Measurements Table • eDataDRF

Introduction

The Measurements data table represents the core data table of the eData format. This table records actual measured parameter values (including uncertainty), and references most other tables using foreign keys.

This table is built from the Samples data table and optionally the Biota data table if present. Both tables are bound together (that is, the rows of one are added below the other) and then extended with additional columns. The inclusion of columns in this table and their order is somewhat a

library(eDataDRF)

initialise_measurements_tibble()
#> # A tibble: 0 × 27
#> # ℹ 27 variables: SITE_CODE <chr>, PARAMETER_NAME <chr>, SAMPLING_DATE <chr>,
#> #   ENVIRON_COMPARTMENT_SUB <chr>, SUBSAMPLE <chr>, MEASURED_FLAG <chr>,
#> #   MEASURED_VALUE <dbl>, UNCERTAINTY_TYPE <chr>, UNCERTAINTY_UPPER <dbl>,
#> #   UNCERTAINTY_LOWER <dbl>, MEASURED_UNIT <chr>, MEASURED_N <dbl>,
#> #   LOQ_VALUE <dbl>, LOQ_UNIT <chr>, LOD_VALUE <dbl>, LOD_UNIT <chr>,
#> #   SAMPLING_PROTOCOL <chr>, EXTRACTION_PROTOCOL <chr>,
#> #   FRACTIONATION_PROTOCOL <chr>, ANALYTICAL_PROTOCOL <chr>, …

Variables

Site Code

SITE_CODE - string, free, mandatory

Site Code is a foreign key that references the Sites data table. During Samples table creation the user selects relevant sites using their code and name.

Parameter Name

PARAMETER_NAME - string, free, mandatory

Parameter name is a foreign key that references the Parameter data table. During Samples table creation the user selects relevant parameters using their name and type.

Sampling Date

SAMPLING_DATE - string, free, mandatory

Transcribed from Sampling Date in the Samples data.

Environmental Sub-Compartment

ENVIRON_COMPARTMENT_SUB - string, controlled, mandatory

Transcribed from Environmental Sub-Compartment in the Samples data table.

Subsample

SUBSAMPLE - string, free, mandatory

Transcribed from Subsample in the Samples data table.

Measured Flag

MEASURED_FLAG - string, controlled, mandatory

A flag to indicate if the data source reported a measured value (blank) or that it was below the limit of detection or limit of quantification. In the latter cases, Measured value becomes optional, but it is mandatory to complete at least one of LOQ/LOD.

Controlled Vocabulary

measured_flag_vocabulary()
#> [1] ""      "< LOQ" "< LOD"

Measured Value

MEASURED_VALUE - numeric, free, conditionally mandatory

The numeric measured value of the parameter, if available.

Uncertainty Type

UNCERTAINTY_TYPE - string, controlled, mandatory

Many Measured values are reported as aggregated statistics with uncertainty bounds (mean, mode, etc; 95% CI, SD, SE, range, etc.). Uncertainty Type provides a non-exhaustive classification system for these.

Where the data source reports uncertaintly, the Upper and Lower should also be reported.

Controlled Vocabulary

uncertainty_types_vocabulary()
#>  [1] "Not Reported"                    "Not Relevant"                   
#>  [3] "Arithmetic Mean"                 "Geometric Mean"                 
#>  [5] "Standard Deviation"              "Standard Error"                 
#>  [7] "95% Confidence Interval"         "90% Confidence Interval"        
#>  [9] "99% Confidence Interval"         "Min-Max Range"                  
#> [11] "Interquartile Range (Q1-Q3)"     "10th-90th Percentile"           
#> [13] "5th-95th Percentile"             "Coefficient of Variation (%)"   
#> [15] "Median Absolute Deviation"       "First-Third Quartile Range"     
#> [17] "Minimum-Maximum"                 "Variance"                       
#> [19] "Standard Error of Mean"          "Relative Standard Deviation (%)"
#> [21] "95% Credible Interval"           "95% Prediction Interval"        
#> [23] "95% Tolerance Interval"          "95% Bootstrap CI"               
#> [25] "Other"

Uncertainty Upper Bound

UNCERTAINTY_UPPER - numeric, free, conditionally mandatory

The upper bound of any reported uncertainty.

Uncertainty Lower Bound

UNCERTAINTY_LOWER - numeric, free, conditionally mandatory

The lower bound of any reported uncertainty.

Measured Unit

MEASURED_UNIT - string, controlled, conditionally mandatory

The unit of measurement associated with the data. A non-exhaustive list of options with conversion factors is provided as part of the format. Mandatory when a Measured value is provided.

