In usgs/nabatr: R Tools for Accessing and Manipulating North American Bat Monitoring Data

Extract Colony Count NABat Data and Build a Report

Get a token for NABat Database

library(nabatr)
# Enter your NABat username here
username = 'NABat_Username'
token = get_nabat_gql_token(username)
token

# Note: if you leave run token = get_nabat_gql_token(),
#   it will prompt you for a username and then a password

Get Project dataframe which contains all of your NABat projects in the NABat Database

# Refresh token
token = get_refresh_token(token)
# Get your projects lookup table
project_df = get_projects(token)
# Display your projects lookup table
project_df

Get all Colony Count Surveys within a single Project set with project_id

# Refresh token
token = get_refresh_token(token)
# Fill in project id using the project_df lookup table
project_id = 000 # Set equal to one of your project ids

# Get survey dataframe 
cc_survey_df = get_cc_project_summary(token,
                                      project_df,
                                      project_id)
# Display survey dataframe
cc_survey_df

Get all Colony Count data within a single Project set with project_id

# Refresh token
token = get_refresh_token(token)
# Get species dataframe
species_df = get_species(token = token)
# Get Colony Count bulk dataframe
cc_bulk_df = get_colony_bulk_counts(token,
                                    cc_survey_df,
                                    project_id,
                                    species_df)

# Display Colony Count dataframe
cc_bulk_df

Build a Colony Count Report

# Edit these two variables below to your local system (file_name, out_dir)
file_name = 'name_of_ma_report.docx'  
out_dir   = '/directory/to/download/report' # Make sure this ends without a '/'

cc_doc = build_col_doc(out_dir = out_dir,
                         project_df = project_df,
                         project_id = project_id,
                         cc_bulk_df = cc_bulk_df)

# Save out your report
print(cc_doc, target = paste0(out_dir, '/', file_name))

usgs/nabatr documentation built on Jan. 28, 2024, 7:10 a.m.