This tool is useful for those who want to extract large volumes of data from DataStream. This R package allows users to call DataStream's Public API using R functions and specific search queries. The package includes several functions which accept a selection of filtering queries and returns a dataframe with the desired data from DataStream.
You might use this tool, for example, if you:
- Cross-dataset downloads (i.e., to download all available pH data in Ontario on DataStream)
- Want to count how many sites in New Brunswick have cesium data on DataStream
To have full API permissions, users must request an API token which is required to call to the API
To install the most recent version in R:
# install.packages("devtools")
remotes::install_github("datastreamapp/datastreamr")Thank you ahead of time for using this data responsibly and providing the appropriate citations when necessary when presenting work to external parties. These dataset citations must be accompanied by a link to the DOI (https://doi.org/{value}). The dataset licence, citation, and DOI can be retrieved from the /Metadata endpoint.
The API returns the URL for a dataset's licence, these should be mapped to the full licence name with a link to the full licence details.
Attribution Licence:- EN: Attribution Licence (ODC-By) v1.0
- FR: Licence d'attribution (ODC-By) v1.0
- URL: https://opendatacommons.org/licenses/by/1-0/
Public Domain Dedication and Licence:- EN: Public Domain Dedication and Licence (ODC-PDDL) v1.0
- FR: Dédicace et licence du domaine public (ODC-PDDL) v1.0
- URL: https://opendatacommons.org/licenses/pddl/1-0/
Open Government Licence:- EN: Open Government Licence (OGL)
- FR: Licence du gouvernement ouvert (OGL)
- URL: Dataset-dependent, entered by data provider (eg. https://open.canada.ca/en/open-government-licence-canada)
The following functions are used to call DataStream's API and pull desired information.
Description
By default the environment variable "DATASTREAM_API_KEY" is used for setting the API key. Click here to request an api token
Usage
library(datastreamr)
# To set API Key for the current session, use:
setAPIKey('xxxxxxxxxx')
# Preferably, save the API key as an environmental variable
usethis::edit_r_environ()
# add DATASTREAM_API_KEY="xxxxxxxxxx" to the file, save, and restart R, then there is no need to include `setAPIKey()` within the script.
# Saving the API key as an environmental variable means it will remain private but be available when neededDescription
Pulls only the dataset level metadata information including dataset name, citation, licence, abstract, etc.
Usage
metadata(
list(
`$select` = NULL,
`$filter` = NULL,
`$top` = NULL,
`$count` = "false"
)
)Description
Pulls only the location data including Location ID, Location Name, Latitude, and Longitude.
Usage
locations(
list(
`$select` = NULL,
`$filter` = NULL,
`$top` = NULL,
`$count` = "false"
)
)Description
Pulls data formatted the same as the downloaded DataStream CSV’s including all columns listed in the DataStream schema .
Usage
- This function will take longer than
observations, but provides all available columns in one request. - Use this function if you aim to pull all location and parameter data in one call
records(
list(
`$select` = NULL,
`$filter` = NULL,
`$top` = NULL,
`$count` = "false"
)
)Description
Pulls data in a condensed format that must be joined with other endpoints to create a full dataset with all the DataStream columns. Specifically, location rows are not pulled, instead LocationId is pulled for each observation and then can be used in combination with locations().
Usage
- This function will be quicker than
records, but if location specifics are needed, needs to be paired withlocations() - Use this function if you are uninterested in specific location coordinates, or in combination with
locations()when you plan to pull >200,000 of rows of data
observations(
list(
`$select` = NULL,
`$filter` = NULL,
`$top` = NULL,
`$count` = "false"
)
)All of the functions above accept query parameters. The ones supported are:
-
select: A list of allowable columns to return
- Fields to be selected are entered as a list.
- Example:
select="DatasetName,Abstract" - Default: All columns available.
-
filter: A list of conditions to filter by
- Available operators:
- eq: Used for exact matches.
- ne: Used for not equal to.
- gt: Used for greater than.
