Record API Demo

# Load core libraries; install these packages if you have not already
library(ridigbio)
library(tidyverse)

# Load library for making nice HTML output
library(kableExtra)

# Let's start with a simple search introducing the primary arguments for the
# function `idig_search_records`
records_1A <- idig_search_records(
  # `rq` is where you adjust your record query
  rq = list(genus = "shortia"),
  # `fields` is where you adjust what fields you want returned by the API
  fields = c("uuid",
             "family",
             "genus",
             "specificepithet",
             "scientificname",
             "stateprovince"),
  # `limit` is where you can set a limit on the number of records to return in
  # order to speed up your query; max is 100000
  limit = 10,
  # `sort` is where you can specify fields for sorting
  sort = c("stateprovince",
           "scientificname"))

# Display the data frame we just created above in a nice pretty table for HTML
knitr::kable(records_1A) %>% 
    kable_styling(bootstrap_options = 
                         c("striped", "hover", "condensed", "responsive")) %>% 
  scroll_box(height = "300px")

# Now let's repeat the same search but remove all arguments other than `rq` to
# see what the defaults for the other arguments look like
records_1B <- idig_search_records(
  rq = list(genus = "shortia"))

records_1B$occurrenceid <- if_else(grepl("^http://", records_1B$occurrenceid),
  gsub("^http://", "", records_1B$occurrenceid),
  records_1B$occurrenceid
)

records_1B$occurrenceid <- if_else(grepl("data.biodiversitydata.nl/naturalis", records_1B$occurrenceid),
  gsub("data.biodiversitydata.nl/naturalis", "bioportal.naturalis.nl/nl", records_1B$occurrenceid),
  records_1B$occurrenceid
)

records_1B$occurrenceid <- if_else(grepl("https://grbio.org/cool", records_1B$occurrenceid),
  gsub("https://grbio.org/cool", "grbio.org/cool", records_1B$occurrenceid),
  records_1B$occurrenceid
)

records_1B$occurrenceid <- if_else(grepl("https://biocol.org", records_1B$occurrenceid),
  gsub("https://biocol.org", "biocol.org", records_1B$occurrenceid),
  records_1B$occurrenceid
)

# Display the data frame we just created above in a nice pretty table for HTML
knitr::kable(records_1B) %>% 
    kable_styling(bootstrap_options = 
                         c("striped", "hover", "condensed", "responsive")) %>% 
  scroll_box(height = "300px")