namc-utah/NAMCr
NAMC Database Access API

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info: Describe the NAMC API.

info: Describe the NAMC API.
In namc-utah/NAMCr: NAMC Database Access API

View source: R/api_info.R

infoR Documentation

Describe the NAMC API.

Description

info prints text to the console describing the NAMC API options.

Usage

info(endpoint = NA, no_paging = TRUE, format = "text", to_console = TRUE)

Arguments

endpoint

api endpoint name to get information about.

no_paging

Logical that omits the paging arguments by default

format

One of: 'text (default), 'markdown'

to_console

Logical TRUE(default), FALSE to print output to console

Details

This function presents a text block describing the available API endpoints and their corresponding input parameters. Inputs are marked as required where applicable. Endpoint descriptions can be subset by providing an endpoint name as input. NAMC API:

auth

Description

:

Input Parameters

none

Output Fields
loggedIn

data type :Boolean

is numeric :FALSE

is expandable :FALSE

userPool

data type :String

is numeric :FALSE

is expandable :FALSE

clientId

data type :String

is numeric :FALSE

is expandable :FALSE

region

data type :String

is numeric :FALSE

is expandable :FALSE

domain

data type :String

is numeric :FALSE

is expandable :FALSE

organizations

Description

:API endpoint that calls entity.fn_organizations

Input Parameters
searchTerm

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields
entityId

data type :Int

is numeric :TRUE

is expandable :FALSE

organizationName

data type :String

is numeric :FALSE

is expandable :FALSE

organizationType

data type :String

is numeric :FALSE

is expandable :FALSE

isLab

data type :Boolean

is numeric :FALSE

is expandable :FALSE

address1

data type :String

is numeric :FALSE

is expandable :FALSE

address2

data type :String

is numeric :FALSE

is expandable :FALSE

city

data type :String

is numeric :FALSE

is expandable :FALSE

usState

data type :String

is numeric :FALSE

is expandable :FALSE

country

data type :String

is numeric :FALSE

is expandable :FALSE

zipCode

data type :String

is numeric :FALSE

is expandable :FALSE

phone

data type :String

is numeric :FALSE

is expandable :FALSE

fax

data type :String

is numeric :FALSE

is expandable :FALSE

website

data type :String

is numeric :FALSE

is expandable :FALSE

notes

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

siteInfo

Description

:Detailed information about a single site. Includes the point location and upstream catchment geometries as GeoJSON.

Input Parameters
siteId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
siteId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :Unique database generated integer that uniquely identifies each site

siteName

data type :String

is numeric :FALSE

is expandable :FALSE

description :Unique text identifier for each site

system

data type :String

is numeric :FALSE

is expandable :FALSE

description :The ecological system (e.g. lake, pond, reservoir) in which the site is located.

ecosystem

data type :String

is numeric :FALSE

is expandable :FALSE

description :The ecosystem in which the site is located.

location

data type :String

is numeric :FALSE

is expandable :FALSE

description :GeoJSON point location of the site in EPSG:4326 spatial reference.

longitude

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Longtidue of the site location in decimal degrees.

latitude

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Latitude of the site location in decimal degrees.

usState

data type :String

is numeric :FALSE

is expandable :FALSE

description :US State in which the site is located.

waterbodyType

data type :String

is numeric :FALSE

is expandable :FALSE

description :If the site has a waterbody code, then the waterbody type identifies the system that this identifier pertains to. The waterbody type might be NHDPlus 1:100,000 or NHDPlusHR 1:24,000 etc.

waterbodyCode

data type :String

is numeric :FALSE

is expandable :FALSE

description :The identifier of the waterbody on which this site occurs. Can be null. If a waterbody code exists, then the waterbodyType can be used to determine which system the code belongs to, such as NHDPlus or NHDPlusHR.

waterbodyName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The string name of the waterbody on which the site occurs. Typicall this is the stream name.

geographyChanged

data type :String

is numeric :FALSE

is expandable :FALSE

description :The latest date and time that either the site location (point) or catchment (polygon) were changed.

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

description :The system generated date and time that the site record was created in the database.

