Merge pull request #56 from ropensci/fix/cran-notes

Fix/cran notes

CITATION.cff

@@ -8,9 +8,9 @@ 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
+version: 0.2.1
 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
+  (2019) <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.
@@ -69,6 +69,18 @@ references:
   institution:
     name: R Foundation for Statistical Computing
   version: '>= 3.4'
+- 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: data.table
   abstract: 'data.table: Extension of `data.frame`'
@@ -84,51 +96,6 @@ references:
     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'
@@ -163,17 +130,59 @@ references:
     orcid: https://orcid.org/0000-0002-1416-3412
   year: '2023'
 - type: software
-  title: testthat
-  abstract: 'testthat: Unit Testing for R'
+  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: stats
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
+- 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: asnipe
+  abstract: 'asnipe: Animal Social Network Inference and Permutations for Ecologists'
   notes: Suggests
-  url: https://testthat.r-lib.org
-  repository: https://CRAN.R-project.org/package=testthat
+  repository: https://CRAN.R-project.org/package=asnipe
   authors:
-  - family-names: Wickham
-    given-names: Hadley
-    email: hadley@posit.co
+  - family-names: Farine
+    given-names: Damien R.
+    email: dfarine@ab.mpg.de
   year: '2023'
-  version: '>= 2.1.0'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -186,6 +195,22 @@ references:
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
   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'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -230,28 +255,14 @@ references:
     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'''
+  title: testthat
+  abstract: 'testthat: Unit Testing for R'
   notes: Suggests
-  url: https://github.com/rstudio/markdown
-  repository: https://CRAN.R-project.org/package=markdown
+  url: https://testthat.r-lib.org
+  repository: https://CRAN.R-project.org/package=testthat
   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
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
   year: '2023'
+  version: '>= 2.1.0'

DESCRIPTION

@@ -1,43 +1,43 @@
 Package: spatsoc
 Title: Group Animal Relocation Data by Spatial and Temporal Relationship
-Version: 0.2.0
-Authors@R: 
-    c(person(given = "Alec L.",
-             family = "Robitaille",
-             role = c("aut", "cre"),
-             email = "robit.alec@gmail.com",
-             comment = c(ORCID = "0000-0002-4706-1762")),
-      person(given = "Quinn",
-             family = "Webber",
-             role = "aut",
-             comment = c(ORCID = "0000-0002-0434-9360")),
-      person(given = "Eric",
-             family = "Vander Wal",
-             role = "aut",
-             comment = c(ORCID = "0000-0002-8534-4317")))
-Description: 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. 
-Depends: R (>= 3.4)
+Version: 0.2.1
+Authors@R: c(
+    person("Alec L.", "Robitaille", , "robit.alec@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-4706-1762")),
+    person("Quinn", "Webber", role = "aut",
+           comment = c(ORCID = "0000-0002-0434-9360")),
+    person("Eric", "Vander Wal", role = "aut",
+           comment = c(ORCID = "0000-0002-8534-4317"))
+  )
+Description: Detects spatial and temporal groups in GPS relocations
+    (Robitaille et al. (2019) <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.
 License: GPL-3 | file LICENSE
-Encoding: UTF-8
-Imports: data.table (>= 1.10.5),
-    sf,
-    units,
+URL: https://docs.ropensci.org/spatsoc/,
+    https://github.com/ropensci/spatsoc
+BugReports: https://github.com/ropensci/spatsoc/issues
+Depends: 
+    R (>= 3.4)
+Imports: 
     adehabitatHR (>= 0.4.21),
-    igraph
+    data.table (>= 1.10.5),
+    igraph,
+    sf,
+    stats,
+    units
 Suggests: 
-    testthat (>= 2.1.0),
+    asnipe,
     knitr,
+    markdown,
     rmarkdown,
-    asnipe,
-    markdown
-SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3
-RoxygenNote: 7.2.3
-VignetteBuilder: knitr
+    testthat (>= 2.1.0)
+VignetteBuilder: 
+    knitr
+Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-BugReports: https://github.com/ropensci/spatsoc/issues
-URL: https://docs.ropensci.org/spatsoc/, https://github.com/ropensci/spatsoc
+RoxygenNote: 7.2.3
+SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0),
+    sqlite3

NEWS.md

@@ -1,4 +1,9 @@
-# v 0.2.0
+# v 0.2.1 (2023-08-23)
+
+* fixed CRAN notes [PR 56](https://github.com/ropensci/spatsoc/pull/56)
+
+
+# v 0.2.0 (2023-08-22)
 
 * following [R-spatial evolution](https://r-spatial.org/r/2022/04/12/evolution.html),
 removed dependencies on retired spatial packages (

R/edge_nn.R

@@ -69,6 +69,9 @@
 #' # Read example data
 #' DT <- fread(system.file("extdata", "DT.csv", package = "spatsoc"))
 #'
+#' # Select only individuals A, B, C for this example
+#' DT <- DT[ID %in% c('A', 'B', 'C')]
+#'
 #' # Cast the character column to POSIXct
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'

R/group_pts.R

@@ -73,6 +73,9 @@
 #' # Read example data
 #' DT <- fread(system.file("extdata", "DT.csv", package = "spatsoc"))
 #'
+#' # Select only individuals A, B, C for this example
+#' DT <- DT[ID %in% c('A', 'B', 'C')]
+#'
 #' # Cast the character column to POSIXct
 #' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 #'

R/randomizations.R

@@ -74,7 +74,7 @@
 #' @param iterations The number of iterations to randomize
 #'
 #' @references
-#' \url{https://doi.org/10.1111/2041-210X.12553}
+#' <doi:10.1111/2041-210X.12553>
 #' @export
 #'
 #' @family Social network tools
@@ -86,6 +86,9 @@
 #' # Read example data
 #' DT <- fread(system.file("extdata", "DT.csv", package = "spatsoc"))
 #'
+#' # Select only individuals A, B, C for this example
+#' DT <- DT[ID %in% c('A', 'B', 'C')]
+#'
 #' # Date time columns
 #' DT[, datetime := as.POSIXct(datetime)]
 #' DT[, yr := year(datetime)]

README.Rmd

@@ -12,11 +12,11 @@ knitr::opts_chunk$set(message = FALSE,
 # spatsoc 
 
 <!-- badges: start -->
-[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![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)
-[![codecov](https://codecov.io/gh/ropensci/spatsoc/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/spatsoc)
+[![codecov](https://app.codecov.io/gh/ropensci/spatsoc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/spatsoc)
 [![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)
 <!-- badges: end -->
 

README.md

@@ -5,12 +5,12 @@
 
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
-developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+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)
-[![codecov](https://codecov.io/gh/ropensci/spatsoc/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/spatsoc)
+[![codecov](https://app.codecov.io/gh/ropensci/spatsoc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/spatsoc)
 [![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)
 <!-- badges: end -->