MazamaLocationUtils v0.1.6

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Manage Spatial Metadata for Known Locations

A suite of utility functions for discovering and managing metadata associated with sets of spatially unique "known locations".

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MazamaLocationUtils

A suite of utility functions for discovering and managaing metadata associated
with sets of spatially unique "known locations".

Background

This package is intended to be used in support of data management activities associated with fixed locations in space. The motivating fields include both air and water quality monitoring where fixed sensors report at regular time intervals.

When working with environmental monitoring time series, one of the first things you have to do is create unique identifiers for each individual time series. In an ideal world, each environmental time series would have both a locationID and a sensorID that uniquely identify the spatial location and specific instrument making measurements. A unique timeseriesID could be produced as locationID_sensorID. Location metadata associated with each time series would contain basic information needed for downstream analysis including at least:

timeseriesID, locationID, sensorID, longitude, latitude, ...

  • Multiple sensors placed at a location could be be grouped by locationID.
  • An extended time series for a mobile sensor would group by sensorID.
  • Maps would be created using longitude, latitude.
  • Time series would be accessed from a secondary data table with timeseriesID.

Unfortunately, we are rarely supplied with a truly unique and truly spatial locationID. Instead we often use sensorID or an associated non-spatial identifier as a standin for locationID.

Complications we have seen include:

  • GPS-reported longitude and latitude can have jitter in the fourth or fifth decimal place making it challenging to use them to create a unique locationID.
  • Sensors are sometimes repositioned in what the scientist considers the "same location".
  • Data for a single sensor goes through different processing pipelines using different identifiers and is later brought together as two separate timeseries.
  • The radius of what constitutes a "single location" depends on the instrumentation and scientific question being asked.
  • Deriving location-based metadata from spatial datasets is computationally intensive unless saved and identified with a unique locationID.
  • Automated searches for spatial metadata occasionally produce incorrect results because of the non-infinite resolution of spatial datasets and must be corrected by hand.

A Solution

A solution to all these problems is possible if we store spatial metadata in simple tables in a standard directory. These tables will be referred to as collections. Location lookups can be performed with geodesic distance calculations where a location is assigned to a pre-existing known location if it is within radius meters. These will be extremely fast.

If no previously known location is found, the relatively slow (seconds) creation of a new known location metadata record can be performed and then added to the growing collection.

For collections of stationary environmental monitors that only number in the thousands, this entire collection (i.e. "database") can be stored as either a .rda or .csv file and will be under a megabyte in size making it fast to load. This small size also makes it possible to store multiple known location files, each created with different locations and different radii to address the needs of different scientific studies.

Immediate Advantages

Working in this manner will solve the problems initially mentioned but also provides further useful functionality:

  • Administrators can correct entries in an individual collection. (e.g. locations in river bends that even high resolution spatial datasets mis-assign)
  • Additional, non-automatable metadata can be added to a collection. (e.g. commonly used location names within a community of practice)
  • Different field campaigns can maintain separate collections.
  • .csv or .rda versions of well populated tables can be downloaded from a URL and used locally, giving scientists working with known locations instant access to spatial data that otherwise requires special skills, large datasets and many compute cycles to generate.

This project is supported by Mazama Science.

Functions in MazamaLocationUtils

Name Description
table_removeRecord Remove location records from a table
or_monitors_500 Oregon monitor locations dataset
%>% Pipe operator
table_save Save a known location table
table_updateSingleRecord Update a single known location record in a table
table_getNearestLocation Return known locations
location_getSingleElevation_USGS Get elevation data from a USGS web service
table_updateColumn Update a column of metadata in a table
location_getSingleAddress_Photon Get address data from the Photon API to OpenStreetMap
table_getNearestDistance Return distances to nearest known locations
validateMazamaSpatialUtils Validate proper setup of MazamaSpatialUtils
coreMetadataNames Names of standard spatial metadata columns
wa_airfire_meta Washington monitor metadata dataset
validateLonLat Validate longitude and latitude values
setLocationDataDir Set location data directory
table_addColumn Add a new column of metadata to a table
MazamaLocationUtils Manage Spatial Metadata for Known Locations
LocationDataDir Directory for location data
validateLonsLats Validate longitude and latitude vectors
table_addSingleLocation Add a single new known location record to a table
table_addLocation Add new known location records to a table
getLocationDataDir Get location data directory
location_initialize Create known location record with core metadata
mazama_initialize Initialize with MazamaScience standard directories
table_load Load a known location table
table_export Export a known location table
table_getRecordIndex Return indexes of known location records
table_getLocationID Return IDs of known locations
table_initialize Create an empty known location table
wa_monitors_500 Wshington monitor locations dataset
table_removeColumn Remove a column of metadata in a table
id_monitors_500 Idaho monitor locations dataset
location_createID Create one or more unique locationIDs
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Details

Type Package
License GPL-3
URL https://github.com/MazamaScience/MazamaCoreUtils
BugReports https://github.com/MazamaScience/MazamaCoreUtils/issues
Encoding UTF-8
VignetteBuilder knitr
LazyData true
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2019-11-02 00:34:58 UTC; jonathan
Repository CRAN
Date/Publication 2019-11-20 16:40:02 UTC

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