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

description :The system generated date and time that the site record was last changed in the database.

catchment

data type :String

is numeric :FALSE

is expandable :FALSE

description :GeoJSON polygon of the upstream area that drains into this site in EPSG:4326 spatial reference.

sampleCount

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The number of samples that are available for this site.

modelInfo

Description

:Detailed information about a single model, including the number of predictors associated with the model.

Input Parameters
modelId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
modelId

data type :Int

is numeric :TRUE

is expandable :FALSE

modelName

data type :String

is numeric :FALSE

is expandable :FALSE

abbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

modelType

data type :String

is numeric :FALSE

is expandable :FALSE

translationId

data type :Int

is numeric :TRUE

is expandable :FALSE

translation

data type :String

is numeric :FALSE

is expandable :FALSE

extentDescription

data type :String

is numeric :FALSE

is expandable :FALSE

platform

data type :String

is numeric :FALSE

is expandable :FALSE

referenceSites

data type :Int

is numeric :TRUE

is expandable :FALSE

groupCount

data type :Int

is numeric :TRUE

is expandable :FALSE

minimumCount

data type :Int

is numeric :TRUE

is expandable :FALSE

oeMean

data type :Float

is numeric :TRUE

is expandable :FALSE

oeStdev

data type :Float

is numeric :TRUE

is expandable :FALSE

taxonomicEffort

data type :String

is numeric :FALSE

is expandable :FALSE

isActive

data type :Boolean

is numeric :FALSE

is expandable :FALSE

fixedCount

data type :Int

is numeric :TRUE

is expandable :FALSE

units

data type :String

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

predictorCount

data type :Int

is numeric :TRUE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

extent

data type :String

is numeric :FALSE

is expandable :FALSE

modelConditions

Description

:List of all model conditions (e.g. good, fair, poor) for a particular model

Input Parameters
modelId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
modelId

data type :Int

is numeric :TRUE

is expandable :FALSE

conditionId

data type :Int

is numeric :TRUE

is expandable :FALSE

condition

data type :String

is numeric :FALSE

is expandable :FALSE

displayText

data type :String

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

boxInfo

Description

:Detailed information about a single box, including information about the customer and number of samples associated with the box.

Input Parameters
boxId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
boxId

data type :Int

is numeric :TRUE

is expandable :FALSE

customerId

data type :Int

is numeric :TRUE

is expandable :FALSE

customerName

data type :String

is numeric :FALSE

is expandable :FALSE

customerAbbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

submitterId

data type :Int

is numeric :TRUE

is expandable :FALSE

submittedBy

data type :String

is numeric :FALSE

is expandable :FALSE

boxStateId

data type :Int

is numeric :TRUE

is expandable :FALSE

boxState

data type :String

is numeric :FALSE

is expandable :FALSE

boxReceivedDate

data type :String

is numeric :FALSE

is expandable :FALSE

processingCompleteDate

data type :String

is numeric :FALSE

is expandable :FALSE

projectedCompleteDate

data type :String

is numeric :FALSE

is expandable :FALSE

sampleCount

data type :Int

is numeric :TRUE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

measurements

data type :Boolean

is numeric :FALSE

is expandable :FALSE

sorterQa

data type :Boolean

is numeric :FALSE

is expandable :FALSE

taxaQa

data type :Boolean

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

samples

Description

:List of all samples in the system, including high level information about the associated box and customer.