- lt: Used for less than.
- ge: Used for greater than or equal to.
- le: Used for less than or equal to.
- and: Used to combine multiple filters with an “and” condition.
- Grouping:
filter="CharacteristicName eq 'Dissolved oxygen saturation' and DOI eq '10.25976/n02z-mm23'" - Temporal (Dataset creation):
filter="CreateTimestamp gt 2020-03-23" - Temporal (Data date-range):
filter="ActivityStartYear gt '2019'" - Spatial:
filter=RegionId eq 'hub.atlantic'RegionIdValues (these values are subject to change):- DataStream Hubs:
hub.{atlantic,lakewinnipeg,mackenzie,greatlakes,pacific } - Countries:
admin.2.{ca} - Provinces/Territories:
admin.4.ca.{ab,bc,mb,nb,nl,ns,nt,nu,on,pe,qc,sk,yt}
-
top:
- Maximum: 10000
- Example:
top=10
-
count: When TRUE, returns number of observations rather than the data itself
- Return only the count for the request. When the value is large enough it becomes an estimate (~0.0005% accurate)
- Example:
count=true - Default:
false
- Use
selectto request only the parameters you need. This will decrease the amount of data needed to process and transfer.
The allowed select and filter options for each of the functions are listed HERE.
filter field, a useful resource is the "allowed values" tab of our upload template . This will give you available strings for:
MonitoringLocationTypeActivityMediaNameCharacteristicName
Get Locations from a dataset
setAPIKey('xxxxxxxxxx')
qs <- list(
`$select` = "Id,DOI,Name,Latitude,Longitude",
`$filter` = "DOI eq '10.25976/xxxx-xx00'",
`$top` = 10000
)
result = locations(qs)Get Locations from multiple datasets
qs <- list(
`$select` = "Id,DOI,Name,Latitude,Longitude",
`$filter` = "DOI in ('10.25976/xxxx-xx00', '10.25976/xxxx-xx11', '10.25976/xxxx-xx22')",
`$top` = 10000)
result = locations(qs)Get Temperature and pH observations from multiple datasets
qs <- list(
`$select` = "DOI,ActivityType,ActivityMediaName,ActivityStartDate,ActivityStartTime,SampleCollectionEquipmentName,CharacteristicName,MethodSpeciation,ResultSampleFraction,ResultValue,ResultUnit,ResultValueType",
`$filter` = "DOI in ('10.25976/xxxx-xx00', '10.25976/xxxx-xx11', '10.25976/xxxx-xx22') and CharacteristicName in ('Temperature, water', 'pH')",
`$top` = 10000)
result = observations(qs)Get select fields from a dataset
qs <- list(
`$select` = "DOI,ActivityType,ActivityMediaName,ActivityStartDate,ActivityStartTime,SampleCollectionEquipmentName,CharacteristicName,MethodSpeciation,ResultSampleFraction,ResultValue,ResultUnit,ResultValueType",
`$filter` = "DOI eq '10.25976/xxxx-xx00'",
`$top` = 10000)
result = records(qs)Get the DOI, Version, and DatasetName for a dataset
qs <- list(
`$select` = "DOI,Version,DatasetName",
`$filter` = "DOI eq '10.25976/xxxx-xx00'",
`$top` = 10000)
result = metadata(qs)qs <- list(
`$filter` = "DOI eq '10.25976/xxxx-xx00'",
`$count` = "true")
count = observations(qs)Dockerfile is provided to run the unit tests and the integration tests. To build the docker image for running tests and other debugging purposes you can run:
docker build -t datastreamr .To run the unit tests:
docker run --rm -e DATASTREAM_API_KEY=$(cat api_key.txt) datastreamr R -e "library(testthat); test_file('tests/testthat/test_unit.R')"To run the integration tests:
docker run --rm -e DATASTREAM_API_KEY=$(cat api_key.txt) datastreamr R -e "library(testthat); test_file('tests/testthat/test_integration.R')"