R/check_dc_cols.R
In nationalparkservice/IMDQC: NPS Inventory and Monitoring Quality Control Toolkit
Defines functions
DC_col_check
check_dc_cols
Documented in
check_dc_cols
DC_col_check
#' TDWG Darwin Core Column Name Check 08-23-2022
#'
#' @description `check_dc_cols()` checks to see if the column names in your dataframe match the standardized simple Darwin Core names established by the Taxonomic Databases Working Group
#'
#' @details A dataframe is created with all the simple DarwinCore terms, drawn from Darwin Core reference guide: https://dwc.tdwg.org/terms/ last updated 07-15-2021. We have chosen to align ourselves mostly with the simple Darwin Core rules: https://dwc.tdwg.org/simple/. The function runs through each of the column names in your working dataframe to see if they match 1. A standard simple DarwinCore name 2. A name with a pattern of strings matching "custom_", indicating a custom made column or 3. A name with a pattern of strings matching "_DQ", indicating a data quality flag. If the column name does not fit within any of the three categories, a "Fix me" statement is printed alongside the column name. The function then counts all of the names fitting within each category and prints a summary table.
#'
#' @param working_df - This is the dataframe you want to run against the function. To call, simply write working_df = "the name of your dataframe".
#'
#' @return - The function returns a list of the column names you should fix (not fitting with simple Darwin Core terms, custom name formatting, data quality flagging formatting). Additionally, a small summary table is printed with the counts of the columns falling under each category (DarwinCore, Custom, DQ, Fix Me).
#'
#' @export
#'
#' @examples
#' \dontrun{
#' check_dc_cols(yourdataframe)
#' }
check_dc_cols <- function(working_df) {
#does not include measurementOrFact or resourceRelationship classes and thus has 179 items vs 196 in the list below.
dwcterms <- data.frame(
DarwinCore = c("type", "modified", "language", "license", "rightsHolder",
"accessRights", "bibliographicCitation", "references",
"institutionID", "collectionID", "datasetID",
"institutionCode", "collectionCode", "datasetName",
"ownerInstitutionCode", "basisOfRecord",
"informationWithheld", "dataGeneralizations",
"dynamicProperties", "occurrenceID", "catalogNumber",
"recordNumber", "recordedBy", "recordedByID",
"individualCount", "organismQuantity",
"organismQuantityType", "sex", "lifeStage",
"reproductiveCondition", "behavior", "establishmentMeans",
"degreeOfEstablishment", "pathway",
"georeferenceVerificationStatus", "occurrenceStatus",
"preparations", "disposition", "associatedMedia",
"associatedOccurrences", "associatedReferences",
"associatedSequences", "associatedTaxa",
"otherCatalogNumbers", "occurrenceRemarks", "organismID",
"organismName", "organismScope", "associatedOrganisms",
"previousIdentifications", "organismRemarks",
"materialSampledID", "eventID", "parentEventID",
"fieldNumber", "eventDate", "eventTime", "startDayOfYear",
"endDayOfYear", "year", "month", "day", "verbatimEventDate",
"habitat", "samplingProtocol", "sampleSizeValue",
"sampleSizeUnit", "samplingEffort", "fieldNotes",
"eventRemarks", "locationID", "higherGeographyID",
"higherGeography", "continent", "waterBody", "islandGroup",
"island", "country", "countryCode", "stateProvince",
"county", "municipality", "locality", "verbatimLocality",
"minimumElevationInMeters", "maximumElevationInMeters",
"verbatimElevation", "verticalDatum", "minimumDepthInMeters",
"maximumDepthInMeters", "verbatimDepth",
"minimumDistanceAboveSurfaceInMeters",
"maximumDistanceAboveSurfaceInMeters", "locationAccordingTo",
"locationRemarks", "decimalLatitude", "decimalLongitude",
"geodeticDatum", "coordinateUncertaintyInMeters",
"coordinatePrecision", "pointRadiusSpatialFit",
"verbatimCoordinates", "verbatimLatitude",
"verbatimLongitude", "verbatimCoordinateSystem",
