Run all congruence checks

Usage

run_congruence_checks(
  directory = here::here(),
  metadata = load_metadata(directory),
  check_metadata_only = FALSE,
  skip_cols = NA,
  output_filename,
  output_dir = here::here()
)

Arguments

directory: the directory where the data file(s) are found (i.e. your data package). Defaults to the current working directory. On exit, returns to the current working directory.
metadata: The metadata object returned by load_metadata. If parameter not provided, defaults to calling load_metadata in current project directory.
check_metadata_only: Only run checks on the metadata and skip anything involving data files.
skip_cols: String. Defaults to NA. A list of one or more columns in the data to skip when testing whether the dates within data fall within the dates range specified in metadata. Useful if, for instance, there are columns within the data associated with the QA/QC process and these dates are expected to fall outside the date range specified for the data.
output_filename: Optional. If specified, saves results of congruence checks to this file. If omitted, prints results to console. If the file already exists, results will be appended to the existing file.
output_dir: Location in which to save the output file, if using.

Value

Invisibly returns metadata.

Examples

dir <- DPchecker_example("BICY_veg")
#> Data are provided for example use only. Do not assume that they are complete, accurate, or up to date.
run_congruence_checks(dir)
#> 
#> ── Running all congruence checks ───────────────────────────────────────────────
#> 
#> ── Reading metadata ──
#> 
#> ── Checking metadata compliance ──
#> 
#> ✔ Your metadata is schema valid.
#> ✔ Each data file name is used exactly once in the metadata file.
#> ✔ Your EML version is supported.
#> ✔ Metadata indicates that each data file contains a field delimiter that is a
#>   single character
#> ✔ Metadata indicates that each data file contains exactly one header row.
#> ✔ Metadata indicates data files do not have footers.
#> ✔ Metadata contains taxonomic coverage element.
#> ✔ Metadata contains geographic coverage element
#> ✔ Metadata contains a digital object identifier, "doi:
#>   https://doi.org/10.57830/2295086".
#> ✔ Metadata Digital Object Identifier appears to be properly formatted.
#> ✔ Metadata contains URLs for all data tables.
#> ✔ Data table URLs are properly formmatted and correspond to the specified DOI.
#> ✔ Metadata contains publisher element.
#> ✔ Field names begin with a letter and do not contain spaces or special
#>   characters.
#> ✔ File names begin with a letter and do not contain spaces or special
#>   characters.
#> ✔ Metadata does not appear to contain any personal emails.
#> 
#> ── Checking that metadata contains required elements for DataStore extraction ──
#> 
#> ✔ Any individual Creators in metadata have a surNames with less than three
#>   words.
#> ! Publication date, 2022, predates the Data Package Reference Type.
#> ✔ Data package title is present in metadata.
#> ✔ Metadata contains keyword(s).
#> ✔ Metadata states data was created by or for NPS.
#> ✔ Metadata indicates the publisher is the National Park Service.
#> ✔ Metadata indicates the publisher state is CO.
#> ✔ Metadata indicates the publisher city is Fort Collins.
#> ! The data package abstract contains non-standard characters: &amp;#13;. Use
#> `EMLeditor::set_abstract()` to revise.
#> ! The metadata methods contains non-standard characters such as \r or
#> &amp;#13;. Use `EMLeditor::set_methods()` to revise.
#> ✔ All dataTables listed in metadata have a unique file description.
#> ! Data file 3 description is greater than 15 words. Consider a more concise
#> description.
#> ✖ The CUI dissemination code PUBVER is not a valid code. Use
#>   `EMLeditor::set_cui()`.
#> ✖ Metadata does not contain a license name. Use `EMLeditor::set_int_rights()`
#>   to add a license name.
#> ✔ Metadata contains an Intellectual Rights statement.
#> ✔ All attributes listed in metadata have attribute definitions.
#> ✔ All attributes listed in metadata have a storage type associated with them.
#> ✔ All attribute storage types are valid values.
#> 
#> ── Checking additional metadata elements ──
#> 
#> ✔ All individual creators have associated ORCiDs.
#> ✔ All Creator ORCiDs are properly formatted.
#> ✔ All Creator ORCiDs resolved to a valid ORCiD profile.
#> ✔ All Creator ORCiDs resolve to an ORCiD profile that matches the Creator last
#>   name.
#> ! Metadata does not contain additionalInfo (notes). Use
#> `EMLeditor::set_additional_info()` to add notes.
#> 
#> ── Checking that metadata is consistent with data file(s) ──
#> 
#> ✔ All data files are listed in metadata and all metadata files names refer to
#>   data files.
#> ✔ All columns in data match all columns in metadata.
#> ✖ Undocumented missing data detected. Please document all missing data in
#>   metadata:
#>   ---> Mini_BICY_Veg_Intercept_Cleaned.csv contains missing data without a
#>   corresponding missing data code in metadata.
#>   ---> Mini_BICY_Veg_Transect_Cleaned.csv contains missing data without a
#>   corresponding missing data code in metadata.
#> ✔ Columns indicated as numeric in metadata contain only numeric values and
#>   valid missing value codes.
#> ✔ Metadata and data date formatting is in congruence.
#> ✔ Columns indicated as date/time in metadata are within the stated temporal
#>   coverage range.
#> 
#> ── Checking data and metadata compliance ──
#> 
#> ✔ Data files do not appear to contain any personal emails.
#> ! CUI is not set to PUBLIC. GPS coordinates detected in metadata will be
#> publicly available. Are you sure?
#> 
#> ── Summary ──
#> 
#> ✖ 3 errors to address
#> ! 6 warnings to look into