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53b3a0d
placeholder news and version
robitalec Aug 3, 2023
0e85557
deprecated build polys with sp
robitalec Aug 3, 2023
39150cd
replace spatial points df with sf as spatial
robitalec Aug 3, 2023
dc864b5
deprecated build_lines_sp
robitalec Aug 3, 2023
f20ce11
clarify dep version
robitalec Aug 3, 2023
ba10704
use setorder and st_sf with linestrings by splitBy
robitalec Aug 3, 2023
c89f8d9
fix missing pkgs::
robitalec Aug 7, 2023
6cf217d
fix ensure splitBy col/arg
robitalec Aug 7, 2023
e6735d6
rm library from test file
robitalec Aug 7, 2023
e4033c4
fix replace length with nrow
robitalec Aug 7, 2023
27dca38
fix returns sf lines not spatial
robitalec Aug 7, 2023
5724ea0
fix check ordered lines
robitalec Aug 7, 2023
be55464
mv packages to testthat.R
robitalec Aug 7, 2023
494f507
mv library calls to testthat
robitalec Aug 7, 2023
c56ee7c
fix missing error if hrType not mcp or kernel
robitalec Aug 7, 2023
975e24a
return sf obj
robitalec Aug 7, 2023
8570cd6
fst test for mcp or kernel
robitalec Aug 7, 2023
6213b96
fix splitBy arg/col
robitalec Aug 7, 2023
b5dbf7b
fix tests for sf polygons/multipolygons
robitalec Aug 7, 2023
247f008
fix use expect in
robitalec Aug 7, 2023
136fb4a
update docs
robitalec Aug 7, 2023
aceaf02
update projection arg
robitalec Aug 7, 2023
4b6e9d3
update projection faq
robitalec Aug 17, 2023
2f65458
clarify sf returned
robitalec Aug 17, 2023
36d529d
notes about sf transtion up front
robitalec Aug 17, 2023
dab4c94
defining*
robitalec Aug 17, 2023
2254138
bump roxygen
robitalec Aug 17, 2023
74626a1
man
robitalec Aug 17, 2023
d125c10
use h2
robitalec Aug 17, 2023
44ac15e
mv group polys workflow up
robitalec Aug 17, 2023
1388528
fix use links and markdown
robitalec Aug 17, 2023
b616124
h2
robitalec Aug 17, 2023
a03ca67
show crs as numeric
robitalec Aug 17, 2023
b1ddac9
tidy examples
robitalec Aug 17, 2023
52e2883
tidy
robitalec Aug 17, 2023
f1e183d
clarify
robitalec Aug 17, 2023
b26cea0
rm note about sp warning
robitalec Aug 17, 2023
25436f9
bump roxygen
robitalec Aug 17, 2023
a206a2a
man
robitalec Aug 17, 2023
dfec811
Merge pull request #53 from ropensci/fix/rm-sp-build-lines
robitalec Aug 17, 2023
40ac530
Merge branch 'fix/rm-retired-spatial-pkgs' into fix/rm-sp-build-polys
robitalec Aug 17, 2023
0762009
Merge pull request #52 from ropensci/fix/rm-sp-build-polys
robitalec Aug 17, 2023
60af2c1
fst fix links, markdown
robitalec Aug 17, 2023
0c795be
reorder for clarity
robitalec Aug 17, 2023
2be3f5c
add test if splitBy non NULL but timegroup NULL
robitalec Aug 17, 2023
35ac2fd
flex splitBy only if provided
robitalec Aug 17, 2023
52e523f
clarify lns arent spLines
robitalec Aug 17, 2023
bed5861
use sf buffer, intersects
robitalec Aug 17, 2023
e7cd97d
switch spLines input to sfLines
robitalec Aug 17, 2023
b7670b4
test sfLines
robitalec Aug 17, 2023
8a7a575
preserve names
robitalec Aug 17, 2023
f8d95f0
require id still if sfLines
robitalec Aug 17, 2023
23d4f56
fix check nrow instead
robitalec Aug 17, 2023
84b68fc
add detail id required
robitalec Aug 17, 2023
f776a50
check nrow and uniqueN id
robitalec Aug 17, 2023
20b0e98
test required id
robitalec Aug 17, 2023
708aae3
r spatial evol section
robitalec Aug 17, 2023
d37cfd2
linestring notes
robitalec Aug 17, 2023
943346f
minor details
robitalec Aug 17, 2023
09ad3b9
use utm num
robitalec Aug 17, 2023
fb7a7d9
yes test
robitalec Aug 17, 2023
d78f53e
fix links
robitalec Aug 17, 2023
4874e7a
minor vignette edits
robitalec Aug 17, 2023
0759d49
fix utm
robitalec Aug 17, 2023
0f520a8
man
robitalec Aug 17, 2023
5ff0511
Merge pull request #54 from ropensci/fix/rm-sp-group
robitalec Aug 17, 2023
42767f5
rox -> md
robitalec Aug 17, 2023
3616961
sfPolys not sp
robitalec Aug 17, 2023
ed3055d
test sfPolys
robitalec Aug 17, 2023
50d592f
stop if id null
robitalec Aug 17, 2023
efef67c