"verbatimSRS", "footprintWKT", "footprintSRS",
"footprintSpatialFit", "georeferencedBy",
"georeferencedDate", "georeferenceProtocol",
"georeferenceSources", "georeferenceRemarks",
"geologicalContextID", "earliestEonOrLowestEonothem",
"latestEonOrHighestEonothem", "earliestEraOrLowestErathem",
"latestEraOrHighestErathem", "earliestPeriodOrLowestSystem",
"latestPeriodOrHighestSystem", "earliestEpochOrLowestSeries",
"latestEpochOrHighestSeries", "earliestAgeOrLowestStage",
"latestAgeOrHighestStage", "lowestBiostratigraphicZone",
"highestBiostratigraphicZone", "lithostratigraphicTerms",
"group", "formation", "member", "bed", "identificationID",
"verbatimIdentification", "identificationQualifier",
"typeStatus", "identifiedBy", "identifiedByID",
"dateIdentified", "ientificationReferences",
"identificationVerificationStatus", "identificationRemarks",
"taxonID", "scientificNameID", "acceptedNameUsageID",
"parentNameUsageID", "originalNameUsageID",
"naemAccordingToID", "naemPublishedInID",
"taxonConceptID", "scientificName", "acceptedNameUsage",
"parentNameUsage", "originalNameUsage", "nameAccordingTo",
"namePublishedIn", "namePublishedInYear",
"higherClassification", "kingdom", "phylum", "class",
"order", "family", "subfamily", "genus", "genericName",
"subgenus", "infragenericEpithet", "specificEpithet",
"infraspecificEpithet", "cultivarEpithet", "taxonRank",
"verbatimTaxonRank", "scientificNameAuthorship",
"vernacularName", "nomenclaturalCode", "taxonomicStatus",
"nomenclaturalStatus", "taxonRemarks", "measurementID",
"measurementType", "measurementValue", "measurementAccuracy",
"measurementUnit", "measurementDeterminedBy",
"measurementDeterminedDate", "measurementMethod",
"measurementRemarks", "resourceRelationshipID", "resourceID",
"reationshipOfResourceID", "relatedResourceID",
"relationshipOfResource", "relationshipAccordingTo",
"relationshipEstablishedDate", "relationshipRemarks"))
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = next,
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = next,
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = next,
no = print(paste0(i, " is not a valid Darwin Core name! Fix me!"))
)
)
)
}
DCproper <- 0
CustomNames <- 0
Flags <- 0
FixMe <- 0
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = DCproper <- (DCproper + 1),
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = CustomNames <- (CustomNames + 1),
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = Flags <- (Flags + 1),
no = FixMe <- (FixMe + 1)
)
)
)
}
DCtable <- data.frame(DCproper = DCproper,
CustomNames = CustomNames,
Flags = Flags,
FixMe = FixMe)
return(DCtable)
}
#' TDWG Darwin Core Column Name Check 08-23-2022
#'
#' @description `lifecycle::badge("deprecated")`
#'
#' `DC_col_check()` was deprecated in favor of `check_dc_cols()` to enforce consistency in function naming throughout the package and to be consistent with tidyverse style guides.
#'
#' DC_col_check checks to see if the column names in your dataframe match the standardized simple Darwin Core names established by the Taxonomic Databases Working Group
#'
#' @details A dataframe is created with all the simple DarwinCore terms, drawn from Darwin Core reference guide: https://dwc.tdwg.org/terms/ last updated 07-15-2021. We have chosen to align ourselves mostly with the simple Darwin Core rules: https://dwc.tdwg.org/simple/. The function runs through each of the column names in your working dataframe to see if they match 1. A standard simple DarwinCore name 2. A name with a pattern of strings matching "custom_", indicating a custom made column or 3. A name with a pattern of strings matching "_DQ", indicating a data quality flag. If the column name does not fit within any of the three categories, a "Fix me" statement is printed alongside the column name. The function then counts all of the names fitting within each category and prints a summary table.
