add references

Author: Bart

CITATION.cff

@@ -8,8 +8,11 @@ message: 'To cite package "getRad" in publications use:'
 type: software
 license: MIT
 title: 'getRad: Download Radar Data for Biological Research'
-version: 0.3.0
+version: 0.3.0.9000
 doi: 10.32614/CRAN.package.getRad
+identifiers:
+- type: doi
+  value: 10.32614/CRAN.package.getRad
 abstract: Load polar volume and vertical profile data for aeroecological research
   directly into R. With 'getRad' you can access data from several sources in Europe
   and the US and standardize it to facilitate further exploration in tools such as
@@ -30,6 +33,29 @@ authors:
   email: peter.desmet@inbo.be
   orcid: https://orcid.org/0000-0002-8442-8025
   affiliation: Research Institute for Nature and Forest (INBO)
+preferred-citation:
+  type: manual
+  title: 'getRad: Download Radar Data for Biological Research'
+  authors:
+  - family-names: Kranstauber
+    given-names: Bart
+    email: b.kranstauber@uva.nl
+    orcid: https://orcid.org/0000-0001-8303-780X
+    affiliation: University of Amsterdam
+  - family-names: Huybrechts
+    given-names: Pieter
+    email: pieter.huybrechts@inbo.be
+    orcid: https://orcid.org/0000-0002-6658-6062
+    affiliation: Research Institute for Nature and Forest (INBO)
+  - family-names: Desmet
+    given-names: Peter
+    email: peter.desmet@inbo.be
+    orcid: https://orcid.org/0000-0002-8442-8025
+    affiliation: Research Institute for Nature and Forest (INBO)
+  year: '2026'
+  notes: R package version 0.3.0
+  url: https://CRAN.R-project.org/package=getRad
+  doi: 10.32614/CRAN.package.getRad
 repository: https://CRAN.R-project.org/package=getRad
 repository-code: https://github.com/aloftdata/getRad
 url: https://aloftdata.github.io/getRad/

R/get_vpts.R

@@ -283,7 +283,8 @@ get_vpts <- function(
     fetched_vpts <- purrr::map(
       fetched_vpts,
       ~ .x[lubridate::`%within%`(.x$datetime, date_interval)]
-    )
+    ) |>
+      purrr::map(add_reference_vpts, source = source)
     if (length(fetched_vpts) != 1) {
       return(fetched_vpts)
     } else {
@@ -322,7 +323,11 @@ get_vpts <- function(
             \(df) dplyr::select(df, -source),
             .purrr_error_call = cl
           )
-        vpts_list <- purrr::map(filtered_vpts_no_source, bioRad::as.vpts)
+        vpts_list <- purrr::map(
+          filtered_vpts_no_source,
+          bioRad::as.vpts
+        ) |>
+          purrr::map(add_reference_vpts, source = source)
         # If we are only returning a single radar, don't return a list
         if (length(vpts_list) == 1) {
           return(purrr::chuck(vpts_list, 1))

R/utils_vpts.R

@@ -0,0 +1,4 @@
+add_reference_vpts <- function(x, source) {
+  x$attributes$references <- c(vptsReferences[source], citation("getRad"))
+  x
+}

