In BirdStudiesCanada/rNatureCounts: Access and download data on plant and animal populations from NatureCounts

library(naturecounts)
library(dplyr)

In naturecounts, by default default data is downloaded with a specific set of fields/columns. However, for more advanced applications, users may wish to specify which fields/columns to return. The Bird Monitoring Data Exchange (BMDE) schema keeps track of variables used to augment observation data. There are different versions reflecting different collections of variables.

The following examples use the "testuser" user which is not available to you. You can quickly sign up for a free account of your own to access and play around with these examples. Simply replace testuser with your own username.

BMDE versions

There are several ways to get more information about these different field/columns sets.

1. You can get a list of the different versions with the meta_bmde_versions() function.

meta_bmde_versions()

1. You can get a list of the specific fields/columns included in each version using the meta_bmde_fields() function

meta_bmde_fields(version = "BMDE-BAND-2.00") %>%
  head()

1. You can see which BMDE versions are used by different collections by looking at the metadata associated with that collection.

meta_collections() %>% 
  head()

Specifying fields by version

By default, the BMDE2.00-min or minimum BMDE version is used when downloading data, but you can specify other versions with either the version name, or the shorthand.

cardinals <- nc_data_dl(species = 19360, fields_set = "core", 
                        collection = "ABATLAS2", verbose = FALSE,
                        username = "testuser", info = "nc_vignette")
names(cardinals)

Basic fields

Note that there are extra fields/columns downloaded in every request, which are in addition to the BMDE fields. These are additional, basic, indexed fields used in the database.

You can figure out exactly which fields these are, by removing all the fields from the core BMDE field set.

names(cardinals)[!names(cardinals) %in% meta_bmde_fields(version = "core")$local_name]

Custom fields

The basic fields will always be included in any data request. However, you can choose which fields/columns to include in addition to these basic fields, by specifying fields_set = custom, and listing all additional fields.

cardinals <- nc_data_dl(species = 19360, fields_set = "custom", 
                        fields = c("Sex", "SamplingEventIdentifier"), 
                        collection = "ABATLAS2", verbose = FALSE,
                        username = "testuser", info = "nc_vignette")
head(cardinals)

Adding specific fields to a BMDE version

In a more complex example, if you wished to download data with the minimum set of BMDE fields, but including a couple of extra fields, you could combine the core fields with the extras you want, and pass them on as a custom field set.

For example, first collect the minimum field/column names.

my_fields <- meta_bmde_fields(version = "minimum")$local_name
my_fields

Then add in the extra fields.

my_fields <- c(my_fields, "Sex", "LifeStage")
my_fields

Now download the data.

cardinals <- nc_data_dl(species = 19360, fields_set = "custom", 
                        fields = my_fields, 
                        collection = "ABATLAS2", verbose = FALSE,
                        username = "testuser", info = "nc_vignette")
head(cardinals)

Great!

BirdStudiesCanada/rNatureCounts documentation built on July 3, 2023, 2:06 a.m.