#'
#' @param working_df - This is the dataframe you want to run against the function. To call, simply write working_df = "the name of your dataframe".
#'
#' @return - The function returns a list of the column names you should fix (not fitting with simple Darwin Core terms, custom name formatting, data quality flagging formatting). Additionally, a small summary table is printed with the counts of the columns falling under each category (DarwinCore, Custom, DQ, Fix Me).
#'
#' @export
#'
#' @keywords internal
#'
#' @examples
#' \dontrun{
#' DC_col_check(yourdataframe)
#' }
DC_col_check <- function(working_df) {
#does not include measurementOrFact or resourceRelationship classes and thus has 179 items vs 196 in the list below.
lifecycle::deprecate_warn("1.0.3.0", "DC_col_check()", "check_dc_cols")
dwcterms <- data.frame(DarwinCore = c("type", "modified", "language", "license", "rightsHolder", "accessRights", "bibliographicCitation", "references", "institutionID", "collectionID", "datasetID", "institutionCode", "collectionCode", "datasetName", "ownerInstitutionCode", "basisOfRecord", "informationWithheld", "dataGeneralizations", "dynamicProperties", "occurrenceID", "catalogNumber", "recordNumber", "recordedBy", "recordedByID", "individualCount", "organismQuantity", "organismQuantityType", "sex", "lifeStage", "reproductiveCondition", "behavior", "establishmentMeans", "degreeOfEstablishment", "pathway", "georeferenceVerificationStatus", "occurrenceStatus", "preparations", "disposition", "associatedMedia", "associatedOccurrences", "associatedReferences", "associatedSequences", "associatedTaxa", "otherCatalogNumbers", "occurrenceRemarks", "organismID", "organismName", "organismScope", "associatedOrganisms", "previousIdentifications", "organismRemarks", "materialSampledID", "eventID", "parentEventID", "fieldNumber", "eventDate", "eventTime", "startDayOfYear", "endDayOfYear", "year", "month", "day", "verbatimEventDate", "habitat", "samplingProtocol", "sampleSizeValue", "sampleSizeUnit", "samplingEffort", "fieldNotes", "eventRemarks", "locationID", "higherGeographyID", "higherGeography", "continent", "waterBody", "islandGroup", "island", "country", "countryCode", "stateProvince", "county", "municipality", "locality", "verbatimLocality", "minimumElevationInMeters", "maximumElevationInMeters", "verbatimElevation", "verticalDatum", "minimumDepthInMeters", "maximumDepthInMeters", "verbatimDepth", "minimumDistanceAboveSurfaceInMeters", "maximumDistanceAboveSurfaceInMeters", "locationAccordingTo", "locationRemarks", "decimalLatitude", "decimalLongitude", "geodeticDatum", "coordinateUncertaintyInMeters", "coordinatePrecision", "pointRadiusSpatialFit", "verbatimCoordinates", "verbatimLatitude", "verbatimLongitude", "verbatimCoordinateSystem", "verbatimSRS", "footprintWKT", "footprintSRS", "footprintSpatialFit", "georeferencedBy", "georeferencedDate", "georeferenceProtocol", "georeferenceSources", "georeferenceRemarks", "geologicalContextID", "earliestEonOrLowestEonothem", "latestEonOrHighestEonothem", "earliestEraOrLowestErathem", "latestEraOrHighestErathem", "earliestPeriodOrLowestSystem", "latestPeriodOrHighestSystem", "earliestEpochOrLowestSeries", "latestEpochOrHighestSeries", "earliestAgeOrLowestStage", "latestAgeOrHighestStage", "lowestBiostratigraphicZone", "highestBiostratigraphicZone", "lithostratigraphicTerms", "group", "formation", "member", "bed", "identificationID", "verbatimIdentification", "identificationQualifier", "typeStatus", "identifiedBy", "identifiedByID", "dateIdentified", "ientificationReferences", "identificationVerificationStatus", "identificationRemarks", "taxonID", "scientificNameID", "acceptedNameUsageID", "parentNameUsageID", "originalNameUsageID", "naemAccordingToID", "naemPublishedInID", "taxonConceptID", "scientificName", "acceptedNameUsage", "parentNameUsage", "originalNameUsage", "nameAccordingTo", "namePublishedIn", "namePublishedInYear", "higherClassification", "kingdom", "phylum", "class", "order", "family", "subfamily", "genus", "genericName", "subgenus", "infragenericEpithet", "specificEpithet", "infraspecificEpithet", "cultivarEpithet", "taxonRank", "verbatimTaxonRank", "scientificNameAuthorship", "vernacularName", "nomenclaturalCode", "taxonomicStatus", "nomenclaturalStatus", "taxonRemarks", "measurementID", "measurementType", "measurementValue", "measurementAccuracy", "measurementUnit", "measurementDeterminedBy", "measurementDeterminedDate", "measurementMethod", "measurementRemarks", "resourceRelationshipID", "resourceID", "reationshipOfResourceID", "relatedResourceID", "relationshipOfResource", "relationshipAccordingTo", "relationshipEstablishedDate", "relationshipRemarks"))
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = next,
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = next,
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = next,
no = print(paste0(i, " is not a valid Darwin Core name! Fix me!"))
)
)
)
}
DCproper <- 0
CustomNames <- 0
Flags <- 0
FixMe <- 0
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = DCproper <- (DCproper + 1),
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = CustomNames <- (CustomNames + 1),
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = Flags <- (Flags + 1),
no = FixMe <- (FixMe + 1)
)
)
)
}
DCtable <- data.frame(DCproper = DCproper, CustomNames = CustomNames, Flags = Flags, FixMe = FixMe)
return(DCtable)
}
nationalparkservice/IMDQC documentation built on March 29, 2025, 10:54 p.m.
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Defines functions DC_col_check check_dc_cols
Documented in check_dc_cols DC_col_check
#' TDWG Darwin Core Column Name Check 08-23-2022
#'
#' @description `check_dc_cols()` checks to see if the column names in your dataframe match the standardized simple Darwin Core names established by the Taxonomic Databases Working Group
#'
#' @details A dataframe is created with all the simple DarwinCore terms, drawn from Darwin Core reference guide: https://dwc.tdwg.org/terms/ last updated 07-15-2021. We have chosen to align ourselves mostly with the simple Darwin Core rules: https://dwc.tdwg.org/simple/. The function runs through each of the column names in your working dataframe to see if they match 1. A standard simple DarwinCore name 2. A name with a pattern of strings matching "custom_", indicating a custom made column or 3. A name with a pattern of strings matching "_DQ", indicating a data quality flag. If the column name does not fit within any of the three categories, a "Fix me" statement is printed alongside the column name. The function then counts all of the names fitting within each category and prints a summary table.
#'
#' @param working_df - This is the dataframe you want to run against the function. To call, simply write working_df = "the name of your dataframe".
#'
#' @return - The function returns a list of the column names you should fix (not fitting with simple Darwin Core terms, custom name formatting, data quality flagging formatting). Additionally, a small summary table is printed with the counts of the columns falling under each category (DarwinCore, Custom, DQ, Fix Me).
#'
#' @export
#'
#' @examples
#' \dontrun{
#' check_dc_cols(yourdataframe)
#' }
check_dc_cols <- function(working_df) {
#does not include measurementOrFact or resourceRelationship classes and thus has 179 items vs 196 in the list below.
