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Merge pull request #51 from ropensci/fix/rm-retired-spatial-pkgs
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Fix/rm retired spatial packages
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@robitalec
robitalec committed Aug 23, 2023
2 parents 920aa5f + 577bfba commit 293a7cb
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -15,3 +15,4 @@ Makefile
^doc$
^Meta$
^\.github$
^CITATION\.cff$
4 changes: 2 additions & 2 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -18,7 +18,7 @@ jobs:
fail-fast: false
matrix:
config:
- {os: macOS-latest, r: 'release'}
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
Expand All @@ -29,7 +29,7 @@ jobs:
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-pandoc@v2

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257 changes: 257 additions & 0 deletions CITATION.cff
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@@ -0,0 +1,257 @@
# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------

cff-version: 1.2.0
message: 'To cite package "spatsoc" in publications use:'
type: software
license: GPL-3.0-only
title: 'spatsoc: Group Animal Relocation Data by Spatial and Temporal Relationship'
version: 0.2.0
abstract: Detects spatial and temporal groups in GPS relocations (Robitaille et al.
(2020) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations
to gambit-of-the-group format to build proximity-based social networks In addition,
the randomizations function provides data-stream randomization methods suitable
for GPS data.
authors:
- family-names: Robitaille
given-names: Alec L.
email: robit.alec@gmail.com
orcid: https://orcid.org/0000-0002-4706-1762
- family-names: Webber
given-names: Quinn
orcid: https://orcid.org/0000-0002-0434-9360
- family-names: Vander Wal
given-names: Eric
orcid: https://orcid.org/0000-0002-8534-4317
preferred-citation:
type: article
title: 'Conducting social network analysis with animal telemetry data: applications
and methods using spatsoc'
authors:
- family-names: Robitaille
given-names: Alec L
- family-names: Webber
given-names: Quinn MR
- family-names: Wal
given-names: Eric Vander
journal: Methods in Ecology and Evolution
year: '2019'
url: https://doi.org/10.1111/2041-210X.13215
repository: https://CRAN.R-project.org/package=spatsoc
repository-code: https://github.com/ropensci/spatsoc
url: https://docs.ropensci.org/spatsoc/
contact:
- family-names: Robitaille
given-names: Alec L.
email: robit.alec@gmail.com
orcid: https://orcid.org/0000-0002-4706-1762
keywords:
- animal
- gps
- network
- r
- r-package
- rstats
- social
- spatial
references:
- type: software
title: 'R: A Language and Environment for Statistical Computing'
notes: Depends
url: https://www.R-project.org/
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
version: '>= 3.4'
- type: software
title: data.table
abstract: 'data.table: Extension of `data.frame`'
notes: Imports
url: https://r-datatable.com
repository: https://CRAN.R-project.org/package=data.table
authors:
- family-names: Dowle
given-names: Matt
email: mattjdowle@gmail.com
- family-names: Srinivasan
given-names: Arun
email: asrini@pm.me
year: '2023'
version: '>= 1.10.5'
- type: software
title: sf
abstract: 'sf: Simple Features for R'
notes: Imports
url: https://r-spatial.github.io/sf/
repository: https://CRAN.R-project.org/package=sf
authors:
- family-names: Pebesma
given-names: Edzer
email: edzer.pebesma@uni-muenster.de
orcid: https://orcid.org/0000-0001-8049-7069
year: '2023'
- type: software
title: units
abstract: 'units: Measurement Units for R Vectors'
notes: Imports
url: https://r-quantities.github.io/units/
repository: https://CRAN.R-project.org/package=units
authors:
- family-names: Pebesma
given-names: Edzer
email: edzer.pebesma@uni-muenster.de
orcid: https://orcid.org/0000-0001-8049-7069
- family-names: Mailund
given-names: Thomas
email: mailund@birc.au.dk
- family-names: Kalinowski
given-names: Tomasz
- family-names: Ucar
given-names: Iñaki
email: iucar@fedoraproject.org
orcid: https://orcid.org/0000-0001-6403-5550
year: '2023'
- type: software
title: adehabitatHR
abstract: 'adehabitatHR: Home Range Estimation'
notes: Imports
repository: https://CRAN.R-project.org/package=adehabitatHR
authors:
- family-names: Calenge
given-names: Clement
- family-names: Fortmann-Roe
given-names: contributions from Scott
year: '2023'
version: '>= 0.4.21'
- type: software
title: igraph
abstract: 'igraph: Network Analysis and Visualization'
notes: Imports
url: https://r.igraph.org/
repository: https://CRAN.R-project.org/package=igraph
authors:
- family-names: Csárdi
given-names: Gábor
email: csardi.gabor@gmail.com
orcid: https://orcid.org/0000-0001-7098-9676
- family-names: Nepusz
given-names: Tamás
email: ntamas@gmail.com
orcid: https://orcid.org/0000-0002-1451-338X
- family-names: Traag
given-names: Vincent
orcid: https://orcid.org/0000-0003-3170-3879
- family-names: Horvát
given-names: Szabolcs
email: szhorvat@gmail.com
orcid: https://orcid.org/0000-0002-3100-523X
- family-names: Zanini
given-names: Fabio
email: fabio.zanini@unsw.edu.au
orcid: https://orcid.org/0000-0001-7097-8539
- family-names: Noom
given-names: Daniel
- family-names: Müller
given-names: Kirill
email: kirill@cynkra.com
orcid: https://orcid.org/0000-0002-1416-3412
year: '2023'
- type: software
title: testthat
abstract: 'testthat: Unit Testing for R'
notes: Suggests
url: https://testthat.r-lib.org
repository: https://CRAN.R-project.org/package=testthat
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2023'
version: '>= 2.1.0'
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
notes: Suggests
url: https://yihui.org/knitr/
repository: https://CRAN.R-project.org/package=knitr
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2023'
- type: software
title: rmarkdown
abstract: 'rmarkdown: Dynamic Documents for R'
notes: Suggests
url: https://pkgs.rstudio.com/rmarkdown/
repository: https://CRAN.R-project.org/package=rmarkdown
authors:
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
- family-names: Dervieux
given-names: Christophe
email: cderv@posit.co
orcid: https://orcid.org/0000-0003-4474-2498
- family-names: McPherson
given-names: Jonathan
email: jonathan@posit.co
- family-names: Luraschi
given-names: Javier
- family-names: Ushey
given-names: Kevin
email: kevin@posit.co
- family-names: Atkins
given-names: Aron
email: aron@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Chang
given-names: Winston
email: winston@posit.co
- family-names: Iannone
given-names: Richard
email: rich@posit.co
orcid: https://orcid.org/0000-0003-3925-190X
year: '2023'
- type: software
title: asnipe
abstract: 'asnipe: Animal Social Network Inference and Permutations for Ecologists'
notes: Suggests
repository: https://CRAN.R-project.org/package=asnipe
authors:
- family-names: Farine
given-names: Damien R.
email: dfarine@ab.mpg.de
year: '2023'
- type: software
title: markdown
abstract: 'markdown: Render Markdown with ''commonmark'''
notes: Suggests
url: https://github.com/rstudio/markdown
repository: https://CRAN.R-project.org/package=markdown
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
- family-names: Allaire
given-names: JJ
- family-names: Horner
given-names: Jeffrey
year: '2023'
15 changes: 7 additions & 8 deletions DESCRIPTION
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@@ -1,6 +1,6 @@
Package: spatsoc
Title: Group Animal Relocation Data by Spatial and Temporal Relationship
Version: 0.1.16.9003
Version: 0.2.0
Authors@R:
c(person(given = "Alec L.",
family = "Robitaille",
Expand All @@ -25,19 +25,18 @@ Depends: R (>= 3.4)
License: GPL-3 | file LICENSE
Encoding: UTF-8
Imports: data.table (>= 1.10.5),
sp,
rgeos,
adehabitatHR,
igraph,
methods
sf,
units,
adehabitatHR (>= 0.4.21),
igraph
Suggests:
testthat (>= 2.1.0),
knitr,
rmarkdown,
asnipe,
markdown
SystemRequirements: GEOS (>= 3.2.0)
RoxygenNote: 7.2.2
SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
BugReports: https://github.com/ropensci/spatsoc/issues
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27 changes: 26 additions & 1 deletion NEWS.md
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# v 0.1.17 (unreleased)
# v 0.2.0

