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presto_input_standards.md

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Presto Reconstruction Input Standards

Paramaters

File

yaml (.yml) format
if you are unfamiliar with yaml, see the official documentation here: yaml
comments in document will be preserved, but not visible to GUI form users

see a complete example of the yaml input file here: Holocene_DA_parameters.yml

see the corresponding GUI form here: Customize Holocene DA Parameters

Parameter keys

Paramter keys follow a naming convention of underscore-separated, lowercase terms with the first word being a grouping term and the second word being a specific, unique term as in: group_specific
grouping terms come from a controlled set and include: recon, time, prior, proxy, geo, model, uncertainty
verbose specific terms such as "range_to_reconstruct" are allowed and take the form: time_range_to_reconstruct

PReSto grouping terms

  • recon: parameters relating to the reconstruction broadly, eg. the climate variable to reconstruct
  • time: parameters relating to time, eg. temporal resolution and interval for reconstruction
  • prior: parameters relating to Bayesian priors, eg. percentage of the prior states to assimilate
  • proxy: parameters relating to proxies, eg. seasonality of proxies to assimilate
  • psm: parameters relating to proxy system models, eg. the calibration period for the PSMs
  • geo: parameters relating to geospatial, eg. coordinate bounds of proxy records to gather
  • model: paramters relating to climate models, eg. choice of linear_global or linear_spatial processing
  • uncertainty: paramters relating to error and confidence intervals, eg. choice of confidence interval width

PReSto specific terms

Please make an effort to conform specific terms to those used in existing PReSto reconstructions. New terms may occassionaly be added due to novelty of specific parameters.

Parameter Values

Each paramter holds 10 key:value pairs
values required by all data types denoted by bold typescript

  • value: the parameter input, to be adjusted as desired
  • default: the default parameter input, does not change
  • limits: upper and lower bounds (inclusive) for value key, required for numeric, lat-lon, and range data_type, eg. [0,12000]
  • options: list of valid choices for value key, required for character and list data types, eg. [linear_global, linear_spatial]. Also used for lat-lon to describe the units of longitude.
  • precision: minimum possible increment between valid options for value key, required for numeric, lat-lon and range data types, eg. 0.1
  • long_name: displayed parameter name for GUI, eg. time interval for reconstruction
  • description: notes for the user, eg. define a start and end year in units years BP
  • data_type: type of parameter, informs design of GUI form (see section below for deatils and options), eg. character
  • complexity: level of understanding required to make use of the parameter (details is section below), eg. experimental
  • URL: web page with additional information, eg. https://lipdverse.org/vocabulary/paleodata_proxy/

Parameter data type

The data type controls the strucure of the form element in the "Reconstruction Parameters" GUI, which is automatically generated from the yaml file. For instance, a "numeric" data type is given a range-slider form element.

free-form:
  special note: this data type dhould be used only as a last resort
  additonal requirement: none
  form element: text box
  example: experiment name
    default: default

boolean:
  additonal requirement: none
  form element: radio buttons (true/false)
  example: Allow the mean of the prior to change through time
    default: false

character:
  additional requirements: options
  form element: radio buttons allow user to select one from a list of options
  example: reconstruction in absolute or relative values
    default: relative
    options: [relative, absolute]

list:
  additional requirements: options
  form element: check boxes allow user to select multiple from a list of options
  example: models used for prior
    default: [hadcm3_regrid,trace_regrid]
    options: [hadcm3_regrid,trace_regrid,famous_regrid]

numeric:
  additional requirements: limits, precision
  form element: range slider and linked numeric input box
  example: minimum resolution of proxies
    default: 200
    limits: [10, 1000]
    precision: 10

range:
  additional requirements: limits, precision
  form element: dual range slider and linked numeric input boxes (min/max)
  example: time interval for reconstruction     default: [0,12000]
    limits: [0,12000]
    precision: 1

lat-lon:
  special note: this data type can only be used once for a given reconstruction
  additional requirements: limits, precision, options
  form element: world map with adjustable selection box and corresponging numeric inputs for lat/lon min and max
  example: coordinate bounds for assimilating proxies
    default: [-90, 90, -180, 180]
    limits: [-90, 90, -180, 180]
    precision: 0.001
    options: [double, 180]

Parameter complexity

Parameter complextity has three options: standard, advanced, experimental.

standard: displayed in GUI form by default, simplest parameters

advanced: displayed in GUI if "show advanced parameters" checkbox is selected, deeper understanding required

experimental: can not be adjusted through GUI form, exceedingly deep understanding necessary and/or may break code

Data

Data should be pulled from a curated repository such as lipdverse.org each time the reconstruction is run rather than being saved in the container. This allows for newly generated data to be incorporated, and limits container size.