R/zzz.R

@@ -63,6 +63,125 @@
   invisible()
 }
 rlang::on_load(rlang::local_use_cli(inline = TRUE))
+
+# References
+
+vptsReferences <- c(
+  "ecog-04003" = bibentry(
+    bibtype = "Misc",
+    key = "ecog-04003",
+    author = c(
+      person(given = "Cecilia", family = "Nilsson"),
+      person(given = "Adriaan", family = "Dokter"),
+      person(given = "Liesbeth", family = "Verlinden"),
+      person(given = "Judy", family = "Shamoun-Baranes"),
+      person(given = "Baptiste", family = "Schmid"),
+      person(given = "Peter", family = "Desmet"),
+      person(given = "Silke", family = "Bauer"),
+      person(given = "Jason", family = "Chapman"),
+      person(given = c("Jose", "A."), family = "Alves"),
+      person(given = c("Phillip", "M."), family = "Stepanian"),
+      person(given = "Nir", family = "Sapir"),
+      person(given = "Charlotte", family = "Wainwright"),
+      person(given = "Mathieu", family = "Boos"),
+      person(given = "Anna", family = "Górska"),
+      person(given = c("Myles", "H.", "M."), family = "Menz"),
+      person(given = "Pedro", family = "Rodrigues"),
+      person(given = "Hidde", family = "Leijnse"),
+      person(given = "Pavel", family = "Zehtindjiev"),
+      person(given = "Robin", family = "Brabant"),
+      person(given = "Günther", family = "Haase"),
+      person(given = "Nadja", family = "Weisshaupt"),
+      person(given = "Michał", family = "Ciach"),
+      person(given = "Felix", family = "Liechti")
+    ),
+    title = "Supplementary material for 'Revealing patterns of nocturnal migration using the European weather radar network'",
+    month = "apr",
+    year = "2018",
+    publisher = "Zenodo",
+    doi = "10.5281/zenodo.1172801",
+    url = "https://doi.org/10.5281/zenodo.1172801"
+  ),
+  uva = bibentry(
+    bibtype = "Misc",
+    key = "uva",
+    author = c(
+      person(given = "Judy", family = "Shamoun-Baranes"),
+      person(given = "Berend-Christiaan", family = "Wijers"),
+      person(given = "Bart", family = "Kranstauber"),
+      person(given = "Bart", family = "Hoekstra"),
+      person(given = "Pieter", family = "Huybrechts"),
+      person(given = c("Adriaan", "M."), family = "Dokter"),
+      person(given = "Hidde", family = "Leijnse"),
+      person(given = "Maarten", family = "Reyniers"),
+      person(given = "Klaus", family = "Stephan"),
+      person(given = "Peter", family = "Desmet")
+    ),
+    title = "UVA_VPTS - Vertical profiles of biological targets derived from weather radars in Belgium, Germany and the Netherlands",
+    month = "jan",
+    year = "2025",
+    publisher = "Research Institute for Nature and Forest (INBO)",
+    doi = "10.5281/zenodo.14711244",
+    url = "https://doi.org/10.5281/zenodo.14711244"
+  ),
+  baltrad = bibentry(
+    bibtype = "Misc",
+    key = "baltrad",
+    author = c(
+      person(given = "Peter", family = "Desmet"),
+      person(given = "Judy", family = "Shamoun-Baranes"),
+      person(given = "Bart", family = "Kranstauber"),
+      person(given = c("Adriaan", "M."), family = "Dokter"),
+      person(given = "Nadja", family = "Weisshaupt"),
+      person(given = "Baptiste", family = "Schmid"),
+      person(given = "Silke", family = "Bauer"),
+      person(given = "Günther", family = "Haase"),
+      person(given = "Bart", family = "Hoekstra"),
+      person(given = "Pieter", family = "Huybrechts"),
+      person(given = "Hidde", family = "Leijnse"),
+      person(given = "Nicolas", family = "Noé"),
+      person(given = "Stijn", family = "Van Hoey"),
+      person(given = "Berend-Christiaan", family = "Wijers"),
+      person(given = "Cecilia", family = "Nilsson")
+    ),
+    title = "BALTRAD_VPTS - Vertical profiles of biological targets derived from European weather radars",
+    month = "jan",
+    year = "2025",
+    publisher = "Research Institute for Nature and Forest (INBO)",
+    doi = "10.5281/zenodo.14711024",
+    url = "https://doi.org/10.5281/zenodo.14711024"
+  ),
+  dark_ecology = bibentry(
+    bibtype = "Article",
+    key = "dark_ecology",
+    author = c(
+      person(given = "Daniel", family = "Sheldon"),
+      person(given = "Kevin", family = "Winner"),
+      person(given = "Iman", family = "Deznabi"),
+      person(given = "Garrett", family = "Bernstein"),
+      person(given = "Pankaj", family = "Bhambani"),
+      person(given = "Tsung-Yu", family = "Lin"),
+      person(given = "Peter", family = "Desmet"),
+      person(given = c("Adriaan", "M."), family = "Dokter"),
+      person(given = c("Kyle", "G."), family = "Horton"),
+      person(given = "Cecilia", family = "Nilsson"),
+      person(given = c("Benjamin", "M."), family = "Van Doren"),
+      person(given = "Andrew", family = "Farnsworth"),
+      person(given = c("Frank", "A."), family = "La Sorte"),
+      person(given = "Subhransu", family = "Maji")
+    ),
+    title = "The Dark Ecology Dataset: Measurements of Aerial Biomass in US Weather Radar from 1995 to 2025",
+    year = "2026",
+    doi = "10.64898/2026.06.20.733536",
+    publisher = "Cold Spring Harbor Laboratory",
+    abstract = "The US NEXRAD radar network has monitored the aerosphere over the US and its territories continuously since the 1990s and archived nearly 300 million radar volume scans. These data contain a wealth of information about the movements of birds, bats, and insects. Historically, this biological information was difficult to access due to the amount of data and challenges in analyzing it. In the last 15 years, fueled by computational and methodological advances, large-scale aeroecology research has blossomed. However, comprehensive analyses of the NEXRAD archive remain very costly. We collected measurements of biological activity from every volume scan in the NEXRAD archive{\\textemdash}nearly 300 million data files total{\\textemdash}to assemble a dataset of aerial biomass over the US from 1995 to 2025. The core data are vertical profiles, which summarize biological activity at different heights above the radar station for each volume scan. We also provide time series data products that aggregate vertical profiles to point measurements at radar stations across time. These data products can support a range of aeroecology analyses at significantly reduced effort.Competing Interest StatementThe authors have declared no competing interest.U.S. National Science Foundation, https://ror.org/021nxhr62, 1661259, 1661329, 2210979Swiss National Science Foundation, https://ror.org/00yjd3n13, 31BD30_216840Belgian Federal Science Policy Office, RT/24/HiRADNetherlands Organisation for Applied Scientific Research, https://ror.org/01bnjb948, EP.1512.22.003Academy of Finland, 359864Leon Levy Foundation, https://ror.org/033hnyq61Lyda Hill Philanthropies, https://ror.org/032sf2845",
+    url = "https://www.biorxiv.org/content/early/2026/06/23/2026.06.20.733536",
+    eprint = "https://www.biorxiv.org/content/early/2026/06/23/2026.06.20.733536.full.pdf",
+    journal = "bioRxiv"
+  )
+)
+
+
 # see ?usethis::use_release_issue() #nolint
 release_bullets <- function() {
   c(