Input Parameters
sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

boxIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

projectIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

entityIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

siteIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

polygon

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

pointDistance

data type :QueryDistance

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

boxId

data type :Int

is numeric :TRUE

is expandable :FALSE

customerName

data type :String

is numeric :FALSE

is expandable :FALSE

customerAbbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

submittedBy

data type :String

is numeric :FALSE

is expandable :FALSE

boxState

data type :String

is numeric :FALSE

is expandable :FALSE

siteId

data type :Int

is numeric :TRUE

is expandable :FALSE

siteName

data type :String

is numeric :FALSE

is expandable :FALSE

usState

data type :String

is numeric :FALSE

is expandable :FALSE

siteLocation

data type :String

is numeric :FALSE

is expandable :FALSE

siteLongitude

data type :Float

is numeric :TRUE

is expandable :FALSE

siteLatitude

data type :Float

is numeric :TRUE

is expandable :FALSE

visitId

data type :String

is numeric :FALSE

is expandable :FALSE

customerSiteCode

data type :String

is numeric :FALSE

is expandable :FALSE

sampleDate

data type :String

is numeric :FALSE

is expandable :FALSE

sampleTime

data type :String

is numeric :FALSE

is expandable :FALSE

sampleType

data type :String

is numeric :FALSE

is expandable :FALSE

sampleMethod

data type :String

is numeric :FALSE

is expandable :FALSE

habitat

data type :String

is numeric :FALSE

is expandable :FALSE

sampleLocation

data type :String

is numeric :FALSE

is expandable :FALSE

sampleLongitude

data type :Float

is numeric :TRUE

is expandable :FALSE

sampleLatitude

data type :Float

is numeric :TRUE

is expandable :FALSE

area

data type :Float

is numeric :TRUE

is expandable :FALSE

fieldSplit

data type :Float

is numeric :TRUE

is expandable :FALSE

fieldNotes

data type :String

is numeric :FALSE

is expandable :FALSE

labSplit

data type :Float

is numeric :TRUE

is expandable :FALSE

jarCount

data type :Int

is numeric :TRUE

is expandable :FALSE

qualitative

data type :Boolean

is numeric :FALSE

is expandable :FALSE

labNotes

data type :String

is numeric :FALSE

is expandable :FALSE

mesh

data type :Int

is numeric :TRUE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

sampleDateChanged

data type :String

is numeric :FALSE

is expandable :FALSE

qaSampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

sites

Description

:Summary information for all sites, including location coordinates and number of samples. Use the siteInfo query to get more detailed information about a single site.

Input Parameters
usState

data type :String

is numeric :FALSE

is array :TRUE

is required :FALSE

is for paging :FALSE

sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

boxIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

projectIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

entityIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

siteIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

polygon

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

pointDistance

data type :QueryDistance

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields
siteId

data type :Int

is numeric :TRUE

is expandable :FALSE

siteName

data type :String

is numeric :FALSE

is expandable :FALSE

system

data type :String

is numeric :FALSE

is expandable :FALSE

ecosystem

data type :String

is numeric :FALSE

is expandable :FALSE

longitude

data type :Float

is numeric :TRUE

is expandable :FALSE

latitude

data type :Float

is numeric :TRUE

is expandable :FALSE

usState

data type :String

is numeric :FALSE

is expandable :FALSE

waterbodyType

data type :String

is numeric :FALSE

is expandable :FALSE

waterbodyCode

data type :String

is numeric :FALSE

is expandable :FALSE

waterbodyName

data type :String

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

hasCatchment

data type :Boolean

is numeric :FALSE

is expandable :FALSE

boxes

Description

:Summary information for all boxes, including the customer name and number of samples within the box. Use the boxInfo query to get more detailed information about a single box.

Input Parameters
boxIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

entityIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

Output Fields
boxId

data type :Int

is numeric :TRUE

is expandable :FALSE

customerId

data type :Int

is numeric :TRUE

is expandable :FALSE

customerName

data type :String

is numeric :FALSE

is expandable :FALSE

submitterId

data type :Int

is numeric :TRUE

is expandable :FALSE

submittedBy

data type :String

is numeric :FALSE

is expandable :FALSE

boxState

data type :String

is numeric :FALSE

is expandable :FALSE

boxReceivedDate

data type :String

is numeric :FALSE

is expandable :FALSE

sampleCount

data type :Int

is numeric :TRUE

is expandable :FALSE

processingCompleteDate

data type :String

is numeric :FALSE

is expandable :FALSE

projectedCompleteDate

data type :String

is numeric :FALSE

is expandable :FALSE

projects

Description

:Summary information about all projects in the system. Use the projectInfo query to get more detailed about a single project.

Input Parameters

none

Output Fields
projectId

data type :Int

is numeric :TRUE

is expandable :FALSE

projectName

data type :String

is numeric :FALSE

is expandable :FALSE

isPrivate

data type :Boolean

is numeric :FALSE

is expandable :FALSE

contactId

data type :Int

is numeric :TRUE

is expandable :FALSE

contactName

data type :String

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

sampleCount

data type :Int

is numeric :TRUE

is expandable :FALSE

modelCount

data type :Int

is numeric :TRUE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

predictors

Description

:List of all predictors in the system. Includes summary information about how many models rely on each predictor.

