRce10

I am an evolutionary behavioral ecologist that ended up doing a lot of coding just to be able to customize my data analyses

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "PhenotypeSpace" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'PhenotypeSpace: Quantifying phenotypic spaces'
version: 0.1.1
abstract: Facilitates quantifying phenotypic trait spaces and comparing spaces across
  groups.
authors:
- family-names: Araya-Salas
  given-names: Marcelo
  email: marcelo.araya@ucr.ac.cr
  orcid: https://orcid.org/0000-0003-3594-619X
- family-names: Odom
  given-names: Karan
  email: kjodom@gmail.com
preferred-citation:
  type: generic
  title: 'PhenotypeSpace: an R package to quantify and compare phenotypic trait spaces'
  authors:
  - family-names: Araya-Salas
    given-names: M.
  - family-names: Odom
    given-names: K.
  year: '2022'
repository: https://CRAN.R-project.org/package=PhenotypeSpace
repository-code: https://github.com/maRce10/PhenotypeSpace/issues/
url: https://marce10.github.io/PhenotypeSpace/
contact:
- family-names: Araya-Salas
  given-names: Marcelo
  email: marcelo.araya@ucr.ac.cr
  orcid: https://orcid.org/0000-0003-3594-619X
references:
- type: software
  title: pbapply
  abstract: 'pbapply: Adding Progress Bar to ''*apply'' Functions'
  notes: Imports
  url: https://github.com/psolymos/pbapply
  repository: https://CRAN.R-project.org/package=pbapply
  authors:
  - family-names: Solymos
    given-names: Peter
    email: psolymos@gmail.com
    orcid: https://orcid.org/0000-0001-7337-1740
  - family-names: Zawadzki
    given-names: Zygmunt
    email: zygmunt@zstat.pl
  year: '2025'
  doi: 10.32614/CRAN.package.pbapply
- type: software
  title: viridis
  abstract: 'viridis: Colorblind-Friendly Color Maps for R'
  notes: Imports
  url: https://sjmgarnier.github.io/viridis/
  repository: https://CRAN.R-project.org/package=viridis
  authors:
  - family-names: Garnier
    given-names: Simon
    email: garnier@njit.edu
  year: '2025'
  doi: 10.32614/CRAN.package.viridis
- type: software
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  abstract: 'adehabitatHR: Home Range Estimation'
  notes: Imports
  repository: https://CRAN.R-project.org/package=adehabitatHR
  authors:
  - family-names: Calenge
    given-names: Clement
    email: clement.calenge@ofb.gouv.fr
  year: '2025'
  doi: 10.32614/CRAN.package.adehabitatHR
- type: software
  title: sp
  abstract: 'sp: Classes and Methods for Spatial Data'
  notes: Imports
  url: https://github.com/edzer/sp/
  repository: https://CRAN.R-project.org/package=sp
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
  - family-names: Bivand
    given-names: Roger
    email: Roger.Bivand@nhh.no
  year: '2025'
  doi: 10.32614/CRAN.package.sp
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: raster
  abstract: 'raster: Geographic Data Analysis and Modeling'
  notes: Imports
  url: https://rspatial.org/raster
  repository: https://CRAN.R-project.org/package=raster
  authors:
  - family-names: Hijmans
    given-names: Robert J.
    email: r.hijmans@gmail.com
    orcid: https://orcid.org/0000-0001-5872-2872
  year: '2025'
  doi: 10.32614/CRAN.package.raster
- type: software
  title: MASS
  abstract: 'MASS: Support Functions and Datasets for Venables and Ripley''s MASS'
  notes: Imports
  url: http://www.stats.ox.ac.uk/pub/MASS4/
  repository: https://CRAN.R-project.org/package=MASS
  authors:
  - family-names: Ripley
    given-names: Brian
    email: Brian.Ripley@R-project.org
  - family-names: Venables
    given-names: Bill
  year: '2025'
  doi: 10.32614/CRAN.package.MASS
- type: software
  title: vegan
  abstract: 'vegan: Community Ecology Package'
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  url: https://github.com/vegandevs/vegan
  repository: https://CRAN.R-project.org/package=vegan
  authors:
  - family-names: Oksanen
    given-names: Jari
    email: jhoksane@gmail.com
  - family-names: Simpson
    given-names: Gavin L.
    email: ucfagls@gmail.com
  - family-names: Blanchet
    given-names: F. Guillaume
  - family-names: Kindt
    given-names: Roeland
  - family-names: Legendre
    given-names: Pierre
  - family-names: Minchin
    given-names: Peter R.
  - family-names: O'Hara
    given-names: R.B.
  - family-names: Solymos
    given-names: Peter
  - family-names: Stevens
    given-names: M. Henry H.
  - family-names: Szoecs
    given-names: Eduard
  - family-names: Wagner
    given-names: Helene
  - family-names: Barbour
    given-names: Matt
  - family-names: Bedward
    given-names: Michael
  - family-names: Bolker
    given-names: Ben
  - family-names: Borcard
    given-names: Daniel
  - family-names: Carvalho
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  - family-names: Chirico
