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 4+4 character CEP names as default, but it can also use other lengths. The function is based on abbreviate and will produce longer names if constructed names are not unique. If generic name is shorter than specified minimum length, more characters can be used by the epithet. If uniqgenera = TRUE, unique generic name may need more characters than the minimum length, 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 in the final attempt to abbreviate abbreviations, starting with lower-case vowels. The constructed names are based on binomial names with two components. If there is only one component (typically a genus), it can use also the space reserved for the second component. If there are more than two components of input names, the function selects only two: always the first, and either the last or second depending on the argument seconditem. Function will issue a warning of duplicated input names or of duplicated inferred binomial names, but resulting CEP names are made unique by adding a sequence number (with a warning listing these names).

Value

Function returns a vector of abbreviated names.

Author

Jari Oksanen

See also

abbreviate.

Note

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

Examples

names <- c("Aa maderoi", "Capsella bursa-pastoris", "Taraxacum",
  "Cladina rangiferina", "Cladonia rangiformis", "Cladonia cornuta",
  "Cladonia cornuta var. groenlandica", "Euphorbia cf. enopla",
  "Rumex acetosa", "Rumex acetosella")
make.cepnames(names)
#>  [1] "Aamadero"    "Capsburs"    "Taraxacu"    "Cladrangife" "Cladrangifo"
#>  [6] "Cladcorn"    "Cladgroe"    "Euphenop"    "Rumeacetosa" "Rumeacetose"
make.cepnames(names, uniqgenera = TRUE)
#>  [1] "Aamadero"    "Capsburs"    "Taraxacu"    "Cladiran"    "Cladoran"   
#>  [6] "Cladocor"    "Cladogro"    "Euphenop"    "Rumeacetosa" "Rumeacetose"
make.cepnames(names, method = "both.sides")
#>  [1] "Aamadero" "Capsburs" "Taraxacu" "Cladrngf" "Cldrngfo" "Cladcorn"
#>  [7] "Cladgroe" "Euphenop" "Rumeacts" "Rmcetose"
## seconditem=TRUE makes subspecies duplicates
data(BCI)
names <- make.cepnames(names(BCI), seconditem=TRUE)
#> Warning: some inferred binomial names were duplicated: Swartzia simplex
#> Warning: these cepnames were made unique by appending a number:
#> Swarsimp1 (Swartzia.simplex.continentalis)