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ebvcube (version 0.5.2)

ebv_metadata: Create the metadata file (json) for the EBV netCDF creation

Description

This function collects the metadata terms of the EBV netCDF to create and collects them in a text file in JSON format. Use ebv_create() with the output file of this function to create your EBV netCDF. During the actual creation you will be asked for more information regarding the spatial resolution, CRS etc.

Usage

ebv_metadata(
  outputpath,
  title,
  summary,
  references = NULL,
  source,
  project_name = NULL,
  project_url = NULL,
  date_created,
  creator_name,
  creator_email = NULL,
  creator_institution,
  contributor_name = NULL,
  license,
  comment = NULL,
  ebv_class,
  ebv_name,
  ebv_scenario_classification_name = NULL,
  ebv_scenario_classification_version = NULL,
  ebv_scenario_classification_url = NULL,
  ebv_spatial_scope,
  ebv_spatial_description = NULL,
  ebv_domain,
  coverage_content_type,
  ebv_entity_type,
  ebv_entity_scope,
  ebv_entity_classification_name = NULL,
  ebv_entity_classification_url = NULL,
  time_coverage_start,
  time_coverage_end,
  time_coverage_resolution,
  metric = list(standard_name = "", long_name = "", units = ""),
  scenario = list(standard_name = "", long_name = ""),
  overwrite = FALSE,
  verbose = TRUE
)

Value

Returns the outputpath of the JSON file with the metadata.

Arguments

outputpath

Character. Outputpath of the text-file (JSON format) containing the metadata. File ending: *.json

title

Character. A short phrase or sentence describing the dataset.

summary

Character. A paragraph describing the dataset, analogous to an abstract for a paper. Maximum character length: 1500.

references

Character. Optional. DOIs (URLs) that describe the data or methods used to produce it. Multiple DOIs can be given in a vector.

source

Character. The method of production of the original data. If it was model-generated, source should name the model and its version. If it is observational, source should characterize it. Corresponding term in the EBV Data Portal: 'methods'.

project_name

Character. Optional. The name of the project principally responsible for originating this data.

project_url

Character. Optional. The URL of the project.

date_created

Character. The date on which this version of the data was created in YYYY-MM-DD format.

creator_name

Character. The name of the person principally responsible for creating this data.

creator_email

Character. Optional. The email address of the person principally responsible for creating this data.

creator_institution

Character. The institution of the creator; should uniquely identify the creator's institution.

contributor_name

Character. Optional. The name of any individuals, projects, or institutions that contributed to the creation of this data. Corresponding term in the EBV Data Portal: 'Co-creators'. Multiple contributors can be given in a vector.

license

Character. License of the dataset. Will be stored in the netCDF as the URL to the CC license. Choose one of: 'CC0', 'CC BY', 'CC BY-SA', 'CC BY-NC', 'CC BY-NC-SA', 'CC BY-ND', 'CC BY-NC-ND'.

comment

Character. Optional. Miscellaneous information about the data, not captured elsewhere.

ebv_class

Character. EBV Class of the data set. One of: 'Genetic composition', 'Species populations', 'Species traits', 'Community composition', 'Ecosystem functioning', 'Ecosystem structure', 'Ecosystem services'. For more info see note.

ebv_name

Character. EBV Name of the data set. The possible options depend on the EBV Class. One of: 'Intraspecific genetic diversity', 'Genetic differentiation', 'Effective population size', 'Inbreeding', 'Species distributions', 'Species abundances', 'Morphology', 'Physiology', 'Phenology', 'Movement', 'Community abundance', 'Taxonomic and phylogenetic diversity', 'Trait diversity', 'Interaction diversity', 'Primary productivity', 'Ecosystem phenology', 'Ecosystem disturbances', 'Live cover fraction', 'Ecosystem distribution', 'Ecosystem Vertical Profile', 'Pollination' For more info see note.

ebv_scenario_classification_name

Character. Optional. Name of the classification system used for the scenarios.

ebv_scenario_classification_version

Character. Optional. Version of the classification system used for the scenarios.

ebv_scenario_classification_url

Character. Optional. URL of the classification system used for the scenarios.

ebv_spatial_scope

Character. Spatial scope of the data set. One of: 'Continental/Regional', 'National', 'Sub-national/Local' or 'Global'.

ebv_spatial_description

Character. Specific information about the spatial scope. Mandatory if spatial scope is not Global.

ebv_domain

Character. Environmental domain of the data set. Choose one or several of: 'Terrestrial', 'Marine' or 'Freshwater'. Multiple domains can be given in a vector.

