R/rename_data.R

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

#############################################################################
#     _   _____    ____        __  ____
#    / | / /   |  / __ )____ _/ /_/ __ \
#   /  |/ / /| | / __  / __ `/ __/ /_/ /
#  / /|  / ___ |/ /_/ / /_/ / /_/ _, _/
# /_/ |_/_/  |_/_____/\__,_/\__/_/ |_|
#
# R Tools for accessing and manipulating North American Bat Monitoring data
#
# Written by: Kyle Enns
#
# FILE DESCRIPTION:  This file contains functions that rename field
# headers from certain dataframes
#
# USGS DISCLAIMER:  This software is in the public domain because it contains
# materials that originally came from the U.S. Geological Survey, an agency
# of the United States Department of Interior. For more information, see the
# [official USGS copyright policy]
# (https://www.usgs.gov/visual-id/credit_usgs.html#copyright/
# "official USGS # copyright policy")
#
# Although this software program has been used by the U.S. Geological Survey
# (USGS), no warranty, expressed or implied, is made by the USGS or the U.S.
# Government as to the accuracy and functioning of the program and related
# program material nor shall the fact of distribution constitute any such
# warranty, and no responsibility is assumed by the USGS in connection
# therewith.
#
# This software is provided "AS IS."
#############################################################################


rename_project_df = function(project_df){
  #' Return the project dataframe renamed with appropriate field headers
  #'
  #' @param project_df Dataframe output from get_projects()
  #'
  names(project_df)[names(project_df) == 'data.allProjects.nodes.id'] =
    'project_id'
  names(project_df)[names(project_df) == 'data.allProjects.nodes.projectName'] =
    'project_name'
  names(project_df)[names(project_df) == 'data.allProjects.nodes.projectKey'] =
    'project_key'
  names(project_df)[names(project_df) == 'data.allProjects.nodes.description'] =
    'project_description'
  names(project_df)[names(project_df) == 'data.allProjects.nodes.mrOwnerEmail'] =
    'owner_email'
  names(project_df)[names(project_df) == 'data.allProjects.nodes.sampleFrameId'] =
    'sample_frame_id'
  names(project_df)[names(project_df) ==
      'data.allProjects.nodes.organizationByOrganizationId.name'] =
    'organization'
  names(project_df)[names(project_df) ==
      'data.allProjects.nodes.organizationByOrganizationId.address'] =
    'organization_address'
  names(project_df)[names(project_df) ==
      'data.allProjects.nodes.organizationByOrganizationId.city'] =
    'organization_city'
  names(project_df)[names(project_df) ==
      'data.allProjects.nodes.organizationByOrganizationId.stateProvince'] =
    'organization_state_province'
  names(project_df)[names(project_df) ==
      'data.allProjects.nodes.organizationByOrganizationId.postalCode'] =
    'organization_postal_code'

  row.names(project_df) = c()
  return (project_df)
}

rename_geoms_df = function(geoms_df){
  #' Return the geometry dataframe renamed with appropriate field headers
  #'
  #' @param geoms_df dataframe from geom gql query
  #'
  names(geoms_df)[names(geoms_df) ==
      'data.allEventGeometries.nodes.name'] = 'location_name'
  names(geoms_df)[names(geoms_df) ==
      'data.allEventGeometries.nodes.id'] = 'event_geometry_id'
  names(geoms_df)[names(geoms_df) ==
      'data.allEventGeometries.nodes.geom.geojson.type'] = 'geom_type'
  names(geoms_df)[names(geoms_df) ==
      'data.allEventGeometries.nodes.geom.geojson.coordinates'] = 'geom_coordinates'
  row.names(geoms_df) = c()
  return (geoms_df)
}

rename_species_df = function(species_df){
  #' Return the species dataframe renamed with appropriate field headers
  #'
  #' @param species_df Dataframe output from get_species()
  #'
  names(species_df)[names(species_df) ==
      'data.allSpecies.nodes.id'] = 'id'
  names(species_df)[names(species_df) ==
      'data.allSpecies.nodes.speciesCode'] = 'species_code'
  names(species_df)[names(species_df) ==
      'data.allSpecies.nodes.species'] = 'species'
  names(species_df)[names(species_df) ==
      'data.allSpecies.nodes.commonName'] = 'common_name'
  row.names(species_df) = c()
  return (species_df)
}

rename_survey_df = function(survey_df){
  #' Return the survey dataframe renamed with appropriate field headers
  #'
  #' @param survey_df Dataframe output from get_project_surveys()
  #'
  names(survey_df)[names(survey_df) ==
      'data.allSurveys.nodes.id'] = 'survey_id'
  names(survey_df)[names(survey_df) ==
      'data.allSurveys.nodes.projectId'] = 'project_id'
  names(survey_df)[names(survey_df) ==
      'data.allSurveys.nodes.grtsId'] = 'grts_cell_id'
  row.names(survey_df) = c()
  return (survey_df)
}

