{"id":19508110,"url":"https://github.com/r-spatialecology/shar","last_synced_at":"2025-04-13T10:58:08.932Z","repository":{"id":38553667,"uuid":"118471130","full_name":"r-spatialecology/shar","owner":"r-spatialecology","description":":package: Analyse species-habitat associations in R","archived":false,"fork":false,"pushed_at":"2025-02-13T07:12:14.000Z","size":206585,"stargazers_count":20,"open_issues_count":0,"forks_count":10,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-10T15:37:30.894Z","etag":null,"topics":["habitat-association","landscape-ecology","point-pattern-analysis","spatial-analysis"],"latest_commit_sha":null,"homepage":"https://r-spatialecology.github.io/shar","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/r-spatialecology.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2018-01-22T14:53:01.000Z","updated_at":"2025-02-13T07:07:10.000Z","dependencies_parsed_at":"2023-01-25T22:15:18.030Z","dependency_job_id":"eba6a414-259c-49d3-b8a8-80ccafed1934","html_url":"https://github.com/r-spatialecology/shar","commit_stats":{"total_commits":606,"total_committers":9,"mean_commits":67.33333333333333,"dds":0.08415841584158412,"last_synced_commit":"f07fd09ddb305ef2c932335a6beea2a3bc09f1b6"},"previous_names":[],"tags_count":25,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/r-spatialecology%2Fshar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/r-spatialecology%2Fshar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/r-spatialecology%2Fshar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/r-spatialecology%2Fshar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/r-spatialecology","download_url":"https://codeload.github.com/r-spatialecology/shar/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248381795,"owners_count":21094528,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["habitat-association","landscape-ecology","point-pattern-analysis","spatial-analysis"],"created_at":"2024-11-10T23:03:43.405Z","updated_at":"2025-04-13T10:58:08.913Z","avatar_url":"https://github.com/r-spatialecology.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: \n    github_document:\n      html_preview: false\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r setup, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE, \n  fig.path = \"man/figures/README-\"\n)\n```\n\n# **shar** | **S**pecies **h**abitat **a**ssociations in **R** \u003cimg src=\"man/figures/logo.png\" align=\"right\" alt=\"\" width=\"150\" /\u003e\n\nREADME Last updated: `r Sys.Date()`\n\n\u003c!-- badges: start --\u003e\n\n| CI | Development | CRAN | License |\n|----|-------------|------|---------|\n| [![R-CMD](https://github.com/r-spatialecology/shar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatialecology/shar/actions/workflows/R-CMD-check.yaml) | [![Project-status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![CRAN-status](https://www.r-pkg.org/badges/version/shar)](https://cran.r-project.org/package=shar) | [![DOI](https://img.shields.io/badge/JOSS-10.21105/joss.03811-yellow.svg)](https://doi.org/10.21105/joss.03811) | \n[![Codecov](https://codecov.io/gh/r-spatialecology/shar/graph/badge.svg)](https://app.codecov.io/gh/r-spatialecology/shar) | [![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN-logs](https://cranlogs.r-pkg.org/badges/grand-total/shar)](http://cran.rstudio.com/web/packages/shar/index.html) | [![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) |\n\n\u003c!-- badges: end --\u003e\n\n**S**pecies-**h**abitat **a**ssociations in **R** provides a toolset of functions in the `R` programming language to analyze species-habitat associations. Therefore, information about the location of the species (as a point pattern) and the environmental conditions (as a raster) is needed. In order to analyse the data for significant habitat associations either the location data or the environmental data is randomized *n*-times. Then, counts within the habitats are compared between the observed and the randomized data. Positive or negative associations are present if the observed counts are higher or lower than the randomized counts (using quantile thresholds). Methods are described in Plotkin et al. (2000), Harms et al. (2001) and Wiegand \u0026 Moloney (2014). **shar** is mainly based on the [`spatstat`](http://spatstat.org) (Baddeley et al. 2015) and [`terra`](https://rspatial.org/terra/) (Hijmans 2022) package.\n\nYou can find more information and help using the corresponding [homepage](https://r-spatialecology.github.io/shar/).\n\n## Installation\n\nYou can install the released version of **shar** from [CRAN](https://cran.r-project.org/web/packages/shar/index.html) with:\n\n```{r install-CRAN, eval = FALSE}\ninstall.packages(\"shar\")\n```\n\nAnd the development version from [GitHub](https://github.com/r-spatialecology/shar) with:\n\n```{r install-github, eval = FALSE}\n# install.packages(\"remotes\")\nremotes::install_github(\"r-spatialecology/shar\")\n```\n\nThis also automatically installs all non-base `R` package dependencies, namely: `classInt`, `spatstat.explore`, `spatstat.geom`, `spatstat.model`, `spatstat.random`, and `terra`.\n\n## How to use **shar**\n\nPlease refer to `vignette(\"Get started\")` and the [homepage](https://r-spatialecology.github.io/shar/) to get an introduction to **shar**.\n\n### Citation\n\nThe **shar** package is part of our academic work. To cite the package or acknowledge its use in publications, please cite the following paper.\n\n\u003e Hesselbarth, M.H.K., (2021). shar: A R package to analyze species-habitat associations using point pattern analysis. Journal of Open Source Software, 6(67), 3811. \u003chttps://doi.org/10.21105/joss.03811\u003e.\n\nIf you use the `reconstruct_pattern_multi()` function, please also cite.\n\n\u003e Wudel C., Schlicht R., Berger U. (2023). Multi-trait point pattern reconstruction of plant ecosystems. Methods in Ecology and Evolution, 14, 2668–2679. \u003chttps://doi.org/10.1111/2041-210X.14206\u003e.\n\nThe get a BibTex entry, please use `citation(\"shar\")`.\n\n## Contributing and Code of Conduct\n\nContributions to **shar** are highly welcomed and appreciated. This includes any form of feedback, bug reports, feature requests/suggestions, or general questions about the usage.\n\nPlease note that the **shar** package is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.\n\nTo contribute to this project, please see the [Contributing guidelines](CONTRIBUTING.md).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fr-spatialecology%2Fshar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fr-spatialecology%2Fshar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fr-spatialecology%2Fshar/lists"}