Introduction to the finbif package

#> [[1]]
#> [[1]]$matchingName
#> [1] "Betula pendula var. pendula"
#> 
#> [[1]]$nameType
#> [1] "MX.scientificName"
#> 
#> [[1]]$id
#> [1] "MX.37994"
#> 
#> [[1]]$scientificName
#> [1] "Betula pendula var. pendula"
#> 
#> [[1]]$taxonRank
#> [1] "MX.variety"
#> 
#> [[1]]$cursiveName
#> [1] TRUE
#> 
#> [[1]]$finnish
#> [1] TRUE
#> 
#> [[1]]$species
#> [1] TRUE
#> 
#> [[1]]$vernacularName
#> [[1]]$vernacularName$sv
#> [1] "vanlig vårtbjörk"
#> 
#> [[1]]$vernacularName$fi
#> [1] "vihtakoivu"
#> 
#> 
#> [[1]]$informalGroups
#> [[1]]$informalGroups[[1]]
#> [[1]]$informalGroups[[1]]$id
#> [1] "MVL.343"
#> 
#> [[1]]$informalGroups[[1]]$name
#> [[1]]$informalGroups[[1]]$name$fi
#> [1] "Putkilokasvit"
#> 
#> [[1]]$informalGroups[[1]]$name$sv
#> [1] "Kärlväxter"
#> 
#> [[1]]$informalGroups[[1]]$name$en
#> [1] "Vascular plants"
#> 
#> 
#> 
#> 
#> [[1]]$type
#> [1] "partialMatches"
#> 
#> 
#> [[2]]
#> [[2]]$matchingName
#> [1] "Betula nana × pendula"
#> 
#> [[2]]$nameType
#> [1] "MX.scientificName"
#> 
#> [[2]]$id
#> [1] "MX.38005"
#> 
#> [[2]]$scientificName
#> [1] "Betula nana × pendula"
#> 
#> [[2]]$taxonRank
#> [1] "MX.infragenericHybrid"
#> 
#> [[2]]$cursiveName
#> [1] TRUE
#> 
#> [[2]]$finnish
#> [1] TRUE
#> 
#> [[2]]$species
#> [1] TRUE
#> 
#> [[2]]$vernacularName
#> named list()
#> 
#> [[2]]$informalGroups
#> [[2]]$informalGroups[[1]]
#> [[2]]$informalGroups[[1]]$id
#> [1] "MVL.343"
#> 
#> [[2]]$informalGroups[[1]]$name
#> [[2]]$informalGroups[[1]]$name$fi
#> [1] "Putkilokasvit"
#> 
#> [[2]]$informalGroups[[1]]$name$sv
#> [1] "Kärlväxter"
#> 
#> [[2]]$informalGroups[[1]]$name$en
#> [1] "Vascular plants"
#> 
#> 
#> 
#> 
#> [[2]]$type
#> [1] "partialMatches"
#> 
#> 

#> Records downloaded: 10
#> Records available: 36710
#> A data.frame [10 x 12]
#>     record_id scientific_name abundance lat_wgs84 lon_wgs84           date_time
#> 1   …41168#42     Cygnus olor  10        60.42799  22.20051 2022-09-12 12:00:00
#> 2   …40986#60     Cygnus olor  3         60.42797  22.20056 2022-09-11 12:00:00
#> 3    …41017#3   Cygnus cygnus  5         62.01636  22.99255 2022-09-11 12:00:00
#> 4    …40997#3   Cygnus cygnus  2         61.09915  21.55087 2022-09-11 09:55:00
#> 5   …40730#75     Cygnus olor  6         60.42796  22.20057 2022-09-10 12:00:00
#> 6   …40539#51     Cygnus olor  7         61.10534  21.45097 2022-09-09 08:55:00
#> 7  …38974#119   Cygnus cygnus  6         63.6616   29.22317 2022-09-08 12:00:00
#> 8  …38974#140   Cygnus cygnus  3         63.50457  29.39159 2022-09-08 12:00:00
#> 9  …38974#110   Cygnus cygnus  4         63.73461  29.37687 2022-09-08 12:00:00
#> 10 …40443#120     Cygnus olor  3         60.42797  22.20054 2022-09-08 12:00:00
#> ...with 0 more records and 6 more variables:
#> coordinates_uncertainty, any_issues, requires_verification, requires_identification,
#> record_reliability, record_quality

# Download all the occurrences of Eurasian Jay in Finland
# that have coordinates accurate to at least 100m
jays <- finbif_occurrence(
  taxa   = "Eurasian Jay",
  filter = c(
    coordinates_uncertainty_max = 100,
    country                     = "Finland"
  ),
  n      = 2e4,
  quiet  = TRUE
)

# Compute the density of occurrences in 1/4 degree cells and plot as a heatmap
with(
  data = c(jays, finland_map),
  expr = {
    par(mar = c(5, 5, 1, 1), las = 1)
    # compute a 2d histogram from the occurrences
    breaks  <- breaks_xy(bbox, .25) # breakpoints every 1/4 of a degree
    density <- hist_xy(xy = list(lon_wgs84, lat_wgs84), breaks)
    # plot the histogram as a heatmap
    image(density,
          asp    = 2.4,
          breaks = 2^seq(0, 12), # breakpoints for the gridcell colours
          col    = hcl.colors(12, rev = TRUE),
          xlab   = "Longitude",
          ylab   = "Latitude",
          panel.first = grid())
    legend("topright",
           inset  = c(0, .01),
           legend = expression(2^12, "", "", 2^6, "", "", 2^0),
           fill   = hcl.colors(7),
           border = NA,
           bty    = "n",
           adj    = c(0, 0.25),
           x.intersp = .2,
           y.intersp = .5)
    # add the Finnish border
    polygon(x = vertices, lwd = .2)
  }
)