Abbreviates a Two-Part Botanical or Zoological Latin Name into Character String

Function is based on abbreviate, and will take given number of characters from the first (genus) and last (epithet) component of botanical or zoological Latin name and combine these into one shorter character string. The names will be unique and more characters will be used if needed. The default usage makes names with 4+4 characters popularized in Cornell Ecology Programs (CEP) and often known as CEP names. Abbreviated names are useful in ordination plots and other graphics to reduce clutter.

Usage

make.cepnames(names, minlengths = c(4,4), seconditem = FALSE,
   uniqgenera = FALSE, named = FALSE, method)

Arguments

names: The names to be abbreviated into a vector abbreviated names.
minlengths: The minimum lengths of first and second part of the abbreviation. If abbreviations are not unique, the parts can be longer.
seconditem: Take always the second part of the original name to the abbreviated name instead of the last part.
uniqgenera: Should the first part of the abbreviation (genus) also be unique. Unique genus can take space from the second part (epithet).
method: The abbreviate argument in last attempt to abbreviate the abbreviation. The default method tries to drop character from the end, but "both.sides" can remove characters from any position, including the genus part, and same genus can be abbreviated differently.
named: Should the result vector be named by original names.

Details

Cornell Ecology Programs (CEP) used eight-letter abbreviations for species and site names. In species, the names were formed by taking four first letters of the generic name and four first letters of the specific or subspecific epithet. The current function produces CEP names as default, but it can also use other lengths. The function is based on abbreviate and can produce longer names if basic names are not unique. If generic name is shorter than specified minimun length, more characters can be used by the epithet. If uniqgenera = TRUE genus can use more characters, and these reduce the number of characters available for the epithet. The function drops characters from the end, but with method = "both.sides" the function tries to drop characters from other positions, starting with lower-case wovels, in the final attempt to abbreviate abbreviations.

Value

Function returns a vector of abbreviated names.

Author

Jari Oksanen

Note

The function does not handle Author names except strictly two-part names with seconditem = TRUE. It is often useful to edit abbreviations manually.

Examples

names <- c("Aa maderoi", "Capsella bursa-pastoris", "Taraxacum",
  "Cladina rangiferina", "Cladonia rangiformis", "Cladonia cornuta",
  "Cladonia cornuta var. groenlandica", "Rumex acetosa",
  "Rumex acetosella")
make.cepnames(names)
#> [1] "Aamadero"    "Capsburs"    "Taraxacu"    "Cladrangife" "Cladrangifo"
#> [6] "Cladcorn"    "Cladgroe"    "Rumeacetosa" "Rumeacetose"
make.cepnames(names, uniqgenera = TRUE)
#> [1] "Aamadero"    "Capsburs"    "Taraxacu"    "Cladiran"    "Cladoran"   
#> [6] "Cladocor"    "Cladogro"    "Rumeacetosa" "Rumeacetose"
make.cepnames(names, method = "both.sides")
#> [1] "Aamadero" "Capsburs" "Taraxacu" "Cladrngf" "Cldrngfo" "Cladcorn" "Cladgroe"
#> [8] "Rumeacts" "Rmcetose"