compact_ids: compact id numbers

In taxotools: Taxonomic List Processing

compact id numbers

Description

Compacting and converting the id values to numeric if required to make sure dependent functions work well

Usage

compact_ids(dat, id = "id", accid = "accid", startid = 1, verbose = TRUE)

Arguments

dat	taxonomic list in a data frame with id and accid columns
id	column name for 'id'. Default 'id'
accid	column name for 'accid'. Default 'accid'
startid	starting id number for the list. Default 1
verbose	verbose output on the console

Details

Helper function to make sure values for ids are in right format and are compact

Value

returns data frame

See Also

Other List functions: DwC2taxo(), cast_cs_field(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples

mylist <- data.frame("id" = c("1","2","3","4","5"),
                     "canonical" = c("Hypochlorosis ancharia",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", 
                                  "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c("0","1","1","0","0"),
                     "source" = c("itis","wiki","wiki","itis",
                                  "itis"),
                     stringsAsFactors = FALSE)

mylist_c <- compact_ids(mylist)

mylist_c <- compact_ids(mylist,startid=1001)

mylist <- data.frame("id" = c(11,12,13,14,15),
                     "canonical" = c("Hypochlorosis ancharia",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", 
                                  "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c(0,11,11,0,0),
                     "source" = c("itis","wiki","wiki","itis",
                                  "itis"),
                     stringsAsFactors = FALSE)
                     
mylist_c <- compact_ids(mylist)

taxotools documentation built on May 29, 2024, 3:09 a.m.