rename_acoustic_df = function(acoustic_df){
  #' Return the acoustic dataframe renamed with appropriate field headers
  #'
  #' @param acoustic_df Dataframe output from get_acoustic_bulk_df()
  #'
  names(acoustic_df)[names(acoustic_df) ==
      'projectId'] = 'project_id'
  names(acoustic_df)[names(acoustic_df) ==
      'recordingTime'] = 'recording_time'
  names(acoustic_df)[names(acoustic_df) ==
      'grtsId'] = 'grts_cell_id'
  names(acoustic_df)[names(acoustic_df) ==
      'id'] = 'stationary_acoustic_values_id'
  names(acoustic_df)[names(acoustic_df) ==
      'locationName'] = 'location_name'
  names(acoustic_df)[names(acoustic_df) ==
      'surveyId'] = 'survey_id'
  names(acoustic_df)[names(acoustic_df) ==
      'wavFileName'] = 'audio_recording_name'
  names(acoustic_df)[names(acoustic_df) ==
      'waterType'] = 'water_type'
  names(acoustic_df)[names(acoustic_df) ==
      'activationStartTime'] = 'survey_start_time'
  names(acoustic_df)[names(acoustic_df) ==
      'activationEndTime'] = 'survey_end_time'
  names(acoustic_df)[names(acoustic_df) ==
      'microphoneHeight'] = 'microphone_height'
  names(acoustic_df)[names(acoustic_df) ==
      'distanceToClutterMeters'] = 'distance_to_nearest_clutter'
  names(acoustic_df)[names(acoustic_df) ==
      'softwareBySoftwareId.name'] = 'software_name'
  names(acoustic_df)[names(acoustic_df) ==
      'distanceToWater'] = 'distance_to_nearest_water'
  names(acoustic_df)[names(acoustic_df) ==
      'percentClutterMethod'] = 'percent_clutter'
  names(acoustic_df)[names(acoustic_df) ==
      'clutterTypeByClutterTypeId.description'] = 'clutter_type'
  names(acoustic_df)[names(acoustic_df) ==
      'habitatTypeByHabitatTypeId.description']= 'broad_habitat_type'
  names(acoustic_df)[names(acoustic_df) ==
      'microphoneOrientationByMicrophoneOrientationId'] = 'microphone_orientation'
  names(acoustic_df)[names(acoustic_df) ==
      'softwareBySoftwareId.versionNumber'] = 'software_version'
  names(acoustic_df)[names(acoustic_df) ==
      'speciesBySpeciesId.speciesCode']= 'auto_id'
  names(acoustic_df)[names(acoustic_df) ==
      'speciesByManualId.speciesCode']= 'manual_id'
  names(acoustic_df)[names(acoustic_df) ==
      'deviceByDeviceId.deviceTypeByDeviceTypeId.manufacturer']=
    'device_manufacturer'
  names(acoustic_df)[names(acoustic_df) ==
      'deviceByDeviceId.deviceTypeByDeviceTypeId.model'] =
    'device_model'
  names(acoustic_df)[names(acoustic_df) ==
      'microphoneByMicrophoneId.microphoneTypeByMicrophoneTypeId.model'] =
    'microphone_model'
  names(acoustic_df)[names(acoustic_df) ==
      'microphoneByMicrophoneId.microphoneTypeByMicrophoneTypeId.manufacturer'] =
    'microphone_manufacturer'
  names(acoustic_df)[names(acoustic_df) ==
      'speciesId'] = 'auto_id'
  names(acoustic_df)[names(acoustic_df) ==
      'manualId'] = 'manual_id'
  names(acoustic_df)[names(acoustic_df) ==
      'id1'] = 'location_id'
  names(acoustic_df)[names(acoustic_df) ==
      'deviceId'] = 'device_id'
  names(acoustic_df)[names(acoustic_df) ==
      'microphoneId'] = 'microphone_id'
  names(acoustic_df)[names(acoustic_df) ==
      'microphoneOrientationId'] = 'microphone_orientation'
  names(acoustic_df)[names(acoustic_df) ==
      'clutterTypeId'] = 'clutter_type_id'
  names(acoustic_df)[names(acoustic_df) ==
      'habitatTypeId'] = 'habitat_type_id'
  names(acoustic_df)[names(acoustic_df) ==
      'softwareId'] = 'software_id'
  names(acoustic_df)[names(acoustic_df) ==
      'location.geojson.type'] = 'location_type'

  row.names(acoustic_df) = c()
  return (acoustic_df)
}

rename_colony_df = function(colony_df){
  #' Return the colony dataframe renamed with appropriate field headers
  #'
  #' @param colony_df Dataframe output from get_colony_bulk_df()
  #'
  names(colony_df)[names(colony_df) ==
      'grtsId'] = 'grts_id'
  names(colony_df)[names(colony_df) ==
      'surveyId'] = 'survey_id'
  names(colony_df)[names(colony_df) ==
      'dateTimeStart'] = 'date_sampled'
  names(colony_df)[names(colony_df) ==
      'eventId'] = 'event_id'
  names(colony_df)[names(colony_df) ==
      'siteId'] = 'site_id'
  names(colony_df)[names(colony_df) ==
      'siteBySiteId.siteName'] = 'site_name'
  names(colony_df)[names(colony_df) ==
      'speciesBySpeciesId.species'] = 'species'
  names(colony_df)[names(colony_df) ==
      'countValue'] = 'count'
  row.names(colony_df) = c()
  return(colony_df)
}