fix return id as provided
robitalec Aug 18, 2023
8feef42
test if id returned as provided
robitalec Aug 18, 2023
701a7bd
fix modify by reference in build_polys, breaks group_polys by
robitalec Aug 18, 2023
aeaaf9f
flex return if DT/sfPolys provided
robitalec Aug 18, 2023
4b50752
intersection
robitalec Aug 18, 2023
09e99c7
area, proportions return units
robitalec Aug 18, 2023
d51f900
set agr to constant to avoid warnings
robitalec Aug 18, 2023
e44278b
check disjointed, return 0 area proportion
robitalec Aug 18, 2023
b5961ce
fix col checks
robitalec Aug 18, 2023
e03e7d8
use epsg num
robitalec Aug 18, 2023
3344ed9
fix unnecessary promises, warnings
robitalec Aug 18, 2023
306856e
test lengths returned expected
robitalec Aug 18, 2023
f8d8bb7
test area, proportions returned expected
robitalec Aug 18, 2023
f894ebf
fix quote percent
robitalec Aug 18, 2023
bf92aa3
intro
robitalec Aug 18, 2023
3a3916e
r spatial evol
robitalec Aug 18, 2023
aef937b
projection edits
robitalec Aug 18, 2023
83f8bd7
note units returned
robitalec Aug 18, 2023
ded91bc
note splitBy cant be used with sfPolys
robitalec Aug 18, 2023
b8f3310
use epsg numb
robitalec Aug 18, 2023
de7a5df
double |
robitalec Aug 18, 2023
7f8bd53
update group polys descriptions in vignettes
robitalec Aug 18, 2023
6650588
man
robitalec Aug 18, 2023
9d9d211
fix typos
robitalec Aug 18, 2023
1d12bf3
Merge pull request #55 from ropensci/fix/rm-sp-group-polys
robitalec Aug 18, 2023
c80071c
rm old sp versions
robitalec Aug 18, 2023
71e1eda
man
robitalec Aug 18, 2023
aa82ec6
rm sp, rgeos, methods and add sf, units
robitalec Aug 18, 2023
7c12010
update system requirements
robitalec Aug 18, 2023
600d007
minimum adehabitatHR version
robitalec Aug 18, 2023
9b3e852
update workflow
robitalec Aug 21, 2023
84c562c
more informative test
robitalec Aug 21, 2023
10de20a
use set units
robitalec Aug 21, 2023
1a9df5a
fix non convertible units error
robitalec Aug 21, 2023
3da121e
rm links to rgeos
robitalec Aug 21, 2023
0dffe53
fix simpler units
robitalec Aug 21, 2023
faaee37
fix set >100 to 100
robitalec Aug 21, 2023
2736cbf
fix no waldo...
robitalec Aug 21, 2023
c8fecf7
cheat avoid tiny differences
robitalec Aug 22, 2023
6a269c9
test id provided
robitalec Aug 22, 2023
aa3f12d
test sfPolys has area
robitalec Aug 22, 2023
1630f4c
test timegroup required
robitalec Aug 22, 2023
7b12989
fix test missing timegroup
robitalec Aug 22, 2023
861fd41
test sfLines id, uniqueN id
robitalec Aug 22, 2023
ea0b25a
update r-spatial evolution details
robitalec Aug 23, 2023
d2a5e7f
bump version
robitalec Aug 23, 2023
287f039
add (temporary) package startup message
robitalec Aug 23, 2023
b7da7a2
man
robitalec Aug 23, 2023
01b171f
note temp startup msg
robitalec Aug 23, 2023
2c05f56
add news r-spatial evolution and new install help
robitalec Aug 23, 2023
82f8f5b
fix missing v0.1.17 news
robitalec Aug 23, 2023
7e05e50
update codemeta
robitalec Aug 23, 2023
577bfba
fst CITATION
robitalec Aug 23, 2023
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1 change: 1 addition & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -15,3 +15,4 @@ Makefile
^doc$
^Meta$
^\.github$
^CITATION\.cff$
4 changes: 2 additions & 2 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
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

Expand Down
257 changes: 257 additions & 0 deletions CITATION.cff
Original file line number Diff line number Diff line change
@@ -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
Original file line number Diff line number Diff line change
@@ -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
Expand Down
27 changes: 26 additions & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
@@ -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
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).
Expand Down
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