Input Parameters
modelId

data type :Int

is numeric :TRUE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields
predictorId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The unique system generated identifier for the predictor.

predictorName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The unique textual name for the predictor.

abbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

description :The unique shorthand abbreviation for the predictor.

units

data type :String

is numeric :FALSE

is expandable :FALSE

description :The units in which the predictor values are stored.

predictorType

data type :String

is numeric :FALSE

is expandable :FALSE

description :The predictor type (e.g. metrics, atmosphere, geology, anthro).

isTemporal

data type :Boolean

is numeric :FALSE

is expandable :FALSE

description :Boolean representing whether the predictor varies over time or whether there is just a single value for the site. True indicates that the predictor is temporal and values are stored for each sample. False indicates that there is only one predictor value for each site.

description

data type :String

is numeric :FALSE

is expandable :FALSE

description :Long form information about the predictor.

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

description :Miscellaneou structured metadata in GeoJSON format.

modelCount

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The number of models that use the predictor

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

description :The system generated date and time that the site record was created in the database.

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

description :The system generated date and time that the site record was last changed in the database.

calculationScript

data type :String

is numeric :FALSE

is expandable :FALSE

description :Optional name of the R function that performs the calculation for this predictor.

source

data type :String

is numeric :FALSE

is expandable :FALSE

description :Source information about the predictors

models

Description

:List of all models in the system. Includes summary information about how many predictors are used by the model as well as the translation that might be required.

Input Parameters

none

Output Fields
modelId

data type :Int

is numeric :TRUE

is expandable :FALSE

modelName

data type :String

is numeric :FALSE

is expandable :FALSE

abbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

isActive

data type :Boolean

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

predictorCount

data type :Int

is numeric :TRUE

is expandable :FALSE

sitePredictorValues

Description

:List of predictor values at a single site. Site predictors are non-temporal. The value is common to all samples at the specific site.

Input Parameters
siteId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
predictorId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The unique system generated identifier for the predictor.

predictorName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The unique textual name for the predictor.

abbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

description :The unique shorthand abbreviation for the predictor.

description

data type :String

is numeric :FALSE

is expandable :FALSE

description :Long form information about the predictor.

predictorType

data type :String

is numeric :FALSE

is expandable :FALSE

description :The predictor type (e.g. metrics, atmosphere, geology, anthro).

predictorValue

data type :String

is numeric :FALSE

is expandable :FALSE

description :The predictor value for this site. The value is always a string, even if it represents an integer or floating point value.

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

description :The system generated date and time that the site record was created in the database.

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

description :The system generated date and time that the site record was last changed in the database.

calculationScript

data type :String

is numeric :FALSE

is expandable :FALSE

description :Optional name of the R function that performs the calculation for this predictor.

samplePredictorValues

Description

:List of all predictor values for a single sample. This includes both temporal and non-temporal predictors as well as their calculation status (current, missing, expired).

Input Parameters
sampleId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
predictorId

data type :Int

is numeric :TRUE

is expandable :FALSE

abbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

calculationScript

data type :String

is numeric :FALSE

is expandable :FALSE

isTemporal

data type :Boolean

is numeric :FALSE

is expandable :FALSE

predictorMetadata

data type :String

is numeric :FALSE

is expandable :FALSE

predictorValue

data type :String

is numeric :FALSE

is expandable :FALSE

predictorValueUpdatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

status

data type :String

is numeric :FALSE

is expandable :FALSE

modelResults

Description

:

Input Parameters
sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

siteId

data type :Int

is numeric :TRUE

is expandable :FALSE

siteName

data type :String

is numeric :FALSE

is expandable :FALSE

modelId

data type :Int

is numeric :TRUE

is expandable :FALSE

modelName

data type :String

is numeric :FALSE

is expandable :FALSE

modelVersion

data type :String

is numeric :FALSE

is expandable :FALSE

modelResult

data type :Float

is numeric :TRUE

is expandable :FALSE

condition

data type :String

is numeric :FALSE

is expandable :FALSE

fixCount

data type :Int

is numeric :TRUE

is expandable :FALSE

notes

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

taxonomy

Description

:List of all taxa in the system. Includes information about each level of the taxonomic hierarchy above each taxa.

