nounoursusvsbears

https://github.com/nmouquet/nounoursusvsbears

Science Score: 44.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (8.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: nmouquet
License: mit
Language: R
Default Branch: master
Size: 6.15 MB

Statistics

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

Created 9 months ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Codemeta

README.md

Too cute to be wild

Research compendium to reproduce analyses and figures of the following article:

Too cute to be wild: what teddy bears reveal about our disconnection from nature, by Mouquet N., Blanc, N., Brassac T., Casajus N. & Tribot A.-S. Bioscience.

Content

This repository is structured as follow:

data/: contains data required to reproduce figures and tables
analysis/: contains subfolders organized by theme. Each folder contains R scripts to run specific analysis
results/: follows the structure of analyses. Contains intermediate results and the numeric results used to produce the figures
outputs/: contains the figures produced for the article
DESCRIPTION: contains project metadata (author, date, dependencies, etc.)

Workflow

The script analysis/Cludy_toys.R computes functional insurance with simulated metacommunities.
The script analysis/Bear_vs_nounoursus.R gets the morphometric and colorimetric features from the analysis of images for Teddy bears and Real bears; and perform the main analysis
The script analysis/features/cluster.R extracts information on color clusters heterogeneity in images.
The script analysis/features/lumsat.R extracts information on lightness and saturation in images.
The script analysis/morpho/morpho.R computes the morphometric measures from the analysis of teady and real bears images.

Big files

Some files were not uploaded to GitHub due to their large size. They are available upon request:

data/illustrations_figures
data/images_real
data/images_real_croped
data/images_real_tocrop
data/nounoursus

Figures

Figures are stored in outputs/.

The following Figures and Tables can be reproduced with the script indicated in brackets (stored in analysis/):

cuddly.tiff, was produced by Cludy_toys.R
fig_pca wad produced by Bearvsnounoursus.R`
fig1-sup, was produced by Bearvsnounoursus.R`
fig2-sup, was produced by Bearvsnounoursus.R`

Installation

To install this compendium:

Fork this repository using the GitHub interface.
Clone your fork using git clone fork-url (replace fork-url by the URL of your fork). Alternatively, open RStudio IDE and create a New Project from Version Control.

Then, run the following command to install required packages:

```r

Install < remotes > package (if not already installed) ----

if (!requireNamespace("remotes", quietly = TRUE)) { install.packages("remotes") }

Install required packages ----

remotes::install_deps() ```

Contributing

All types of contributions are encouraged and valued. For more information, check out our Contributor Guidelines.

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

Name: Nicolas Mouquet
Login: nmouquet
Kind: user
Location: Montpellier
Company: CNRS

Website: http://nicolasmouquet.free.fr
Twitter: NicolasMouquet
Repositories: 1
Profile: https://github.com/nmouquet

I am primarily a theoretical community ecologist, with some complementary experience in experimental ecology, microbiology, evolution and biogeography.

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 "NOUNOURSUSvsBEARS" in publications use:'
type: software
license: MIT
title: 'NOUNOURSUSvsBEARS: Too Cute to Be Wild'
version: 0.0.1
abstract: 'Research compendium of the article ''Too cute to be wild: what teddy bears
  reveal about our disconnection from nature'' by Mouquet N. et al. submited to Trends
  in Ecology and Evolution in 2025.'
authors:
- family-names: Mouquet
  given-names: Nicolas
  email: nicolas.mouquet@cnrs.fr
  orcid: https://orcid.org/0000-0003-1840-6984
repository-code: https://github.com/nmouquet/NOUNOURSUSvsBEARS
url: https://github.com/nmouquet/NOUNOURSUSvsBEARS
contact:
- family-names: Mouquet
  given-names: Nicolas
  email: nicolas.mouquet@cnrs.fr
  orcid: https://orcid.org/0000-0003-1840-6984
references:
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Depends
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Depends
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
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  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
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  - family-names: Brand
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  year: '2025'
  doi: 10.32614/CRAN.package.ggplot2
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  notes: Depends
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  authors:
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  year: '2025'
  doi: 10.32614/CRAN.package.imager
- type: software
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  url: https://tidyverse.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyverse
  authors:
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    given-names: Hadley
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  year: '2025'
  doi: 10.32614/CRAN.package.tidyverse
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  notes: Imports
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  authors:
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    given-names: Kirill
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    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2025'
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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  institution:
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    address: Vienna, Austria
  year: '2025'
- type: software
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  notes: Imports
  repository: https://CRAN.R-project.org/package=RColorBrewer
  authors:
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  year: '2025'
  doi: 10.32614/CRAN.package.RColorBrewer
- type: software
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  abstract: 'readxl: Read Excel Files'
  notes: Imports
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  repository: https://CRAN.R-project.org/package=readxl
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Bryan
    given-names: Jennifer
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    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.readxl
- type: software
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  notes: Imports
  url: https://github.com/markvanderloo/stringdist
  repository: https://CRAN.R-project.org/package=stringdist
  authors:
  - family-names: Loo
    given-names: Mark
    name-particle: van der
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    orcid: https://orcid.org/0000-0002-9807-4686
  year: '2025'
  doi: 10.32614/CRAN.package.stringdist
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  notes: Imports
  url: https://stringi.gagolewski.com/
  repository: https://CRAN.R-project.org/package=stringi
  authors:
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  year: '2025'
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  notes: Imports
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  repository: https://CRAN.R-project.org/package=tidytext
  authors:
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    email: julia.silge@gmail.com
    orcid: https://orcid.org/0000-0002-3671-836X
  year: '2025'
  doi: 10.32614/CRAN.package.tidytext

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Dependencies

DESCRIPTION cran

SDMTools * depends
colorspace * depends
dplyr * depends
ggplot2 * depends
gridExtra * depends
imager * depends
reshape2 * depends
splancs * depends
tidyverse * depends
GGally * imports
RColorBrewer * imports
ade4 * imports
cowplot * imports
factoextra * imports
here * imports
parallel * imports
pbmcapply * imports
readxl * imports
spatstat.geom * imports
stringdist * imports
stringi * imports
tidytext * imports

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