dwcterms <- data.frame(
DarwinCore = c("type", "modified", "language", "license", "rightsHolder",
"accessRights", "bibliographicCitation", "references",
"institutionID", "collectionID", "datasetID",
"institutionCode", "collectionCode", "datasetName",
"ownerInstitutionCode", "basisOfRecord",
"informationWithheld", "dataGeneralizations",
"dynamicProperties", "occurrenceID", "catalogNumber",
"recordNumber", "recordedBy", "recordedByID",
"individualCount", "organismQuantity",
"organismQuantityType", "sex", "lifeStage",
"reproductiveCondition", "behavior", "establishmentMeans",
"degreeOfEstablishment", "pathway",
"georeferenceVerificationStatus", "occurrenceStatus",
"preparations", "disposition", "associatedMedia",
"associatedOccurrences", "associatedReferences",
"associatedSequences", "associatedTaxa",
"otherCatalogNumbers", "occurrenceRemarks", "organismID",
"organismName", "organismScope", "associatedOrganisms",
"previousIdentifications", "organismRemarks",
"materialSampledID", "eventID", "parentEventID",
"fieldNumber", "eventDate", "eventTime", "startDayOfYear",
"endDayOfYear", "year", "month", "day", "verbatimEventDate",
"habitat", "samplingProtocol", "sampleSizeValue",
"sampleSizeUnit", "samplingEffort", "fieldNotes",
"eventRemarks", "locationID", "higherGeographyID",
"higherGeography", "continent", "waterBody", "islandGroup",
"island", "country", "countryCode", "stateProvince",
"county", "municipality", "locality", "verbatimLocality",
"minimumElevationInMeters", "maximumElevationInMeters",
"verbatimElevation", "verticalDatum", "minimumDepthInMeters",
"maximumDepthInMeters", "verbatimDepth",
"minimumDistanceAboveSurfaceInMeters",
"maximumDistanceAboveSurfaceInMeters", "locationAccordingTo",
"locationRemarks", "decimalLatitude", "decimalLongitude",
"geodeticDatum", "coordinateUncertaintyInMeters",
"coordinatePrecision", "pointRadiusSpatialFit",
"verbatimCoordinates", "verbatimLatitude",
"verbatimLongitude", "verbatimCoordinateSystem",
"verbatimSRS", "footprintWKT", "footprintSRS",
"footprintSpatialFit", "georeferencedBy",
"georeferencedDate", "georeferenceProtocol",
"georeferenceSources", "georeferenceRemarks",
"geologicalContextID", "earliestEonOrLowestEonothem",
"latestEonOrHighestEonothem", "earliestEraOrLowestErathem",
"latestEraOrHighestErathem", "earliestPeriodOrLowestSystem",
"latestPeriodOrHighestSystem", "earliestEpochOrLowestSeries",
"latestEpochOrHighestSeries", "earliestAgeOrLowestStage",
"latestAgeOrHighestStage", "lowestBiostratigraphicZone",
"highestBiostratigraphicZone", "lithostratigraphicTerms",
"group", "formation", "member", "bed", "identificationID",
"verbatimIdentification", "identificationQualifier",
"typeStatus", "identifiedBy", "identifiedByID",
"dateIdentified", "ientificationReferences",
"identificationVerificationStatus", "identificationRemarks",
"taxonID", "scientificNameID", "acceptedNameUsageID",
"parentNameUsageID", "originalNameUsageID",
"naemAccordingToID", "naemPublishedInID",
"taxonConceptID", "scientificName", "acceptedNameUsage",
"parentNameUsage", "originalNameUsage", "nameAccordingTo",
"namePublishedIn", "namePublishedInYear",
"higherClassification", "kingdom", "phylum", "class",
"order", "family", "subfamily", "genus", "genericName",
"subgenus", "infragenericEpithet", "specificEpithet",
"infraspecificEpithet", "cultivarEpithet", "taxonRank",
"verbatimTaxonRank", "scientificNameAuthorship",
"vernacularName", "nomenclaturalCode", "taxonomicStatus",
"nomenclaturalStatus", "taxonRemarks", "measurementID",
"measurementType", "measurementValue", "measurementAccuracy",
"measurementUnit", "measurementDeterminedBy",
"measurementDeterminedDate", "measurementMethod",
"measurementRemarks", "resourceRelationshipID", "resourceID",
"reationshipOfResourceID", "relatedResourceID",
"relationshipOfResource", "relationshipAccordingTo",
"relationshipEstablishedDate", "relationshipRemarks"))
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = next,
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = next,
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = next,
no = print(paste0(i, " is not a valid Darwin Core name! Fix me!"))
