Automatic Curation of Spatially Annotated Data

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Documentation for package ‘CleanGeoStreamR’ version 1.0.0

• DESCRIPTION file.

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analyze_coordinate_country_mismatch	Analyze coordinate-country mismatch
apply_location_normalization	Apply location normalization
are_countries_neighbors	Function to check if two countries are neighbors
assign_average_coords	Assign average coordinates to stations with the same name
check_all_characters	Check if all provided arguments are of type character
check_all_contained	Check if All Columns are Contained in Data
check_country	Check if Coordinates Belong to a Specified Country
check_remaining_missing_ids	Check Remaining Missing IDs
compare_location_files	Modify locations data and write comparison of row differences to CSV
compare_string_modifications	Compare string modifications in two dataframes
coordinate_format_checker	Check if latitude and longitude are in valid format
country_lat_lon_crosscheck	This function checks if the coordinates of locations in a dataset correspond to their actual country. If the coordinates do not match, the function checks if the pair of countries are neighbors. If they are not, then the latitude and longitude are switched and the function checks again if the new coordinates correspond to the country. If they do, then the coordinates in the dataset are modified.
count_lines	Count the Number of Lines in a File
count_values	Count TRUE, FALSE, and NA Values in a Data Frame Column
create_df_coords	Create dataframe with coordinates and perform checks
create_dt	Create DataTable
create_unique_station_identifiers	Create unique station identifiers
cross_check_locations	Cross-check locations dataframe
curate_controversy_station_country_information	Curate controversial station country information
curate_missing_or_inconsistent_information	Curate missing or inconsistent information in locations dataframe
derive_empodat_results	Derive and Print Empodat Results
dms2dec	Convert Degrees, Minutes and Seconds to Decimal
draw_cheos_numbers	Draw CHEOS Numbers
file.path2	#' Custom File Path Generation
find_country_code	Function to find country code by country name
generate_map_for_row	Generate Leaflet Map for a Specified Row
generate_time_point_column	Generate Time Point
get_duplicated_stations	Get Duplicated Stations with Inconsistent Information
get_nonunique_id_associations	Get non-unique id associations
heatmap_and_na_count	Heatmap and NA Counter
identify_missing_ids	Identify Missing IDs
integrate_manual_curation	Integrate manually curated information into the locations dataframe
intersect_groups	Intersection Function for Tibble Columns
loadRData	Load RData Function
locations_format_check	Check and format locations dataframe
location_close_to_border	Check if a Location is Close to a Country Border
main_read_curate_chemical_data	Main Function
main_read_curate_spatial_data	Main function to process and curate environmental data
map_chemical_data_by_susdat_id	Map Chemical Data by SUSDAT ID
map_chemical_name	Map Chemical Name
merge_susdat_with_ct_map_by_cas_number	Merge SUSDAT with CT_MAP by CAS number
merge_susdat_with_ct_map_by_dtxsid	Merge SUSDAT with CT_MAP by DTXSID
modify_dot_position	Modify dot position in a number
normalize_locations	Normalize Locations
normalize_string	#' Normalize String Data
normanid_equals_dtxsid	Identify Duplicated Associations between Norman ID and DTXSID
parse_arguments_r	Parse command line arguments
process_and_save_empodat	Process and save EMPODAT dataframe
process_empodat_unfiltered	Process and save unfiltered EMPODAT dataframe
process_station_information	Process station information
read_ct_map	Read and Save CompTox Map
read_files	Read files into R environment
read_susdat	Read and select relevant columns from the SUSDAT file
remove_CAS_RN_prefix	Remove the CAS_RN prefix from CAS numbers in the SUSDAT data
remove_dots	Remove dots from numeric values
resolve_inconsistent_rb_and_wb_info	Resolve Inconsistent River Basin and Water Body Information
resolve_missing_rb_and_wb_info	Resolve Missing River Basin and Water Body Information
resolve_missing_rb_or_wb_info	Resolve Missing River Basin or Water Body Information
save_chemical_data_files	Save Chemical Data Files
save_empodat_unfiltered_tagged_data	Save tagged empodat unfiltered data
save_susdat	Save the SUSDAT data frame as an RData file
setup_data_directories	Setup Data Directories Function
source_functions	Source External Functions
tag_locations	Tag Locations with Geographic Information
to_camel_case	Convert to Camel Case