DataStream R Package

This is tool is useful for those who want to extract large volumes of data from DataStream. This R package allows users to call to the DataStream Public API using built-in R functions and specific search queries. The package includes several functions which accept a selection of filtering queries and then return a dataframe with the desired data from DataStream.

You might use this tool, for example, if you:

• Want to download all available DataStream pH data in Ontario
• Want to count how many sites in New Brunswick have cesium data on DataStream

Note: DataStream's Custom Download tool is another option that allows users to download csv data from across datasets in a particular DataStream hub using basic filters. This tool has fewer filtering options than the API, but works well for basic searches. You can find it via 'Explore Data' in the header menu from any DataStream regional hub.

Request an API Token

To have full API permissions, users must request an API token which is required to call to the API

Installation

To install the most recent version in R:

# install.packages("devtools")
devtools::install_github("datastreamapp/datastreamr")

Attribution/Citation

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.

Licence representations

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 Functions

The following functions are used to call to the DataStream API and pull desired information.

ds_metadata():

Description
Pulls only the dataset level metadata information including dataset name, citation, licence, abstract, etc.

Usage

ds_metadata( 
  api_token, 
  select = NULL, 
  filter = NULL,  
  top = NULL, 
  count = FALSE 
)

ds_locations():

Description
Pulls only the location data including Location ID, Location Name, Latitude, and Longitude.

Usage

ds_locations( 
  api_token, 
  select = NULL, 
  filter = NULL, 
  top = NULL, 
  count = FALSE
)

ds_records():

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 ds_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
  

ds_records( 
  api_token, 
  select = NULL, 
  filter = NULL,  
  top = NULL, 
  count = FALSE
)

ds_observations():

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 ds_locations().

Usage

• This function will be quicker than ds_records, but if location specifics are needed, needs to be paired with ds_locations()
  
• Use this function either if you are uninterested in specific location coordinates, or in combination with ds_locations() when you plan to pull millions of rows of data
  

ds_observations( 
  api_token, 
  select = NULL, 
  filter = NULL,  
  top = NULL, 
  count = FALSE
)

Function Inputs

All of the functions above accept query parameters. The ones supported are:

• api_token: A character string containing your unique API key
  

  • Click here to request an api token
    

• select: A list of allowable columns to return
  

  • Fields to be selected are entered as a list.
  • Example: select=c("DatasetName","Abstract")
  • Default: All columns available.

Note: $\color{blue}{\text{Below there is a list of allowed </code>select<code> values to choose from for each function}}$

• filter: A list of conditions to filter by
  

  • Available filters: =, <, >, <=, >=, !=
  • Grouping: filter=c("CharacteristicName=Dissolved oxygen saturation", "DOI='10.25976/n02z-mm23'")
  • Temporal (Dataset creation): filter=c("CreateTimestamp>2020-03-23")
  • Temporal (Data date-range): filter=c("ActivityStartDate<1990-01-01")
  • Spatial: filter=c(RegionId=hub.atlantic)
    • RegionId Values (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}

Note: $\color{blue}{\text{Below there is a list of allowed </code>filter<code> values to choose from for each function}}$

• top: Number of rows to return
  

  • 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

  Performance Tips

  • Use select to request only the parameters you need. This will decrease the amount of data needed to process and transfer.

Allowed Values

The allowed select and filter options for each of the functions are below.

$\color{green}{\text{Note:}}$ When using the filter field, a useful resource is the "allowed values" tab of our upload template . This will give you available strings for:

• MonitoringLocationType

• ActivityMediaName

• CharacteristicName

• ds_metadata

select: 'DOI', 'Version', 'DatasetName', 'DataStewardEmail', 'DataCollectionOrganization', 
'DataUploadOrganization', 'ProgressCode', 'MaintenanceFrequencyCode', 'Abstract', 
'DataCollectionInformation', 'DataProcessing', 'FundingSources', 'DataSourceURL', 
'OtherDataSources', 'Citation', 'Licence', 'Disclaimer', 'TopicCategoryCode', 'Keywords', 
'CreateTimestamp'

filter: 'DOI', 'DatasetName', 'RegionId', 'Latitude', 'Longitude', 'CreateTimestamp'

• ds_locations

select: 'Id', 'DOI', 'NameId', 'Name', 'Latitude', 'Longitude', 
'HorizontalCoordinateReferenceSystem', 'HorizontalAccuracyMeasure',
'HorizontalAccuracyUnit', 'VerticalMeasure', 'VerticalUnit', 'MonitoringLocationType'

filter: 'Id', 'DOI', 'MonitoringLocationType', 'ActivityStartYear', 
'ActivityMediaName', 'CharacteristicName', 'RegionId', 'Name'