)
)
)
}
DCproper <- 0
CustomNames <- 0
Flags <- 0
FixMe <- 0
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = DCproper <- (DCproper + 1),
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = CustomNames <- (CustomNames + 1),
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = Flags <- (Flags + 1),
no = FixMe <- (FixMe + 1)
)
)
)
}
DCtable <- data.frame(DCproper = DCproper,
CustomNames = CustomNames,
Flags = Flags,
FixMe = FixMe)
return(DCtable)
}
#' TDWG Darwin Core Column Name Check 08-23-2022
#'
#' @description `lifecycle::badge("deprecated")`
#'
#' `DC_col_check()` was deprecated in favor of `check_dc_cols()` to enforce consistency in function naming throughout the package and to be consistent with tidyverse style guides.
#'
#' DC_col_check checks to see if the column names in your dataframe match the standardized simple Darwin Core names established by the Taxonomic Databases Working Group
#'
#' @details A dataframe is created with all the simple DarwinCore terms, drawn from Darwin Core reference guide: https://dwc.tdwg.org/terms/ last updated 07-15-2021. We have chosen to align ourselves mostly with the simple Darwin Core rules: https://dwc.tdwg.org/simple/. The function runs through each of the column names in your working dataframe to see if they match 1. A standard simple DarwinCore name 2. A name with a pattern of strings matching "custom_", indicating a custom made column or 3. A name with a pattern of strings matching "_DQ", indicating a data quality flag. If the column name does not fit within any of the three categories, a "Fix me" statement is printed alongside the column name. The function then counts all of the names fitting within each category and prints a summary table.
#'
#' @param working_df - This is the dataframe you want to run against the function. To call, simply write working_df = "the name of your dataframe".
#'
#' @return - The function returns a list of the column names you should fix (not fitting with simple Darwin Core terms, custom name formatting, data quality flagging formatting). Additionally, a small summary table is printed with the counts of the columns falling under each category (DarwinCore, Custom, DQ, Fix Me).
#'
#' @export
#'
#' @keywords internal
#'
#' @examples
#' \dontrun{
#' DC_col_check(yourdataframe)
#' }
DC_col_check <- function(working_df) {
#does not include measurementOrFact or resourceRelationship classes and thus has 179 items vs 196 in the list below.
lifecycle::deprecate_warn("1.0.3.0", "DC_col_check()", "check_dc_cols")
dwcterms <- data.frame(DarwinCore = c("type", "modified", "language", "license", "rightsHolder", "accessRights", "bibliographicCitation", "references", "institutionID", "collectionID", "datasetID", "institutionCode", "collectionCode", "datasetName", "ownerInstitutionCode", "basisOfRecord", "informationWithheld", "dataGeneralizations", "dynamicProperties", "occurrenceID", "catalogNumber", "recordNumber", "recordedBy", "recordedByID", "individualCount", "organismQuantity", "organismQuantityType", "sex", "lifeStage", "reproductiveCondition", "behavior", "establishmentMeans", "degreeOfEstablishment", "pathway", "georeferenceVerificationStatus", "occurrenceStatus", "preparations", "disposition", "associatedMedia", "associatedOccurrences", "associatedReferences", "associatedSequences", "associatedTaxa", "otherCatalogNumbers", "occurrenceRemarks", "organismID", "organismName", "organismScope", "associatedOrganisms", "previousIdentifications", "organismRemarks", "materialSampledID", "eventID", "parentEventID", "fieldNumber", "eventDate", "eventTime", "startDayOfYear", "endDayOfYear", "