Skip to content

patterninstitute/azores.rorquals

BranchesTags

Repository files navigation

azores.rorquals

The goal of azores.rorquals is to provide an R Compendium Accompanying Peres dos Santos et al. (2025).

Installation

# install.packages("pak")
pak::pak("patterninstitute/azores.rorquals")

Sightings

A data set of sightings of rorquals in the Azores, during the period of 2012 and 2018:

library(azores.rorquals)
#> Loading required package: sf
#> Linking to GEOS 3.13.0, GDAL 3.10.0, PROJ 9.5.0; sf_use_s2() is TRUE
sightings_sf
#> Simple feature collection with 54946 features and 8 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -839828 ymin: -631183.3 xmax: 840628.2 ymax: 586935
#> Projected CRS: +proj=laea +lat_0=38.5 +lon_0=-28 +datum=WGS84 +units=m +no_defs
#> # A tibble: 54,946 × 9
#>    source species      datetime            date       time     sc    tc presence
#>  * <chr>  <chr>        <dttm>              <date>     <hms> <int> <int> <chr>   
#>  1 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1 1933001…
#>  2 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1 1933001…
#>  3 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     2     1 1933002…
#>  4 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     3     1 1933003…
#>  5 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     4     1 1933004…
#>  6 gbif   Stenella co… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1 1048400…
#>  7 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     1     1 1934001…
#>  8 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     2     1 1934002…
#>  9 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     3     1 1934003…
#> 10 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     4     1 1934004…
#> # ℹ 54,936 more rows
#> # ℹ 1 more variable: geometry <POINT [m]>

Presences

The presences_sf dataset is a filtered version of sightings_sf with redundant observations removed, ensuring that each unique animal is counted only once. The presence column provides a unique identifier for each individual.

The presences_sf2 dataset contains the same observations as presences_sf but includes additional climate and topographical variables.

presences_sf
#> Simple feature collection with 44037 features and 9 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -839797.6 ymin: -631183.3 xmax: 840628.2 ymax: 586935
#> Projected CRS: +proj=laea +lat_0=38.5 +lon_0=-28 +datum=WGS84 +units=m +no_defs
#> # A tibble: 44,037 × 10
#>    source species      datetime            date       time     sc    tc presence
#>  * <chr>  <chr>        <dttm>              <date>     <hms> <int> <int> <chr>   
#>  1 gbif   Stenella co… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1 1048400…
#>  2 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1 1933001…
#>  3 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     2     1 1933002…
#>  4 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     3     1 1933003…
#>  5 gbif   Delphinus d… 2007-04-10 00:00:00 2007-04-10 NA s…     4     1 1933004…
#>  6 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     1     1 1934001…
#>  7 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     2     1 1934002…
#>  8 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     3     1 1934003…
#>  9 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     4     1 1934004…
#> 10 gbif   Delphinus d… 2007-04-11 00:00:00 2007-04-11 NA s…     5     1 1934005…
#> # ℹ 44,027 more rows
#> # ℹ 2 more variables: mixed_sp_grp <chr>, geometry <POINT [m]>
presences_sf2
#> Simple feature collection with 44037 features and 17 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -839797.6 ymin: -631183.3 xmax: 840628.2 ymax: 586935
#> Projected CRS: +proj=laea +lat_0=38.5 +lon_0=-28 +datum=WGS84 +units=m +no_defs
#> First 10 features:
#>    source               species   datetime       date    time sc tc    presence
#> 1    gbif Stenella coeruleoalba 2007-04-10 2007-04-10 NA secs  1  1 10484001001
#> 2    gbif     Delphinus delphis 2007-04-10 2007-04-10 NA secs  1  1  1933001001
#> 3    gbif     Delphinus delphis 2007-04-10 2007-04-10 NA secs  2  1  1933002001
#> 4    gbif     Delphinus delphis 2007-04-10 2007-04-10 NA secs  3  1  1933003001
#> 5    gbif     Delphinus delphis 2007-04-10 2007-04-10 NA secs  4  1  1933004001
#> 6    gbif     Delphinus delphis 2007-04-11 2007-04-11 NA secs  1  1  1934001001
#> 7    gbif     Delphinus delphis 2007-04-11 2007-04-11 NA secs  2  1  1934002001
#> 8    gbif     Delphinus delphis 2007-04-11 2007-04-11 NA secs  3  1  1934003001
#> 9    gbif     Delphinus delphis 2007-04-11 2007-04-11 NA secs  4  1  1934004001
#> 10   gbif     Delphinus delphis 2007-04-11 2007-04-11 NA secs  5  1  1934005001
#>    mixed_sp_grp      mld      sst       chl     depth      slope dst_all_sm
#> 1    0001001001 16.32740 16.57000 0.5599283  831.0224  0.3162881   30619.25
#> 2    0001002001 14.95407 16.51998 2.1153419  616.3859  7.8704503   30526.34
#> 3    0001003001 15.25926 16.55999 0.4679706  786.0898  0.8380182   28066.52
#> 4    0001004001 16.32740 16.60000 0.5599283  868.7615  2.1067018   29314.37
#> 5    0001005001 14.64889 16.60998 0.4254855  919.2671  3.2004743   27873.97
#> 6    0002001001 13.88592 16.77999 0.4627705  777.6098  3.5939226   29992.30
#> 7    0002002001 13.88592 16.82000 0.4815105  828.7536  1.0009347   28829.75
#> 8    0002003001 12.66518 16.73998 0.4886960  356.0018 18.0552602   34012.53
#> 9    0002004001 15.56444 16.77210 0.4784797        NA         NA   37033.25
#> 10   0002005001 12.51259 16.82998 0.4634760 1208.8931  3.9953495   29045.14
#>    dst_lrg_sm dst_sml_sm                    geometry
#> 1    45896.94   30619.25 POINT (-47310.49 -10036.94)
#> 2    38475.54   30526.34 POINT (-52938.36 -2508.946)
#> 3    40816.06   28066.52  POINT (-51663.29 -7790.11)
#> 4    47720.79   29314.37 POINT (-43688.28 -13202.49)
#> 5    49989.31   27873.97 POINT (-40352.78 -15994.97)
#> 6    42554.59   29992.30 POINT (-49768.66 -7357.982)
#> 7    44194.34   28829.75 POINT (-48861.64 -11378.21)
#> 8    45377.20   34012.53 POINT (-46437.58 -5083.639)
#> 9    53504.84   37033.25  POINT (-38022.26 -6811.32)
#> 10   53593.13   29045.14  POINT (-36244.88 -16051.4)

