spatsoc

:package: spatsoc is an R package for detecting spatial and temporal groups in GPS relocations.

https://github.com/ropensci/spatsoc

Keywords

animal gps network r r-package rstats social spatial

Keywords from Contributors

reproducibility ecology

Last synced: 4 months ago · JSON representation ·

Repository

:package: spatsoc is an R package for detecting spatial and temporal groups in GPS relocations.

Basic Info

Host: GitHub
Owner: ropensci
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/spatsoc
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Forks: 2
Open Issues: 15
Releases: 27

Topics

animal gps network r r-package rstats social spatial

Created over 7 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Citation Codemeta

README.Rmd

---
output: github_document
---

```{r opts, include = FALSE}
knitr::opts_chunk$set(message = FALSE, 
                      warning = FALSE,
                      eval = FALSE, 
                      echo = TRUE)
```

# spatsoc 


[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/)
[![peer-review](https://badges.ropensci.org/237_status.svg)](https://github.com/ropensci/software-review/issues/237)
[![CRAN](https://www.r-pkg.org/badges/version/spatsoc)](https://cran.r-project.org/package=spatsoc)
[![cran checks](https://cranchecks.info/badges/summary/spatsoc)](https://cran.r-project.org/web/checks/check_results_spatsoc.html)
[![R-CMD-check](https://github.com/ropensci/spatsoc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/spatsoc/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/ropensci/spatsoc/graph/badge.svg)](https://app.codecov.io/gh/ropensci/spatsoc)




### [News](#news) - [Installation](#installation) - [Usage](#usage) - [Contributing](#contributing)

`spatsoc` is an R package for detecting spatial and temporal groups in GPS relocations. It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks with grouping and edge-list generating functions. In addition, the `randomizations` function provides data-stream randomization methods suitable for GPS data and the `get_gbi` function generates group by individual matrices useful for building networks with `asnipe::get_network`. 

See below for [installation](#installation) and basic [usage](#usage). 

For more details, see the [blog post](https://ropensci.org/blog/2018/12/04/spatsoc/) and vignettes:

* [Introduction to spatsoc](https://docs.ropensci.org/spatsoc/articles/intro.html)
* [Frequently asked questions](https://docs.ropensci.org/spatsoc/articles/faq.html)
* [Using spatsoc in social network analysis](https://docs.ropensci.org/spatsoc/articles/using-in-sna.html)
* [Using edge list and dyad id functions](https://docs.ropensci.org/spatsoc/articles/using-edge-and-dyad.html)


## News
### R-spatial evolution

`spatsoc` has been updated according to the [R-spatial evolution](https://r-spatial.org/r/2022/04/12/evolution.html), to remove
deprecated package dependencies in favour of modern spatial R packages. In 
our case, this means replacing `rgeos`, `rgdal` and `sp` with `sf`. 

Below is a list of user-side differences for `spatsoc` users: 

- spatsoc now depends on `sf`, `units` instead of `rgeos` and `sp`
- `build_lines` now returns an `sf` LINESTRING object
- `build_polys` now returns an `sf` POLYGON/MULTIPOLYGON object
- `group_lines` now accepts an input `sf` LINESTRING object (argument "sfLines") 
and internally uses `sf::st_intersects`, `sf::st_buffer`, etc instead of `rgeos` functions
- `group_polys` now accepts an input `sf` POLYGON/MULTIPOLYGON object (argument "sfPolys") 
and internally uses `sf::st_intersects`, `sf::st_area`, etc instead of `rgeos` functions. 
`group_polys` now returns area and proportion of overlap (%) when `area = TRUE` with 
respective units using the `units` package

The details of these changes are available in [PR 50](https://github.com/ropensci/spatsoc/issues/50). 

If required, the old version using retired spatial packages can be installed 
with the following but please note that in October 2023 `rgeos`, `rgdal` and 
`maptools` will no longer be available on CRAN. 

```{r old_install}
remotes::install_github('ropensci/spatsoc@v0.1.17')
```


---

We wrote a [`targets`](https://github.com/ropensci/targets) workflow, available
at
[github.com/robitalec/targets-spatsoc-networks](https://github.com/robitalec/targets-spatsoc-networks).
`targets` is an incredible package for designing workflows in R and, with it, we
can reproducibly run all steps from raw telemetry data to output networks and
metrics. Check it out and let us know how it works for you!


Edge-list generating functions added:

  * `edge_nn`
  * `edge_dist`
  
and dyad id function:

  * `dyad_id`
  
(feedback welcome as always!)

Both documented further in a vignette: [Using edge list and dyad id functions](https://docs.ropensci.org/spatsoc/articles/using-edge-and-dyad.html).


Also, our article describing `spatsoc` is published at Methods in Ecology and Evolution. [Link here](https://doi.org/10.1111/2041-210X.13215). Thanks to reviewers and editors at [rOpenSci](https://github.com/ropensci/software-review/issues/237) and at [MEE](https://besjournals.onlinelibrary.wiley.com/journal/2041210x). 


More detailed news [here](https://docs.ropensci.org/spatsoc/news/index.html).


