Metadata quality checks list and implementation tracking

[MalditoBarbudo]

Here is a list of Metadata Quality Checks, indicating if their implementation is done yet or not. Please feel free to add checks in the comments and I will add them to the list.

Metadata Quality Checks

(Checked boxes indicates implementation in sapfluxnetr R package)

• [x] Coordinates: Check if provided coordinates are correct and are inside site country. Implemented, using the rgeos and sp packages
• [x] Unique Site & Country name: Check if provided site and country combination is unique, in order to ensure adequate data flow in the scripts. _Implemented in the df_received_to_accepted function._
• [x] Duplicate contributors: Check if a contributor already exists, and if so, that the site is new, in order to avoid duplicate entries. Not fix. It is no needed at the moment
• [x] Adequate range in numerical values: Check if numerical metadata is in a reasonable biological/physiological/environmental/... range. _Implemented in qc_out_of_range function_
• [x] Species names correctness: Check if provided species names are spelled correctly and correspond to the right plant. Implemented, using the tpl and tpldata packages
• [x] Concordance between pl_species and sp_names variables: Check if species provided in both variables are the same. _Implemented in qc_species_verification_
• [x] Number of trees: Check if number of trees per species agrees with number of trees provided in the tree metadata. _Implemented in qc_species_verification_
• [x] Plant treatment: Check if plant treatments, if any, are identical between trees (e.g. Drought and drought). _Implemented in qc_pl_treatments. At the moment only information about treatments is returned, as check and fix probably must be done at hand_
• [x] Enviromental variables data presence: Check if all environmental variables filled in the metadata really have associated data in the environmental data file. _Implemented in qc_env_vars_presence_.
• [x] Timestamp format: Check if the timestamp format is adequate, ~~and if not, fix it (if it is possible)~~. As errors are contributor dependent, automatic fixes are not possible. _Implemented in qc_timestamp_errors function, indicating the intervals where errors are found_
• [x] Metadata columns: Check that all the metadata variables are present and that their classes are correct
• [x] Biomes: Function to assign a biome to the site based on the coordinates (or Annual Mean Temperature and Annual Mean Precipitation).

  Site_md specific checks

• [x] email: Check if si_contact_email and si_addcontr_email are valid email directions. *Implemented in qc_email_check
• [x] Dictionaries for factors: Check if factor variables (si_country, si_dist_mgmt, si_igbp) have valid values.

  Stand_md specific checks

• [x] Dictionaries for factors: Check if factor variables have valid values.
• [x] Soil texture. Implemented by Marie Sirot in qc_soil_texture function

  Species_md specific checks

• [x] Dictionaries for factors: Check if factor variables have valid values.

  Plant_md specific checks

• [x] Dictionaries for factors: Check if factor variables have valid values.

  Environmental_md specific checks

• [x] Dictionaries for factors: Check if factor variables have valid values.
• [x] Conversion between radiation types: Functions to convert between radiation types to standardize metadata. Implemented in qc_rad_conversion function (conversion between sw_in and ppfd_in)

[rafapoyatos]

About #2, we need to change the default settings for the species checks using tpl, so that we keep the contributor-supplied species name if it's a synonym (and we only fix the species name if it's a typo). @MalditoBarbudo

[MalditoBarbudo]

An issue (#16) for the species and synonyms problem has been filed.

[guillembagaria]

Function qc_rad_conversion to convert between sw_in and ppfd_in radiation types has been added, but not tested yet. It also lacks its vignette.

[guillembagaria]

Function qc_rad_conversion has been improved and tested. However, it lacks its vignette and implementing it in the main script.

[MalditoBarbudo]

All items have been implemented, closing the issue.