validateDup: Prepare, Search and Merge Duplicate Specimens

In LimaRAF/plantR: Managing Species Records from Biological Collections

Prepare, Search and Merge Duplicate Specimens

Description

This function search for duplicated specimens within and across collections and it can be used to homogenize the information of different groups of fields and to remove duplicates, leaving only one occurrence for each group of duplicata.

Usage

validateDup(
  occ.df,
  cat.code = "collectionCode.new",
  cat.numb = "catalogNumber",
  merge = TRUE,
  remove = FALSE,
  noYear = "s.d.",
  noName = "s.n.",
  noNumb = "s.n.",
  comb.fields = list(c("family", "col.last.name", "col.number", "col.loc"), c("family",
    "col.year", "col.number", "col.loc"), c("species", "col.last.name", "col.number",
    "col.year"), c("col.year", "col.last.name", "col.number", "col.loc")),
  ignore.miss = TRUE,
  dup.name = "dup.ID",
  prop.name = "dup.prop",
  prop = 0.75,
  rec.ID = "numTombo",
  info2merge = c("tax", "geo", "loc"),
  tax.names = c(family = "family.new", species = "scientificName.new", det.name =
    "identifiedBy.new", det.year = "yearIdentified.new", tax.check = "tax.check", status
    = "scientificNameStatus"),
  geo.names = c(lat = "decimalLatitude.new", lon = "decimalLongitude.new", org.coord =
    "origin.coord", prec.coord = "precision.coord", geo.check = "geo.check"),
  loc.names = c(loc.str = "loc.correct", res.gazet = "resolution.gazetteer", res.orig =
    "resol.orig", loc.check = "loc.check"),
  tax.level = "high",
  overwrite = FALSE,
  print.rm = TRUE
)

Arguments

occ.df	a data frame, containing typical fields from occurrence records from herbarium specimens
cat.code	character. The name of the column containing the code of the collection. Default to the plantR output column "collectionCode.new".
cat.numb	character. The name of the column containing the catalog number (a.k.a. accession number) of the record. Default to "catalogNumber".
merge	logical. Should duplicates be merged? Default to TRUE.
remove	logical. Should all duplicates be removed or only the duplicated entries from the same collection? Default to FALSE.
noYear	character. Standard for missing data in Year. Default to "n.d.".
noName	character. Standard for missing data in collector name. Default to "s.n.".
noNumb	character. Standard for missing data in collector number. Default to "s.n.".
comb.fields	list. A list containing one or more vectors with the information that should be used to create the duplicate search strings. Default to four vectors of information to be combined.
ignore.miss	logical. Should the duplicate search strings with missing/unknown information (e.g. 'n.d.', 's.n.', NA) be excluded from the duplicate search. Default to TRUE.
dup.name	character. The name of column in the input data frame with the duplicate group ID. Default to the plantR output 'dup.ID'.
prop.name	character. The name of column in the input data frame with the proportion of duplicates found within the group ID. Default to the plantR output 'dup.prop'.
prop	numerical. The threshold value of proportion of duplicated values retrieved (i.e. dup.prop) to enter the merging routine. Should be between zero and one. Default to 0.75.
rec.ID	character. The name of the columns containing the unique record identifier (see function getTombo()). Default to 'numTombo'.
info2merge	Vector. The groups of information (i.e. fields) to be merged. Currently, only taxonomic ('tax'), geographic ('geo') and/or locality ('loc') information can be merged. Default to merge all of them.
tax.names	Vector. A named vector containing the names of columns in the input data frame with the taxonomic information to be merged.
geo.names	Vector. A named vector containing the names of columns in the input data frame with the geographical information to be merged.
loc.names	Vector. A named vector containing the names of columns in the input data frame with the locality information to be merged.
tax.level	character. A vector with the confidence level of the identification that should be considered in the merge of taxonomic information. Default to "high".
overwrite	logical. Should the merged information be overwritten or stored in separate, new columns. Default to FALSE (new columns are created).
print.rm	logical. Should the number of records removed be printed? Default to TRUE.

Details

The function works similarly to a wrapper function, where the individuals steps of the proposed plantR workflow for preparing, searching, merging and removal of duplicates are performed altogether (see the plantR tutorial for details).

Value

The input data frame, plus the new columns with the formatted fields.

Author(s)

Renato A. F. de Lima

See Also

prepDup, getDup, mergeDup, rmDup

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.