Input Parameters
searchTerm

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields
taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

parentTaxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

parentScientificName

data type :String

is numeric :FALSE

is expandable :FALSE

parentLevelId

data type :Int

is numeric :TRUE

is expandable :FALSE

parentLevelName

data type :String

is numeric :FALSE

is expandable :FALSE

notes

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

taxonomyTree

Description

:list all parents for a particular taxa

Input Parameters
taxonomyId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

parentId

data type :Int

is numeric :TRUE

is expandable :FALSE

attributes

Description

:List of all attributes in the system.

Input Parameters

none

Output Fields
attributeId

data type :Int

is numeric :TRUE

is expandable :FALSE

attributeName

data type :String

is numeric :FALSE

is expandable :FALSE

attributeType

data type :String

is numeric :FALSE

is expandable :FALSE

label

data type :String

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

taxaAttributes

Description

:List of all attributes that exist for a single taxa

Input Parameters
taxonomyId

data type :Int

is numeric :TRUE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields
taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

attributeName

data type :String

is numeric :FALSE

is expandable :FALSE

attributeType

data type :String

is numeric :FALSE

is expandable :FALSE

label

data type :String

is numeric :FALSE

is expandable :FALSE

attributeValue

data type :String

is numeric :FALSE

is expandable :FALSE

translationTaxa

Description

:List all the taxa within a specific translation (OTU)

Input Parameters
translationId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
translationId

data type :Int

is numeric :TRUE

is expandable :FALSE

translationName

data type :String

is numeric :FALSE

is expandable :FALSE

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

originalScientificName

data type :String

is numeric :FALSE

is expandable :FALSE

translationScientificName

data type :String

is numeric :FALSE

is expandable :FALSE

isFinal

data type :Boolean

is numeric :FALSE

is expandable :FALSE

translations

Description

:List of all translations in the system.

Input Parameters

none

Output Fields
translationId

data type :Int

is numeric :TRUE

is expandable :FALSE

translationName

data type :String

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

isActive

data type :Boolean

is numeric :FALSE

is expandable :FALSE

taxaCount

data type :Int

is numeric :TRUE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

planktonSamples

Description

:List of all plankton samples in the system.

Input Parameters

none

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

diameter

data type :Float

is numeric :TRUE

is expandable :FALSE

subSampleCount

data type :Int

is numeric :TRUE

is expandable :FALSE

towLength

data type :Float

is numeric :TRUE

is expandable :FALSE

volume

data type :Float

is numeric :TRUE

is expandable :FALSE

aliquot

data type :Float

is numeric :TRUE

is expandable :FALSE

sizeInterval

data type :Float

is numeric :TRUE

is expandable :FALSE

towType

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

driftSamples

Description

:List of all drift samples in the system.

Input Parameters

none

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

netArea

data type :Float

is numeric :TRUE

is expandable :FALSE

netDuration

data type :Float

is numeric :TRUE

is expandable :FALSE

streamDepth

data type :Float

is numeric :TRUE

is expandable :FALSE

netDepth

data type :Float

is numeric :TRUE

is expandable :FALSE

netVelocity

data type :Float

is numeric :TRUE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

fishSamples

Description

:List of all fish samples in the system.

Input Parameters

none

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

fishLength

data type :Float

is numeric :TRUE

is expandable :FALSE

fishMass

data type :Float

is numeric :TRUE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

massSamples

Description

:List of all mass samples in the system.