Rorquals occurrences

The rorquals_occurrence dataset is derived from presences_sf2 through the following steps:

  1. Observations with missing (NA) values for any climate or topographical variable are removed.

  2. Observations of the target species—Balaenoptera physalus (Fin whale), Balaenoptera borealis (Sei whale), Balaenoptera musculus (Blue whale), and Megaptera novaeangliae (Humpback whale)—are classified as “presence” in the class column, while all other species are labeled as “absence”.

  3. Observations that could simultaneously represent both presences of target species and absences of others are excluded.

  4. Observations located on land are removed. This issue may arise in a small subset of records sourced from GBIF, or due to rasterization effects in climate and topographical data, when merging locations that are very close to the shore (< 500 m).

rorquals_occurrence
#> Simple feature collection with 43337 features and 19 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -697580.6 ymin: -554293.5 xmax: 684416.8 ymax: 533719.9
#> Projected CRS: +proj=laea +lat_0=38.5 +lon_0=-28 +datum=WGS84 +units=m +no_defs
#> # A tibble: 43,337 × 20
#>    source species         class datetime            date       time     sc    tc
#>  * <chr>  <chr>           <chr> <dttm>              <date>     <drt> <int> <int>
#>  1 gbif   Stenella coeru… abse… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1
#>  2 gbif   Delphinus delp… abse… 2007-04-10 00:00:00 2007-04-10 NA s…     1     1
#>  3 gbif   Delphinus delp… abse… 2007-04-10 00:00:00 2007-04-10 NA s…     2     1
#>  4 gbif   Delphinus delp… abse… 2007-04-10 00:00:00 2007-04-10 NA s…     3     1
#>  5 gbif   Delphinus delp… abse… 2007-04-10 00:00:00 2007-04-10 NA s…     4     1
#>  6 gbif   Delphinus delp… abse… 2007-04-11 00:00:00 2007-04-11 NA s…     1     1
#>  7 gbif   Delphinus delp… abse… 2007-04-11 00:00:00 2007-04-11 NA s…     2     1
#>  8 gbif   Delphinus delp… abse… 2007-04-11 00:00:00 2007-04-11 NA s…     3     1
#>  9 gbif   Delphinus delp… abse… 2007-04-11 00:00:00 2007-04-11 NA s…     5     1
#> 10 gbif   Delphinus delp… abse… 2007-04-11 00:00:00 2007-04-11 NA s…     6     1
#> # ℹ 43,327 more rows
#> # ℹ 12 more variables: presence <chr>, mixed_sp_grp <chr>, mld <dbl>,
#> #   sst <dbl>, chl <dbl>, depth <dbl>, slope <dbl>, dst_all_sm <dbl>,
#> #   dst_lrg_sm <dbl>, dst_sml_sm <dbl>, geometry <POINT [m]>, is_in_eez <lgl>
colours <- c(
  Balaenopteridae = "#0F00FF",
  Physeteridae = "#FFEE00AF",
  Ziphiidae = "#FFA600",
  Delphinidae  = "#E8E8E8AF",
  Kogiidae = "#00E000",
  Balaenidae = "#F404E2",
  Phocoenidae = "#04B3F4"
)

rorquals_occurrence |>
  dplyr::filter(is_in_eez) |>
  dplyr::mutate(season = as_season(date)) |>
  dplyr::left_join(cetaceans(), by = "species") |>
  tidyr::drop_na(family) |>
  ggplot() +
  geom_sf(data = CAOP.RAA.2024::districts(), fill = "black") +
  geom_sf(data = CAOP.RAA.2024::eez(distance = 200), fill = NA, linewidth = 0.5, col = "darkgray") +
  geom_sf(mapping = aes(col = family), size = 0.1) +
  geom_sf(data = CAOP.RAA.2024::eez(distance = 12), fill = NA, linewidth = 0.5, col = "#FF7B7B") +
  scale_color_manual(values = colours, name = "Cetacean Family") +
  guides(colour = guide_legend(override.aes = list(size = 3))) +
  facet_wrap(vars(season)) +
  theme_minimal() +
  theme(legend.title = element_text(hjust = 0.5),
        strip.text = element_text(size = 14))

About

R Compendium Accompanying Peres dos Santos et al. (2025)

Resources

Readme

License

CC-BY-4.0 license
Activity
Custom properties

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

No releases published

Packages

 
 
 

Contributors

Languages