compact_ids {taxotools} | R Documentation |
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)
[Package taxotools version 0.0.139 Index]