Pass strings from a column into a function by using a loop - R

Question

I have a dataset with ~10,000 species. For each species in the dataset I want to query the IUCN database for threats facing each species. I can do this with one species at a time using the rl_threats function from the package rredlist. Below is an example of the function, this example pulls the threats facing Fratercula arctica and assigns them to the object test1 (key is a string that serves as a password for using the IUCN API that stays constant, parse should be TRUE but not as important).

    test1<-rl_threats(name="Fratercula arctica", 
                  key = '1234',
                  parse = TRUE)

I want to get threats for all 10,000 species in my dataset. My idea is to use a loop that passes in the names from my dataset into the name=" " field in the rl_threats command. This is a basic loop I tried to construct to do this but I'm getting lots of errors:

   for (i in 1:df$scientific_name) {
    rl_threats(name=i, 
             key = '1234',
             parse = TRUE)
    }

How would I pass the species names from the scientific_name column into the rl_threats function such that R would loop through and pull threats for every species?

Thank you.

Ronak Shah · Accepted Answer · 2020-11-09 01:53:30Z

1

You can create a list to store the output.

result <- vector('list', length(df$scientific_name))
for (i in df$scientific_name) {
  result[[i]] <- rl_threats(name=i, key = '1234', parse = TRUE)
}

You can also use lapply :

result <- lapply(df$scientific_name, function(x) rl_threats(name=x, key = '1234', parse = TRUE))

answered Nov 9, 2020 at 1:53

Ronak Shah

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