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  url: http://spatstat.org/
  repository: https://CRAN.R-project.org/package=spatstat.explore
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    orcid: https://orcid.org/0000-0002-6675-533X
  year: '2025'
  doi: 10.32614/CRAN.package.spatstat.explore
- type: software
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  abstract: 'spatstat.geom: Geometrical Functionality of the ''spatstat'' Family'
  notes: Imports
  url: http://spatstat.org/
  repository: https://CRAN.R-project.org/package=spatstat.geom
  authors:
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    email: Adrian.Baddeley@curtin.edu.au
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    orcid: https://orcid.org/0000-0001-5521-5218
  - family-names: Rubak
    given-names: Ege
    email: rubak@math.aau.dk
    orcid: https://orcid.org/0000-0002-6675-533X
  year: '2025'
  doi: 10.32614/CRAN.package.spatstat.geom
- type: software
  title: proxy
  abstract: 'proxy: Distance and Similarity Measures'
  notes: Imports
  repository: https://CRAN.R-project.org/package=proxy
  authors:
  - family-names: Meyer
    given-names: David
    email: David.Meyer@R-project.org
  - family-names: Buchta
    given-names: Christian
  year: '2025'
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  title: grDevices
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: sf
  abstract: 'sf: Simple Features for R'
  notes: Imports
  url: https://r-spatial.github.io/sf/
  repository: https://CRAN.R-project.org/package=sf
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
  year: '2025'
  doi: 10.32614/CRAN.package.sf
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  notes: Imports
  url: https://github.com/mlysy/nicheROVER
  repository: https://CRAN.R-project.org/package=nicheROVER
  authors:
  - family-names: Lysy
    given-names: Martin
    email: mlysy@uwaterloo.ca
  - family-names: Stasko
    given-names: Ashley D.
  - family-names: Swanson
    given-names: Heidi K.
  year: '2025'
  doi: 10.32614/CRAN.package.nicheROVER
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  abstract: 'caret: Classification and Regression Training'
  notes: Suggests
  url: https://github.com/topepo/caret/
  repository: https://CRAN.R-project.org/package=caret
  authors:
  - family-names: Kuhn
    given-names: Max
    email: mxkuhn@gmail.com
    orcid: https://orcid.org/0000-0003-2402-136X
  year: '2025'
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  abstract: 'randomForest: Breiman and Cutlers Random Forests for Classification and
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  notes: Suggests
  url: https://www.stat.berkeley.edu/~breiman/RandomForests/
  repository: https://CRAN.R-project.org/package=randomForest
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  - family-names: Cutler
    given-names: Adele
  - family-names: Liaw
    given-names: Andy
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  doi: 10.32614/CRAN.package.randomForest
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  notes: Suggests
  url: https://topepo.github.io/C5.0/
  repository: https://CRAN.R-project.org/package=C50
  authors:
  - family-names: Kuhn
    given-names: Max
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  - family-names: Quinlan
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  doi: 10.32614/CRAN.package.C50
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  url: https://plotly-r.com
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  authors:
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    given-names: Carson
    email: cpsievert1@gmail.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Parmer
    given-names: Chris
    email: chris@plot.ly
  - family-names: Hocking
    given-names: Toby
    email: tdhock5@gmail.com
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    email: myrmecocystus@gmail.com
  - family-names: Ram
    given-names: Karthik
    email: karthik.ram@gmail.com
  - family-names: Corvellec
    given-names: Marianne
    email: marianne.corvellec@igdore.org
    orcid: https://orcid.org/0000-0002-1994-3581
  - family-names: Despouy
    given-names: Pedro
    email: pedro@plot.ly
  year: '2025'
  doi: 10.32614/CRAN.package.plotly
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.0.0'

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Dependencies

DESCRIPTION cran

R >= 4.0.0 depends
warbleR * depends
MASS * imports
adehabitatHR * imports
grDevices * imports
knitr * imports
pbapply * imports
proxy * imports
raster * imports
rgeos * imports
rmarkdown * imports
sp * imports
spatstat * imports
spatstat.core * imports
spatstat.geom * imports
stats * imports
vegan * imports
viridis * imports

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