year", "month", "day", "verbatimEventDate", "habitat", "samplingProtocol", "sampleSizeValue", "sampleSizeUnit", "samplingEffort", "fieldNotes", "eventRemarks", "locationID", "higherGeographyID", "higherGeography", "continent", "waterBody", "islandGroup", "island", "country", "countryCode", "stateProvince", "county", "municipality", "locality", "verbatimLocality", "minimumElevationInMeters", "maximumElevationInMeters", "verbatimElevation", "verticalDatum", "minimumDepthInMeters", "maximumDepthInMeters", "verbatimDepth", "minimumDistanceAboveSurfaceInMeters", "maximumDistanceAboveSurfaceInMeters", "locationAccordingTo", "locationRemarks", "decimalLatitude", "decimalLongitude", "geodeticDatum", "coordinateUncertaintyInMeters", "coordinatePrecision", "pointRadiusSpatialFit", "verbatimCoordinates", "verbatimLatitude", "verbatimLongitude", "verbatimCoordinateSystem", "verbatimSRS", "footprintWKT", "footprintSRS", "footprintSpatialFit", "georeferencedBy", "georeferencedDate", "georeferenceProtocol", "georeferenceSources", "georeferenceRemarks", "geologicalContextID", "earliestEonOrLowestEonothem", "latestEonOrHighestEonothem", "earliestEraOrLowestErathem", "latestEraOrHighestErathem", "earliestPeriodOrLowestSystem", "latestPeriodOrHighestSystem", "earliestEpochOrLowestSeries", "latestEpochOrHighestSeries", "earliestAgeOrLowestStage", "latestAgeOrHighestStage", "lowestBiostratigraphicZone", "highestBiostratigraphicZone", "lithostratigraphicTerms", "group", "formation", "member", "bed", "identificationID", "verbatimIdentification", "identificationQualifier", "typeStatus", "identifiedBy", "identifiedByID", "dateIdentified", "ientificationReferences", "identificationVerificationStatus", "identificationRemarks", "taxonID", "scientificNameID", "acceptedNameUsageID", "parentNameUsageID", "originalNameUsageID", "naemAccordingToID", "naemPublishedInID", "taxonConceptID", "scientificName", "acceptedNameUsage", "parentNameUsage", "originalNameUsage", "nameAccordingTo", "namePublishedIn", "namePublishedInYear", "higherClassification", "kingdom", "phylum", "class", "order", "family", "subfamily", "genus", "genericName", "subgenus", "infragenericEpithet", "specificEpithet", "infraspecificEpithet", "cultivarEpithet", "taxonRank", "verbatimTaxonRank", "scientificNameAuthorship", "vernacularName", "nomenclaturalCode", "taxonomicStatus", "nomenclaturalStatus", "taxonRemarks", "measurementID", "measurementType", "measurementValue", "measurementAccuracy", "measurementUnit", "measurementDeterminedBy", "measurementDeterminedDate", "measurementMethod", "measurementRemarks", "resourceRelationshipID", "resourceID", "reationshipOfResourceID", "relatedResourceID", "relationshipOfResource", "relationshipAccordingTo", "relationshipEstablishedDate", "relationshipRemarks"))
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = next,
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = next,
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = next,
no = print(paste0(i, " is not a valid Darwin Core name! Fix me!"))
)
)
)
}
DCproper <- 0
CustomNames <- 0
Flags <- 0
FixMe <- 0
for (i in dplyr::all_of(colnames(working_df))) {
ifelse(test = i %in% dwcterms$DarwinCore,
yes = DCproper <- (DCproper + 1),
no = ifelse(test = grepl("custom_", i, ignore.case = TRUE) == TRUE,
yes = CustomNames <- (CustomNames + 1),
no = ifelse(test = grepl("_dq", i, ignore.case = TRUE) == TRUE,
yes = Flags <- (Flags + 1),
no = FixMe <- (FixMe + 1)
)
)
)
}
DCtable <- data.frame(DCproper = DCproper, CustomNames = CustomNames, Flags = Flags, FixMe = FixMe)
return(DCtable)
}
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