## Installation

```{r install}
# Stable release
install.packages('spatsoc')

# Development version (choose one option)
install.packages('spatsoc', 
                 repos = c('https://robitalec.r-universe.dev',
                           'https://cloud.r-project.org'))
remotes::install_github('ropensci/spatsoc')
```

`spatsoc` depends on `sf`, see [here](https://github.com/r-spatial/sf#installing)
for help installing. 



## Usage
### Load package, import data
`spatsoc` expects a `data.table` for all of its functions. If you have a `data.frame`, you can use `data.table::setDT()` to convert it by reference. If your data is a text file (e.g.: CSV), you can use `data.table::fread()` to import it as a `data.table`. 

```{r library}
library(spatsoc)
library(data.table)
DT <- fread(system.file("extdata", "DT.csv", package = "spatsoc"))
DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
```


### Temporal grouping
`group_times` groups rows temporally using a threshold defined in units of minutes (B), hours (C) or days (D). 



### Spatial grouping 
`group_pts` groups points spatially using a distance matrix (B) and a spatial threshold defined by the user (50m in this case). Combined with `group_times`, the returned 'group' column represents spatiotemporal, point based groups (D). 




`group_lines` groups sequences of points (forming a line) spatially by buffering each line (A) by the user defined spatial threshold. Combined with `group_times`, the returned 'group' column represents spatiotemporal, line overlap based groups (B). 





`group_polys` groups home ranges by spatial and proportional overlap. Combined with `group_times`, the returned 'group' column represents spatiotemporal, polygon overlap based groups. 





### Edge-list generating functions
`edge_dist` and `edge_nn` generate edge-lists. `edge_dist` measures the spatial distance between individuals (A) and returns all pairs within the user specified distance threshold (B). `edge_nn` measures the distance between individuals (C) and returns the nearest neighbour to each individual (D). 



### Social network analysis functions
`randomizations` for data-stream randomization and `get_gbi` for generating group by individual matrices. 




# Contributing
Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
  
Development of `spatsoc` welcomes contribution of feature requests, bug reports and suggested improvements through the [issue board](https://github.com/ropensci/spatsoc/issues). 

See details in [CONTRIBUTING.md](CONTRIBUTING.md). 

[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

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    "4": {
      "@type": "SoftwareApplication",
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      "sameAs": "https://CRAN.R-project.org/package=igraph"
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      "sameAs": "https://CRAN.R-project.org/package=sf"
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    "6": {
      "@type": "SoftwareApplication",
      "identifier": "lwgeom",
      "name": "lwgeom",
      "version": ">= 0.2.15",
      "provider": {
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        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://github.com/r-spatial/lwgeom"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "CircStats",
      "name": "CircStats",
      "provider": {
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      "sameAs": "https://CRAN.R-project.org/package=CircStats"
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    "8": {
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}

GitHub Events

Total

Create event: 15
Release event: 1
Issues event: 8
Delete event: 14
Issue comment event: 5
Push event: 89
Pull request event: 24

Last Year

Create event: 15
Release event: 1
Issues event: 8
Delete event: 14
Issue comment event: 5
Push event: 89
Pull request event: 24

Committers

Last synced: about 2 years ago

All Time

Total Commits: 1,434
Total Committers: 4
Avg Commits per committer: 358.5
Development Distribution Score (DDS): 0.009

Past Year

Commits: 195
Committers: 1
Avg Commits per committer: 195.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Alec Robitaille	r**c@g**m	1,421
qwebber	w**n@g**m	9
Maëlle Salmon	m**n@y**e	3
Hugo Gruson	B****o	1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 1
Total pull requests: 12
Average time to close issues: 1 day
Average time to close pull requests: about 10 hours
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 12
Average time to close issues: 1 day
Average time to close pull requests: about 10 hours
Issue authors: 1
Pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

robitalec (11)
maelle (1)

Pull Request Authors

robitalec (27)
maelle (1)

Top Labels

Issue Labels

type: enhancement (7) priority: low (1) type: discussion (1) type: documentation (1)

Pull Request Labels

type: enhancement (7) type: documentation (5) status: in progress (2) type: bug (1) status: completed (1)

Packages

Total packages: 1
Total downloads:
- cran 400 last-month
Total docker downloads: 20,392

Total dependent packages: 1
Total dependent repositories: 5
Total versions: 11
Total maintainers: 1

cran.r-project.org: spatsoc

Group Animal Relocation Data by Spatial and Temporal Relationship

Homepage: https://docs.ropensci.org/spatsoc/
Documentation: http://cran.r-project.org/web/packages/spatsoc/spatsoc.pdf
License: GPL-3 | file LICENSE
Latest release: 0.2.2
published over 2 years ago

Versions: 11
Dependent Packages: 1
Dependent Repositories: 5
Downloads: 400 Last month
Docker Downloads: 20,392

Rankings

Stargazers count: 10.3%

Docker downloads count: 12.6%

Dependent repos count: 13.0%

Average: 15.5%

Forks count: 17.0%

Dependent packages count: 18.1%

Downloads: 22.1%

Maintainers (1)

robit.alec@gmail.com

Last synced: 4 months ago

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

spatsoc

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: spatsoc

Rankings

Maintainers (1)