taxotools (version 0.0.129)

compact_ids: 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

Value

returns data frame

Details

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

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

# NOT RUN {
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)
# }