inst/CITATION

@@ -0,0 +1,25 @@
+bibentry(
+  bibtype = "Manual",
+  key = "getRad",
+  title ="getRad: Download Radar Data for Biological Research" ,
+  author = c(person(given = "Bart",
+                           family = "Kranstauber",
+                           role = c("aut", "cre"),
+                           email = "b.kranstauber@uva.nl",
+                           comment = c(ORCID = "0000-0001-8303-780X", affiliation = "University of Amsterdam")),
+                    person(given = "Pieter",
+                           family = "Huybrechts",
+                           role = "aut",
+                           email = "pieter.huybrechts@inbo.be",
+                           comment = c(ORCID = "0000-0002-6658-6062", affiliation = "Research Institute for Nature and Forest (INBO)")),
+                    person(given = "Peter",
+                           family = "Desmet",
+                           role = "aut",
+                           email = "peter.desmet@inbo.be",
+                           comment = c(ORCID = "0000-0002-8442-8025", affiliation = "Research Institute for Nature and Forest (INBO)"))),
+
+     year = "2026",
+         note = "R package version 0.3.0",
+         url = "https://CRAN.R-project.org/package=getRad",
+         doi = "10.32614/CRAN.package.getRad"
+)

tests/testthat/test-get_vpts_references.R

@@ -0,0 +1,79 @@
+test_that("Dark ecology reference", {
+  dk_path <- system.file("extdata", "darkecology", package = "getRad")
+  skip_if(
+    dk_path == "",
+    message = "No local data present for testing local read from dark ecology."
+  )
+  expect_s3_class(
+    kcbx_vpts <- get_vpts(
+      path = dk_path,
+      radar = "KCBX",
+      lubridate::interval(
+        start = "20150101",
+        end = "20150201"
+      ),
+      source = "dark_ecology"
+    ),
+    "vpts"
+  )
+  expect_identical(
+    kcbx_vpts |> purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("dark_ecology")
+  )
+  expect_s3_class(
+    kcbx_vpts |> purrr::pluck("attributes", "references", 2),
+    "bibentry"
+  )
+  expect_identical(
+    kcbx_vpts |> purrr::pluck("attributes", "references", 2) |> attr("key"),
+    "getRad"
+  )
+})
+test_that("aloft reference", {
+  expect_identical(
+    get_vpts("bewid", as.Date("2023-2-1")) |>
+      purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("baltrad")
+  )
+  expect_identical(
+    get_vpts("bewid", as.Date("2023-2-1"), source = "baltrad") |>
+      purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("baltrad")
+  )
+  expect_identical(
+    get_vpts("nlhrw", as.Date("2023-2-1"), source = "uva") |>
+      purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("uva")
+  )
+
+  expect_identical(
+    get_vpts("nlhrw", as.Date("2016-10-6"), source = "ecog-04003") |>
+      purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("ecog-04003")
+  )
+})
+
+
+test_that("rmi reference", {
+  expect_identical(
+    get_vpts("bewid", as.Date("2023-2-1"), source = "rmi") |>
+      purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("rmi")
+  )
+})
+test_that("birdcast reference", {
+  expect_identical(
+    get_vpts("KABX", as.Date("2023-2-1"), source = "birdcast") |>
+      purrr::pluck("attributes", "references", 1),
+    vptsReferences |> purrr::pluck("birdcast")
+  )
+})
+
+
+test_that("references exist for all sources", {
+  expect_identical(
+    vptsReferences |> names() |> sort(),
+    rlang::fn_fmls(get_vpts)$source |> eval() |> sort()
+  )
+  expect_s3_class(vptsReferences, "bibentry")
+})