Extract gbif occurrences within a geographic administrative area with rgbif

I would like to extract all occurrences for a Canadian province for a given taxa with rgbif. I am following this tutorial : https://docs.ropensci.org/rgbif/articles/getting_occurrence_data.html

It mentions that we can use the gadm instead of the polygonal boundaries but I can't figure out the code. My real area that I am want should be CAN11_1. I am trying to simplify the code from here and adapt to my taxa. This simplified code works:

occ_download(
  pred("taxonKey", 2436775),
 pred("gadm","ETH"),
  format = "SIMPLE_CSV")

However, this code using phylumKey instead of taxonKey does not work. The error message says that the problem is the pred("gadm", "ETH").

occ_download(
  pred("phylumKey", 35),
 pred("gadm","ETH"),

  format = "SIMPLE_CSV")

This code works but is not the correct polygon.

occ_download(
  pred_in("phylumKey", c(35, 9, 13)), # important to use pred_in
  pred_within("POLYGON((-70 47,-69 47,-69 49,-70 49,-70 47))"),
  format = "SIMPLE_CSV"
)

What am I missing???

Solution

You can use pred_and() with two separate pred() calls. Two separate unwrapped pred() calls e.g. not using pred_in() should work too.

When that error was returned, it seems like for some reason pred_in() was expecting a list object, although it does work with a single value.

library(rgbif)

# Request data (omit user, pwd, and email if already added to .Renviron)
occ_download(pred_and(pred("phylumKey", 35), pred("gadm","ETH")),
             format = "SIMPLE_CSV",
             user = "your_gbif_username",
             pwd = "your_gbif_password",
             email = "your_gbif_email")

# Check download status using occurrence number,
# see result in console from previous step
occ_download_wait("download occurrence number")

# Load data
df <- occ_download_get("download occurrence number") %>%
  occ_download_import()

head(df)
# # A tibble: 6 × 50
#     gbifID datasetKey    occurrenceID kingdom phylum class order family genus species
#    <int64> <chr>         <chr>        <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>  
# 1 92657932 85042096-f76… ""           Plantae Bryop… Spha… Spha… Sphag… Spha… Sphagn…
# 2 92643197 85042096-f76… ""           Plantae Bryop… Bryo… Brya… Mniac… Pohl… Pohlia…
# 3 92630747 85042096-f76… ""           Plantae Bryop… Bryo… Dicr… Dicra… Para… Parale…
# 4 92629842 85042096-f76… ""           Plantae Bryop… Bryo… Bart… Bartr… Phil… Philon…
# 5 92622427 85042096-f76… ""           Plantae Bryop… Bryo… Brya… Mniac… Mnium Mnium …
# 6 92622418 85042096-f76… ""           Plantae Bryop… Bryo… Brya… Mniac… Plag… Plagio…
# # ℹ 40 more variables: infraspecificEpithet <chr>, taxonRank <chr>,
# #   scientificName <chr>, verbatimScientificName <chr>,
# #   verbatimScientificNameAuthorship <chr>, countryCode <chr>, locality <chr>,
# #   stateProvince <chr>, occurrenceStatus <chr>, individualCount <int>,
# #   publishingOrgKey <chr>, decimalLatitude <dbl>, decimalLongitude <dbl>,
# #   coordinateUncertaintyInMeters <dbl>, coordinatePrecision <dbl>, elevation <dbl>,
# #   elevationAccuracy <dbl>, depth <lgl>, depthAccuracy <lgl>, eventDate <chr>, …