Input Parameters

none

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

typeId

data type :Int

is numeric :TRUE

is expandable :FALSE

typeAbbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

typeName

data type :String

is numeric :FALSE

is expandable :FALSE

methodId

data type :Int

is numeric :TRUE

is expandable :FALSE

methodAbbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

methodName

data type :String

is numeric :FALSE

is expandable :FALSE

mass

data type :Float

is numeric :TRUE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

fishDiet

Description

:List all fish diet samples in the system

Input Parameters
sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

sampleDate

data type :String

is numeric :FALSE

is expandable :FALSE

siteId

data type :Int

is numeric :TRUE

is expandable :FALSE

siteName

data type :String

is numeric :FALSE

is expandable :FALSE

fishWeight

data type :Float

is numeric :TRUE

is expandable :FALSE

fishLength

data type :Float

is numeric :TRUE

is expandable :FALSE

fishTaxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

fishScientificName

data type :String

is numeric :FALSE

is expandable :FALSE

notes

data type :String

is numeric :FALSE

is expandable :FALSE

metadata

data type :String

is numeric :FALSE

is expandable :FALSE

organicWeight

data type :Float

is numeric :TRUE

is expandable :FALSE

inorganicWeight

data type :Float

is numeric :TRUE

is expandable :FALSE

otherWeight

data type :Float

is numeric :TRUE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

lifeStageId

data type :Int

is numeric :TRUE

is expandable :FALSE

lifeStage

data type :String

is numeric :FALSE

is expandable :FALSE

count

data type :Float

is numeric :TRUE

is expandable :FALSE

weight

data type :Float

is numeric :TRUE

is expandable :FALSE

sampleTaxaRaw

Description

:Sample organisms summed by taxonomy only. Includes both raw counts as well as counts corrected for lab and field split. Also includes both raw and corrected big rare counts.

Input Parameters
sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

boxIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

projectIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The sample to which the taxa belong

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxa identified within the laboratory.

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The name of the taxa identified with the laboratory.

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

abundance

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Abundance for the specified taxa and lifestage

sampleTaxaGeneralized

Description

:Sample organisms summed by taxonomy, life stage and bug size. Includes both raw counts as well as counts corrected for lab and field split. Also includes both raw and corrected big rare counts.

Input Parameters
sampleId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

lifeStageId

data type :Int

is numeric :TRUE

is expandable :FALSE

lifeStage

data type :String

is numeric :FALSE

is expandable :FALSE

lifeStageAbbreviation

data type :String

is numeric :FALSE

is expandable :FALSE

bugSize

data type :Float

is numeric :TRUE

is expandable :FALSE

rawCount

data type :Float

is numeric :TRUE

is expandable :FALSE

labSplit

data type :Float

is numeric :TRUE

is expandable :FALSE

fieldSplit

data type :Float

is numeric :TRUE

is expandable :FALSE

correctedCount

data type :Float

is numeric :TRUE

is expandable :FALSE

rawBigRareCount

data type :Int

is numeric :TRUE

is expandable :FALSE

sampleTaxaTranslation

Description

:Sample organisms converted to a translation (OTU). Rolls up counts to those taxa present in the translation and omits any organisms that don't roll up to a taxa in the translation.

Input Parameters
sampleId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

translationId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The sample to which the taxa belong

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxa identified within the laboratory.

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The name of the taxa identified with the laboratory.

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

abundance

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Abundance for the specified taxa and lifestage

sampleTaxaTranslationRarefied

Description

:Sample organisms converted to the translation (OTU) and then rarefied to the specified fixed count.

Input Parameters
sampleId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

translationId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

fixedCount

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The sample to which the taxa belong

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxa identified within the laboratory.

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The name of the taxa identified with the laboratory.

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

abundance

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Abundance for the specified taxa and lifestage

pointTaxaRaw

Description

:Sample organisms within distance (meters) of a point (decimal degrees)

Input Parameters
longitude

data type :Float

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

latitude

data type :Float

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

distance

data type :Float

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The sample to which the taxa belong

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxa identified within the laboratory.

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The name of the taxa identified with the laboratory.

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

abundance

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Abundance for the specified taxa and lifestage

polygonTaxaRaw

Description

:Sample organisms within a polygon

Input Parameters
polygon

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The sample to which the taxa belong

taxonomyId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxa identified within the laboratory.

scientificName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The name of the taxa identified with the laboratory.

levelId

data type :Int

is numeric :TRUE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

levelName

data type :String

is numeric :FALSE

is expandable :FALSE

description :The taxonomic level of the taxa identified within the laboratory.

abundance

data type :Float

is numeric :TRUE

is expandable :FALSE

description :Abundance for the specified taxa and lifestage

metrics

Description

:

Input Parameters

none

Output Fields
metricId

data type :Int

is numeric :TRUE

is expandable :FALSE

metricName

data type :String

is numeric :FALSE

is expandable :FALSE

displayText

data type :String

is numeric :FALSE

is expandable :FALSE

groupId

data type :Int

is numeric :TRUE

is expandable :FALSE

groupName

data type :String

is numeric :FALSE

is expandable :FALSE

formulaId

data type :Int

is numeric :TRUE

is expandable :FALSE

formulaName

data type :String

is numeric :FALSE

is expandable :FALSE

codeFunction

data type :String

is numeric :FALSE

is expandable :FALSE

isStandardized

data type :Boolean

is numeric :FALSE

is expandable :FALSE

perturbDirection

data type :String

is numeric :FALSE

is expandable :FALSE

description

data type :String

is numeric :FALSE

is expandable :FALSE

createdDate

data type :String

is numeric :FALSE

is expandable :FALSE

updatedDate

data type :String

is numeric :FALSE

is expandable :FALSE

sampleMetrics

Description

:

Input Parameters
sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

boxIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

projectIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

translationId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

fixedCount

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields
sampleId

data type :Int

is numeric :TRUE

is expandable :FALSE

groupId

data type :Int

is numeric :TRUE

is expandable :FALSE

groupName

data type :String

is numeric :FALSE

is expandable :FALSE

metricId

data type :Int

is numeric :TRUE

is expandable :FALSE

metricName

data type :String

is numeric :FALSE

is expandable :FALSE

metricValue

data type :String

is numeric :FALSE

is expandable :FALSE

setSitePredictorValue

Description

:Store a non-temporal predictor value for a specific site. See setSamplePredictorValue if you want to store a temporal predictor value associated with a particular sample.

Input Parameters
siteId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

predictorId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

value

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields

none

setSamplePredictorValue

Description

:Store a temporal predictor value for a specific sample. Set setSitePredictorValue if you want to store a temporal predictor value associated with a particular site.

Input Parameters
sampleId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

predictorId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

value

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields

none

setSiteCatchment

Description

:Store the upstream catchment polygon for a specific site. The catchment polygon must be a valid, non-empty GeoJSON polygon that partially or entirely intersects with the United States.

Input Parameters
siteId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

catchment

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields

none

createTranslation

Description

:Create a new translation. The name is mandatory and cannot be an empty string. The description is optional.

Input Parameters
translationName

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

description

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields

none

setTranslationTaxa

Description

:Add or update a taxa associated with a translation

Input Parameters
translationId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

taxonomyId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

alias

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

isFinal

data type :Boolean

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields

none

deleteTranslationTaxa

Description

:Permanently remove a taxa from a translation

Input Parameters
translationId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

taxonomyId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields

none

setTaxonomy

Description

:Update information related to a specific taxa. Change its scientific name, move its level or change its parent

Input Parameters
taxonomyId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

scientificName

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

levelId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

parentId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

author

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

year

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

notes

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

metadata

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields

none

createProject

Description

:

Input Parameters
projectName

data type :String

is numeric :FALSE

is array :FALSE

is required :TRUE

is for paging :FALSE

isPrivate

data type :Boolean

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

description

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

metadata

data type :String

is numeric :FALSE

is array :FALSE

is required :FALSE

is for paging :FALSE

contactId

data type :Int

is numeric :TRUE

is array :FALSE

is required :FALSE

is for paging :FALSE

Output Fields

none

addProjectSamples

Description

:

Input Parameters
projectId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

Output Fields

none

addProjectBoxes

Description

:

Input Parameters
projectId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

boxIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

Output Fields

none

removeProjectSamples

Description

:

Input Parameters
projectId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

sampleIds

data type :Int

is numeric :TRUE

is array :TRUE

is required :FALSE

is for paging :FALSE

Output Fields

none

deleteProject

Description

:

Input Parameters
projectId

data type :Int

is numeric :TRUE

is array :FALSE

is required :TRUE

is for paging :FALSE

Output Fields

none

Value

If format argument is console nothing is returned otherwise text is returned in the format defined.

See Also

browseVignettes("NAMC-API-Overview")

Examples


info()

namc-utah/NAMCr documentation built on Feb. 12, 2024, 4:29 a.m.

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