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codyn

Community dynamics metrics

https://github.com/nceas/codyn

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 16 committers (31.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords from Contributors

carpentries geospatial-data package-creation
Last synced: 11 months ago · JSON representation

Repository

Community dynamics metrics

Basic Info
  • Host: GitHub
  • Owner: NCEAS
  • Language: R
  • Default Branch: master
  • Size: 1.11 MB
Statistics
  • Stars: 34
  • Watchers: 15
  • Forks: 9
  • Open Issues: 12
  • Releases: 0
Created almost 12 years ago · Last pushed about 4 years ago
Metadata Files
Readme Contributing

README.md

codyn - Community Dynamics Metrics

CRAN_Status_Badge Build Status Downloads Project Status: Active – The project has reached a stable, usable state and is being actively developed.

  • Authors: Lauren Hallett [lauren.m.hallett@gmail.com], Meghan Avolio [meghan.avolio@jhu.edu], Ian T. Carroll [carroll.ian@gmail.com], Sydney K. Jones [syd@sevilleta.unm.edu], Andrew A. MacDonald [a.a.m.macdonald@gmail.com], Dan F. B. Flynn [flynn@fas.harvard.edu], Peter Slaughter [slaughter@nceas.ucsb.edu], Julie Ripplinger [julie.ripplinger@asu.edu], Scott L. Collins [scollins@sevilleta.unm.edu], Corinna Gries [cgries@wisc.edu], Matthew B. Jones [jones@nceas.ucsb.edu]
  • Version 1.x: doi:10.5063/F1542KJB
  • Version 2.x: doi:10.5063/F1N877Z6
  • License: Apache 2
  • Package source code on Github
  • Submit Bugs and feature requests

A package to analyze long-term ecological community datasets.

Univariate and multivariate temporal and spatial diversity indices, rank abundance curves, and community stability metrics. The functions implement metrics that are either explicitly temporal and include the option to calculate them over multiple replicates, or spatial and include the option to calculate them over multiple time points. Functions fall into five categories: static diversity indices, temporal diversity indices, spatial diversity indices, rank abundance curves, and community stability metrics. The diversity indices are temporal and spatial analogs to traditional diversity indices. Specifically, the package includes functions to calculate community richness, evenness and diversity at a given point in space and time. In addition, it contains functions to calculate species turnover, mean rank shifts, and lags in community similarity between two time points.

For an overview of codyn, see:

  • Hallett LM, Jones SK, MacDonald AAA, Jones MB, Flynn DFB, Ripplinger J, Slaughter P, Gries C, Collins SL (2016) codyn: An R package of community dynamics metrics. Methods in Ecology and Evolution, 7(10):1146–1151. https://doi.org/10.1111/2041-210X.12569

For a description of the newer spatial methods in codyn v2.x:

  • Avolio ML, Carroll IT, Collins SL, Houseman GR, Hallett LM, Isbell F, Koerner SE, Komatsu KJ, Smith MD, Wilcox KR (2019) A comprehensive approach to analyzing community dynamics using rank abundance curves. Ecosphere, 10(10):e02881. https://doi.org/10.1002/ecs2.2881

Installation

From CRAN, the package can be installed using standard tools: R install.packages("codyn")

Automated R CMD check with Docker via rhub

To simplify the process of running R CMD check on the package, one can easily run the build and tests using the rhub package. Use rhub::platforms() to get a list of platforms that can be used to build and test.

r library(rhub) chks <- check(platform = c("debian-gcc-devel", "fedora-gcc-devel"), show_status = FALSE)

and the checks can be run locally using rhub as well using a docker container:

r library(rhub) local_check_linux(image="rhub/fedora-gcc-devel")

Acknowledgments

Work on this package was supported by NSF-ABI grant #1262458 to C. Gries, M. Jones, and S. Collins. Additional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California, and a SESYNC Synthesis Postdoctoral Fellowship to MLA.

Owner

  • Name: National Center for Ecological Analysis and Synthesis
  • Login: NCEAS
  • Kind: organization
  • Email: help@nceas.ucsb.edu
  • Location: Santa Barbara, CA

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 909
  • Total Committers: 16
  • Avg Commits per committer: 56.813
  • Development Distribution Score (DDS): 0.772
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lauren Hallett l****t@b****u 207
Andrew MacDonald a****d@g****m 183
Matt Jones g****e@m****g 177
Meghan m****o@g****m 82
Ian Carroll i****l@s****g 70
Meghan Avolio m****o@M****l 54
Dan Flynn d****n@g****m 32
Peter Slaughter s****r@n****u 29
Corinna Gries c****s@w****u 29
SydJones s****d@s****u 23
Test c****n@g****m 13
Ian Carroll i****l 4
Ian Carroll i****l@k****m 2
Julie Ripplinger j****r@d****u 2
James Lamb j****0@g****m 1
Gavin L. Simpson u****s@g****m 1
Committer Domains (Top 20 + Academic)
dhcp228.nceas.ucsb.edu: 1 kimetrica.com: 1 sevilleta.unm.edu: 1 wisc.edu: 1 nceas.ucsb.edu: 1 sesync.org: 1 magisa.org: 1 berkeley.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 95
  • Total pull requests: 8
  • Average time to close issues: 4 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 23
  • Total pull request authors: 4
  • Average comments per issue: 1.99
  • Average comments per pull request: 2.25
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mbjones (32)
  • laurenmh (9)
  • mavolio (7)
  • aammd (7)
  • klapierre (7)
  • gothub (4)
  • wilcoxkr (4)
  • SallyKoerner (4)
  • itcarroll (3)
  • dflynn-volpe (3)
  • gsrednick (2)
  • pulidofabs (2)
  • mcrossley3 (1)
  • Gian77 (1)
  • pennockc (1)
Pull Request Authors
  • itcarroll (4)
  • aammd (2)
  • gavinsimpson (1)
  • jameslamb (1)
Top Labels
Issue Labels
enhancement (26) documentation (15) bug (11) testing (9) question (6) next (3) needs review (2) help wanted (1) in progress (1) community metric (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 419 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 9
  • Total maintainers: 1
cran.r-project.org: codyn

Community Dynamics Metrics

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 419 Last month
Rankings
Forks count: 7.9%
Stargazers count: 9.3%
Average: 18.5%
Downloads: 22.7%
Dependent repos count: 23.9%
Dependent packages count: 28.7%
Maintainers (1)
jones@nceas.ucsb.edu
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • assertthat * imports
  • permute * imports
  • stats * imports
  • vegan * imports
  • devtools * suggests
  • dplyr * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • pillar * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • testthat * suggests