rcompendium - Create a Package or Research Compendium Structure

Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown'). This package heavily relies on the R packages 'devtools' and 'usethis' and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.

Last updated 12 days ago

reproducible-researchresearch-compendium

6.77 score 39 stars 20 scripts 782 downloads

forcis - An R Client to Access the FORCIS Database

Provides an interface to the FORCIS database (<https://zenodo.org/doi/10.5281/zenodo.7390791>) on global foraminifera distribution. This package allows to download and to handle FORCIS data. It is part of the FRB-CESAB working group FORCIS. <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/>.

Last updated 1 months ago

5.84 score 3 stars 5 scripts

funbiogeo - Functional Biogeography Analyses

Helps users with analyses in functional biogeogeography by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.

Last updated 4 months ago

functional-biogeography

5.62 score 10 stars 8 scripts

chessboard - Create Network Connections Based on Chess Moves

Provides functions to work with directed (asymmetric) and undirected (symmetric) spatial networks. It makes the creation of connectivity matrices easier, i.e. a binary matrix of dimension n x n, where n is the number of nodes (sampling units) indicating the presence (1) or the absence (0) of an edge (link) between pairs of nodes. Different network objects can be produced by 'chessboard': node list, neighbor list, edge list, connectivity matrix. It can also produce objects that will be used later in Moran's Eigenvector Maps (Dray et al. (2006) <doi:10.1016/j.ecolmodel.2006.02.015>) and Asymetric Eigenvector Maps (Blanchet et al. (2008) <doi:10.1016/j.ecolmodel.2008.04.001>), methods available in the package 'adespatial' (Dray et al. (2023) <https://CRAN.R-project.org/package=adespatial>). This work is part of the FRB-CESAB working group Bridge <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/>.

Last updated 1 years ago

connectivity-matrixdirected-networksneighborhoodnetworkone-dimensional-networksspatial-networkstwo-dimensional-networksundirected-networks

4.78 score 4 stars 181 downloads

rutils - A Collection of R Functions

A collection of R functions commonly used in FRB-CESAB projects.

Last updated 12 months ago

miscellaneous

4.60 score 2 stars 396 scripts

popbayes - Bayesian Model to Estimate Population Trends from Counts Series

Infers the trends of one or several animal populations over time from series of counts. It does so by accounting for count precision (provided or inferred based on expert knowledge, e.g. guesstimates), smoothing the population rate of increase over time, and accounting for the maximum demographic potential of species. Inference is carried out in a Bayesian framework. This work is part of the FRB-CESAB working group AfroBioDrivers <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/afrobiodrivers/>.

Last updated 10 months ago

animalbayesiancountspopulationprecisiontemporal-trend

4.30 score 1 stars 191 downloads

zoteror - Handle Zotero Local Database

Makes a connection to the (local) Zotero database (SQLite) to extract bibliographic references metadata.

Last updated 2 months ago

databasereferenceszotero

3.95 score 6 stars 5 scripts

worldpa - An Interface to the World Database on Protected Areas (WDPA)

This package is an interface to the World Database on Protected Areas <https://www.protectedplanet.net> and its API <https://api.protectedplanet.net>. User can download terrestrial and marine protected areas for the world countries (one country at the time).

Last updated 4 years ago

protected-areasprotected-planetshapefilespatialworld

3.85 score 14 stars 1 scripts

rdeps - Identify External Packages Used in a Project

Screens all '.R', '.Rmd', and '.qmd' files to extract the name of packages used in a project. This package detects packages called with 'library(foo)', 'require(foo)', and 'foo::bar()' and adds these dependencies in the DESCRIPTION file in the sections Depends, Imports, and Suggests.

Last updated 10 months ago

3.40 score 1 stars 1 scripts 132 downloads

rbibtools - Toolbox to Handle BibTeX Files

Imports, cleans, and exports BibTeX references exported by references management softwares (e.g. Mendeley, Zotero).

Last updated 2 months ago

bibtex

3.18 score 3 stars

messages - Print Messages in the Console

A collection of functions to print messages in the R console using the packages 'cli' and 'crayon'. This package is strongly inspired from the functions ui_*() of the package 'usethis'.

Last updated 3 years ago

3.16 score 1 stars 290 scripts

snakedist - Compute Distances along a Linear Shape

Computes distance between pair of points along a linear shape (e.g. a river, a road, etc.). This function uses parallel computing to speed up the distance computation.

Last updated 1 years ago

2.70 score

geoparser - Detect Country Names in Documents

Detects country names in PDF documents imported with the package 'pdftools'.

Last updated 2 years ago

text-miningworld-countries

2.70 score 4 scripts 36 downloads

rsendinblue - R Client for the SENDINBLUE API

Provides an R client for the sendinblue API <https://developers.sendinblue.com>.

Last updated 4 years ago

mailing-listsendinblue-api

2.70 score

rwoslite - R Client for WOS Lite API

R Client for the WOS Lite API.

Last updated 2 years ago

apiweb-of-science

2.48 score 6 stars

refR - An R package to get and manage BibTeX/YAML/JSON references

The package \textbf{refR} retrieves author references from Scopus Search and Crossref APIs and returns references as BibTeX files (function \code{\link[refR]{getRefs}}). It also allows to convert BibTeX files in more readable formats (i.e. YAML and JSON) by calling the software pandoc-citeproc (functions \code{\link[refR]{getRefs}} and \code{\link[refR]{bib2yaml}}). Information in references files can be cleaned using the function \code{\link[refR]{cleanRefs}}. This function translates special characters (accented characters and other LaTeX tags) and also cleans author names (detection of particle in family names, removal of uppercase except for each first letter of family and given names, and shorten given name).

Last updated 6 years ago

2.40 score 5 stars 2 scripts

omdbr - Retrieve Movies Metadata from OMDb Database

This package retrieves movies metadata (title, actors, year, genres, etc.) using the OMDb API <http://www.omdbapi.com/> (an API key is required). Cover can also be downloaded from the YTS API <https://yts.mx/api> (no API key required).

Last updated 10 months ago

coverimdbmetadatamoviesomdb-apiyts-api

2.18 score 3 stars 2 scripts

zenodor - Download Files from a Zenodo Repository

Lists and downloads available files of a Zenodo repository. For restricted repository a token must be provided.

Last updated 1 years ago

curlzenodo

2.18 score 3 stars

rwosstarter - An R Client to the Web of Science Starter API

A client to the 'Web of Science Starter API' (<https://developer.clarivate.com/apis/wos-starter>) dedicated to retrieve metadata (including times-cited counts) of scientific publications matching search terms. It can be used to run a literature synthesis. Note that this API requires an API Key access (<https://developer.clarivate.com/>).

Last updated 2 months ago

2.00 score 2 stars