Fix/rm retired spatial packages

.Rbuildignore

@@ -15,3 +15,4 @@ Makefile
 ^doc$
 ^Meta$
 ^\.github$
+^CITATION\.cff$

.github/workflows/R-CMD-check.yaml

@@ -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'}
@@ -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
 

CITATION.cff

@@ -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'

DESCRIPTION

@@ -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",
@@ -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

NEWS.md

@@ -1,4 +1,26 @@
-# 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
@@ -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).