Controlled Vocabulary

parameter_unit_vocabulary()
#> # A tibble: 64 × 4
#>    MEASURED_UNIT BASE_SI_UNIT CONVERSION_FACTOR UNIT_COMMENTS      
#>    <chr>         <chr>        <chr>             <chr>              
#>  1 mg/L          kg/m³        1e-3              mass concentration 
#>  2 μg/L          kg/m³        1e-6              mass concentration 
#>  3 ng/L          kg/m³        1e-9              mass concentration 
#>  4 pg/L          kg/m³        1e-12             mass concentration 
#>  5 mol/L         mol/m³       1000              molar concentration
#>  6 mmol/L        mol/m³       1                 molar concentration
#>  7 μmol/L        mol/m³       1e-3              molar concentration
#>  8 nmol/L        mol/m³       1e-6              molar concentration
#>  9 pmol/L        mol/m³       1e-9              molar concentration
#> 10 M             mol/m³       1000              molar concentration
#> # ℹ 54 more rows

Measured N

MEASURED_N - numeric, free, mandatory

The sample size of a biota population and/or number of replicates the Measured value represents.

LOQ Value

LOQ_VALUE - numeric, free, conditionally mandatory

Limit of Quantification of the method, if reported.

If no Measured value is reported, at least one of an LOQ and an LOD should be reported with value and unit; implicitly the stressor occurence was below the method’s ability to quantify. If a Measured value, LOQ and/or LOQ are reported, please include as many as possible in the extracted data.

LOQ Unit

LOQ_UNIT - string, controlled, conditionally mandatory

Unit associated with LOQ Value

If no Measured value is reported, at least one of an LOQ and an LOD should be reported with value and unit.

Uses the Measured Unit vocabulary.

LOD Value

LOD_VALUE - numeric, free, conditionally mandatory

Limit of Detection of the method, if reported.

If no Measured value is reported, at least one of an LOQ and an LOD should be reported with value and unit; implicitly the stressor occurence was below the method’s ability to detect. If a Measured value, LOQ and/or LOQ are reported, please include as many as possible in the extracted data.

LOD Unit

LOD_UNIT - string, controlled, conditionally mandatory

Unit associated with LOD Value

If no Measured value is reported, at least one of an LOQ and an LOD should be reported with value and unit.

Uses the Measured Unit vocabulary.

Sampling Protocol

SAMPLING_PROTOCOL - string, controlled, mandatory

The ID of the sampling protocol used to generate the measured sample. Foreign key referencing protocol ID. Limited to sampling protocols.

Extraction Protocol

EXTRACTION_PROTOCOL - string, controlled, mandatory

The ID of the extraction protocol used to generate the measured sample. Foreign key referencing protocol ID. Limited to extraction protocols.

Fractionation Protocol

FRACTIONATION_PROTOCOL - string, controlled, mandatory

The ID of the fractionation protocol used to generate the measured sample. Foreign key referencing protocol ID. Limited to fractionation protocols.

Analytical Protocol

ANALYTICAL_PROTOCOL - string, controlled, mandatory

The ID of the analytical protocol used to generate the measured sample. Foreign key referencing protocol ID. Limited to analytical protocols.

Reference ID

REFERENCE_ID - string, free, mandatory

Identifier for data source, foreign key referencing reference id.

Sample ID

SAMPLE_ID - string, free, mandatory

Campaign Name Short

CAMPAIGN_NAME_SHORT - string, free, mandatory

Identifier for campaign, foreign key referencing Short campaign name.

Environmental Compartment

ENVIRON_COMPARTMENT - string, controlled, mandatory

Transcribed from Environmental Compartment in the Samples data.

Parameter Type

PARAMETER_TYPE - string, controlled, mandatory

Transcribed from Parameter Type in the Parameters data table..

Measured Type

MEASURED_TYPE - string, controlled, mandatory

The type of measurement taken of the sample. Typically concentration, but other options are provided.

Controlled Vocabulary

measured_types_vocabulary()
#>  [1] "Concentration"        "Dose rate"            "Dose"                
#>  [4] "Physical parameter"   "Amount"               "Volume"              
#>  [7] "Fraction of total"    "Percent"              "Irradiance"          
#> [10] "Response"             "Ecological Indicator" "Not relevant"        
#> [13] "Other"

Measurement Comment

MEASUREMENT_COMMENT - string, free, optional

Space for the recording of any additional notes or comments about the sample or measurement deemed relevant.