* following [R-spatial evolution](https://r-spatial.org/r/2022/04/12/evolution.html),
removed dependencies on retired spatial packages (
[PR 50](https://github.com/ropensci/spatsoc/issues/50):
[PR 52](https://github.com/ropensci/spatsoc/issues/50),
[PR 53](https://github.com/ropensci/spatsoc/issues/50),
[PR 54](https://github.com/ropensci/spatsoc/issues/50)
[PR 55](https://github.com/ropensci/spatsoc/issues/50))
- 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
- tests, vignettes, manual updated
- added temporary package startup message until October 2023


# v 0.1.17 (2023-03-16)

* added a link to our `spatsoc` + `targets` workflow example
* changed the error and underlying check for `group_polys` from alphanumeric to
Expand All @@ -8,6 +30,9 @@ spaces in input DT's id column
* fix links in man ([PR 47](https://github.com/ropensci/spatsoc/pull/47))
* fix proportions outside 0-1 due to differences in default units from rgeos::gArea
and polys@area ([PR 49](https://github.com/ropensci/spatsoc/pull/49))
* Add keyword internal by @maelle in https://github.com/ropensci/spatsoc/pull/40
* Rm unnecessary lines by @maelle in https://github.com/ropensci/spatsoc/pull/43


# v 0.1.16 (2021-03-23)
* added an option for `edge_dist` to handle threshold = NULL. If NULL, `edge_dist` will return all neighbours observed (eg. useful if one wanted to calculated mean nearest neighbour distance at each timegroup).
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