coverage_content_type

Character. Describes the source of the data based on an ISO 19115-1 code. Choose one or several of: 'image', 'thematicClassification', 'physicalMeasurement', 'auxiliaryInformation', 'qualityInformation', 'referenceInformation', 'modelResult', or 'coordinate'. Multiple types can be given in a vector.

ebv_entity_type

Character. EBV entity type. This is a free entry field. Still, if one of the following terms fits your entity scope please use: 'Species', 'Communities', 'Ecosystems' or 'None'.

ebv_entity_scope

Character. Specifies the entity scope in more detail, e.g., 'African great apes'. If the entity type is 'None' this term is not applied to the metadata.

ebv_entity_classification_name

Character. Optional. Name of the classification system used for the entity types.

ebv_entity_classification_url

Character. Optional. URL of the classification system used for the entity types.

time_coverage_start

Character. Start date of the time span covered by the dataset in YYYY-MM-DD format.

time_coverage_end

Character. End date of the time span covered by the dataset in YYYY-MM-DD format.

time_coverage_resolution

Character. Describes the targeted time period between each value in the data set (ISO 8601:2004 date format). Provide the definition of your temporal resolution in the ISO 8601:2004 duration format P(YYYY)-(MM)-(DD). Examples: decadal: 'P0010-00-00', daily: 'P0000-00-01', single timestep: 'P0000-00-00' and irregular time intervals: 'Irregular'. For the latter the timesteps can be directly defined when using ebv_create() (timesteps argument).

metric

List. Metric attributes defined accordingly: list(standard_name='', long_name='', units=''). If you have several metrics give a list of lists, e.g. for two: list(list(standard_name='', long_name='', units=''),list(standard_name='', long_name='', units='')) At least one metric is mandatory.

scenario

List. Optional. Scenario attributes defined accordingly: list(standard_name='', long_name=''). If you have several scenarios give a list of lists, e.g. for two: list(list(standard_name='', long_name=''),list(standard_name='', long_name='')). It is not mandatory to have a scenario.

overwrite

Logical. Default: FALSE. Set to TRUE to overwrite the output file defined by 'outputpath'.

verbose

Logical. Default: TRUE. Turn off additional prints and warnings by setting it to FALSE.

Details

See EBV Classes and their corresponding EBV Names:

EBV ClassEBV Names
Genetic composition'Intraspecific genetic diversity', 'Genetic differentiation','Effective population size', 'Inbreeding'
Species populations'Species distributions', 'Species abundances'
Species traits'Morphology', 'Physiology', 'Phenology', 'Movement'
Community composition'Community abundance', 'Taxonomic and phylogenetic diversity', 'Trait diversity', 'Interaction diversity'
Ecosystem functioning'Primary productivity', 'Ecosystem phenology', 'Ecosystem disturbances'
Ecosystem structure'Live cover fraction', 'Ecosystem distribution', 'Ecosystem Vertical Profile'
Ecosystem services'Pollination', 'other'

Examples

Run this code
#create minimal metadata
if (FALSE) {
ebv_metadata(outputpath=out,
  overwrite = TRUE,
  title = 'Not a real title',
  summary = 'Summary summary summary',
  source = 'this was created by doing...',
  date_created = as.Date('2024-07-10'),
  creator_name = 'Name Name',
  creator_institution = 'lame name',
  license = 'CC0',
  ebv_class = 'Genetic composition',
  ebv_name = 'Intraspecific genetic diversity',
  ebv_spatial_scope = 'National',
  ebv_spatial_description = 'Finland',
  ebv_domain = 'Terrestrial',
  ebv_entity_type = 'Species',
  ebv_entity_scope = '50 mammal species',
  coverage_content_type = c('modelResult'),
  time_coverage_start = as.Date('1900-01-01'),
  time_coverage_end =as.Date('1950-01-01'),
  time_coverage_resolution = 'P0010-00-00',
  metric = list(list(standard_name='relative change of habitat',
  long_name='relative change to year 1800', units='percentage'),
              list(standard_name='absolute change habitat',
              long_name='absolute change since year 1800',
              units='square kilometers')),
  scenario = list(list(standard_name='SSP1xRCP2.6 LU',
                long_name='Global Sustainability (SSP1xRCP2.6), with only effects of land-use.'),
                list(standard_name='SSP3xRCP6.0 LU',
                long_name='Regional Rivalry (SSP3xRCP6.0), with only effects of land-use')),
  scenario_classification_name = 'SSP-RCP',
  ebv_scenario_classification_version = 'LUH2, CMIP5/ISIMIP2a',
  verbose = TRUE
)
}

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