Function to abbreviate scientific names

user_7787472 0
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Could you please help me?

I'm trying to modify an R function written by a colleague. This function receives a character vector with scientific names (Latin binomes), just like this one:

Name
Cerradomys scotti
Oligoryzomys sp
Philander frenatus
Byrsonima sp
Campomanesia adamantium
Cecropia pachystachya
Cecropia sp
Erythroxylum sp
Ficus sp
Leandra aurea

Then, it should abbreviate the scientific names, using only the first three letters of the genus (first term) and the epithet (second term) to make a short code. For instance, Cerradomys scotti should become Cersco.

This is the original function:

AbbreviatedNames <- function(vector) {

    abbreviations <- character(length = length(vector))
    
    splitnames <- strsplit(vector, " ")
    
    for (i in 1:length(vector)) {
        vector[i] <- if(splitnames[[i]][2] == "^sp") {
            paste(substr(splitnames[[i]][1],1,3),
                  splitnames[[i]][2], sep = "")
        }
        
        else {
            paste(substr(splitnames[[i]][1],1,3),
                  substr(splitnames[[i]][2],1,3), sep = "")
        }
        
    }
    
    vector
    
    }

With a simple list like that one, the function works perfectly. However, when the list has some missing or extra elements, it does not work. The loop stops when it meets the first row that does not match the pattern. Let's take this more complex list as an example:

Name
Cerradomys scotti
Oligoryzomys sp
Philander frenatus
Byrsonima sp
Campomanesia adamantium
Cecropia pachystachya
Cecropia sp
Erythroxylum sp
Ficus sp
Leandra aurea
Morfosp1
Vismia cf brasiliensis

See that Morfosp1 has only 1 term. And Vismia cf brasiliensis has an additional term (cf) in the middle.

I've tried adapting the function, for instance, this way:

AbbreviatedNames <- function(vector) {

    abbreviations <- character(length = length(vector))
    
    splitnames <- strsplit(vector, " ")
    
    for (i in 1:length(vector)) {
        vector[i] <- if(splitnames[[i]][2] == "^sp" & is.na(splitnames[[i]][2]))) {
            paste(substr(splitnames[[i]][1],1,3),
                  splitnames[[i]][2], sep = "")
        }
        
        else {
            paste(substr(splitnames[[i]][1],1,3),
                  substr(splitnames[[i]][2],1,3), sep = "")
        }
        
    }
    
    vector
    
    }

Nevertheless, it does not work. I get this error message:

Error in if (splitnames[[i]][2] == "^sp" & is.na(splitnames[[i]][2])) { : 
  valor ausente onde TRUE/FALSE necessário

How could I make the function:

  1. Deal also with names that have only 1 term?

Expected outcome: Morfosp1 -> Morfosp1 (stays the same)

  1. Deal also with names that have an additional term in the middle?

Expected outcome: Vismia cf brasiliensis -> Visbra (term in the middle is ignored)

Thank you very much!

logical-operators r list split
3 Answers

Something like this is pretty concise:

test <- c("Cerradomys scotti", "Oligoryzomys sp", "Latingstuff", "Latin staff more")

# function to truncate a given name
trunc_str <- function(latin_name) {
  
  # split it on a space
  name_split <- unlist(strsplit(latin_name, " ", fixed = TRUE))
  
  # if one name, just return it
  if (length(name_split) == 1) return(name_split)
  
  # truncate to first 3 letters
  name_trunc <- substr(name_split, 1, 3)

  # paste the first and last term together (skipping any middle ones)
  paste0(head(name_trunc, 1), tail(name_trunc, 1))
    
}

# iterate over all
vapply(test, trunc_str, "")
# Cerradomys scotti   Oligoryzomys sp       Latingstuff  Latin staff more 
# "Cersco"           "Olisp"     "Latingstuff"          "Latmor"

If you don't want a named vector output, you can use USE.NAMES = FALSE in vapply(). Or feel free to use a loop here.

user_109174790 
AbbreviatedNames <- function(vector) {
  
  abbreviations <- character(length = length(vector))
  
  splitnames <- strsplit(vector, " ")
  
  for (i in 1:length(vector)){
    
    # One name
    if(length(splitnames[[i]])==1){
      vector[i] <- paste(substr(splitnames[[i]][1],1,3),
            substr(splitnames[[i]][2],1,3), sep = "")
    }
    
    # Two names
    else if(length(splitnames[[i]])==2){
      vector[i] <- if(splitnames[[i]][2] == "^sp") {
        paste(substr(splitnames[[i]][1],1,3),
              splitnames[[i]][2], sep = "")
      }
      else {
        paste(substr(splitnames[[i]][1],1,3),
              substr(splitnames[[i]][2],1,3), sep = "")
      }
    }
    
    # Three names
    else if(length(splitnames[[i]])==3){
      vector[i] <- paste(substr(splitnames[[i]][1],1,3),
              substr(splitnames[[i]][3],1,3), sep = "")
      # Assuming that the unwanted word is always in the middle 
    }
    
  }
  
  return(vector)
}

I tested on the list you gave and it seems to work, tell me if you need a more general code

user_130487280

Thank you very much for the help, Ricardo and Adam! I've made the code available on GitHub to other people who work with interaction networks, and need to abbreviate scientific names to be used in graphs.

user_77874720
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