• ds_records

select: 'Id', 'DOI', 'DatasetName', 'MonitoringLocationID', 'MonitoringLocationName', 
'MonitoringLocationLatitude','MonitoringLocationLongitude', 
'MonitoringLocationHorizontalCoordinateReferenceSystem', 
'MonitoringLocationHorizontalAccuracyMeasure', 'MonitoringLocationHorizontalAccuracyUnit',
'MonitoringLocationVerticalMeasure', 'MonitoringLocationVerticalUnit', 'MonitoringLocationType', 
'ActivityType', 'ActivityMediaName', 'ActivityStartDate', 'ActivityStartTime', 'ActivityEndDate', 
'ActivityEndTime', 'ActivityDepthHeightMeasure', 'ActivityDepthHeightUnit', 
'SampleCollectionEquipmentName', 'CharacteristicName', 'MethodSpeciation', 'ResultSampleFraction', 
'ResultValue', 'ResultUnit', 'ResultValueType', 'ResultDetectionCondition', 
'ResultDetectionQuantitationLimitMeasure','ResultDetectionQuantitationLimitUnit', 
'ResultDetectionQuantitationLimitType','ResultStatusID', 'ResultComment', 
'ResultAnalyticalMethodID', 'ResultAnalyticalMethodContext', 'ResultAnalyticalMethodName', 
'AnalysisStartDate', 'AnalysisStartTime', 'AnalysisStartTimeZone', 'LaboratoryName', 
'LaboratorySampleID'

filter: 'DOI', 'MonitoringLocationType', 'ActivityStartDate', 'ActivityMediaName', 
'CharacteristicName', 'RegionId'

• ds_observations

select: 'Id', 'DOI', 'LocationId', 'ActivityType', 'ActivityStartDate', 'ActivityStartTime', 
'ActivityEndDate', 'ActivityEndTime', 'ActivityDepthHeightMeasure', 'ActivityDepthHeightUnit', 
'SampleCollectionEquipmentName', 'CharacteristicName', 'MethodSpeciation', 'ResultSampleFraction', 
'ResultValue', 'ResultUnit', 'ResultValueType','ResultDetectionCondition', 
'ResultDetectionQuantitationLimitUnit', 'ResultDetectionQuantitationLimitMeasure',
'ResultDetectionQuantitationLimitType', 'ResultStatusId', 'ResultComment', 'ResultAnalyticalMethodId',
'ResultAnalyticalMethodContext', 'ResultAnalyticalMethodName', 'AnalysisStartDate', 'AnalysisStartTime', 
'AnalysisStartTimeZone', 'LaboratoryName', 'LaboratorySampleId', 'CreateTimestamp'

filter: 'DOI', 'MonitoringLocationType', 'ActivityStartDate', 'ActivityMediaName', 
'CharacteristicName', 'RegionId', 'LocationId'

Full examples

Get the citation and licence for a dataset:

ds_metadata(api_token,filter=c("DOI='10.25976/1q5q-zy55'"), select=c("DOI","DatasetName","Licence","Citation","Version"))

Get all pH observations in Alberta:

ds_records(api_token,filter=c("CharacteristicName='pH'", "RegionId='admin.4.ca.ab'"))

More Examples:

# Pull all metadata for all datasets in the Atlantic DS Hub 

Example01 = ds_metadata(api_token=key,
                        filter=c("RegionId='hub.atlantic'"))

# Pull all metadata for all datasets in BC

Example02 = ds_metadata(api_token=key,
                        filter=c("RegionId='admin.4.ca.bc'"))

# Pull only the DOI's and contact emails for all datasets in the Great Lakes Hub 

Example03 = ds_metadata(api_token=key,
                        filter=c("RegionId='hub.greatlakes'"),
                        select=c('DOI','DataStewardEmail'))

# Pull all location information for sites in Ontario 

Example04 = ds_locations(api_token=key,
                         filter=c("RegionId='admin.4.ca.on'"))

# Pull the site names and lat/lon coordinates for a particular dataset 

Example05 = ds_locations(api_token=key,
                         filter=c("DOI='10.25976/1q5q-zy55'"),
                         select=c("Name","Latitude","Longitude"))

# Pull all ph data available in the Atlantic DS Hub (only pulling top 1000)

Example06 = ds_records(api_token=key,
                       filter = c("RegionId='hub.atlantic'","CharacteristicName='pH"),
                       top=1000)

# Now, only select desired columns 

Example07 = ds_records(api_token=key,
                       filter = c("RegionId='hub.atlantic'","CharacteristicName='pH"),
                       select = c('DOI','DatasetName','MonitoringLocationName','MonitoringLocationLatitude',
                                  'MonitoringLocationLongitude','ActivityStartDate','ResultValue','ResultUnit'),
                       top=1000)

# Now, only pull data before 2015 

Example08 = ds_records(api_token=key,
                       filter = c("RegionId='hub.atlantic'","CharacteristicName='pH","ActivityStartDate<2015-01-01"),
                       select = c('DOI','DatasetName','MonitoringLocationName','MonitoringLocationLatitude',
                                  'MonitoringLocationLongitude','ActivityStartDate','ResultValue','ResultUnit'),
                       top=1000)

# Try ds_observations()

Example09 = ds_observations(api_token=key,
                            select=c("ResultValue"), 
                            filter=c("CharacteristicName = pH","ActivityStartDate>2019-01-01"),
                            top=1000)

# Use the count filter 

Example10 = ds_observations(api_token=key,
                            select=c("ResultValue"), 
                            filter=c("RegionId = 'hub.atlantic'","CharacteristicName = 'Ammonia'","ActivityStartDate>2019-01-01"),
                            count = TRUE)