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Calling the Traits webservice from R
This example script was written in R version 3.4.4, for newer/older versions just try and see if it works (See http://www.r-project.org/).
Available for MacOS X, Linux & Windows.
Paste the following code in the R Console (this is just an example)
See all available functions at https://marinespecies.org/traits./rest. Just click on the function you want to explore and "try it out"!
#install the required packages (comment if needed)
install.packages("jsonlite", repos="http://cran.r-project.org")
install.packages("httr")
#Use the libraries
library(jsonlite) #https://cran.r-project.org/web/packages/jsonlite/
library(httr)
#Fill in the AphiaID you need
AphiaID <- 127160
#Build the URL to get the data from
url <- sprintf("https://marinespecies.org/traits./rest/AphiaClassificationByAphiaID/%d", AphiaID);
#Get the actual data from the URL
classificationTree <- fromJSON(url)
#Walk the classification tree
currentTreeItem = classificationTree
while (!is.null(currentTreeItem )) {
print(sprintf("ID: %d, RANK: %s, ScientificName: %s",
currentTreeItem$AphiaID,
currentTreeItem$rank,
currentTreeItem$scientificname
));
#You can access the variables individually
#print(currentTreeItem$AphiaID);
#print(currentTreeItem$scientificname);
#print(currentTreeItem$rank);
#Get next item in the tree
currentTreeItem <- currentTreeItem$child;
}
Download this example.
Download elaborate example (match names).
Note there is a complete R package available that you can use. See the rOpenSci library 'worrms', available here: https://github.com/ropensci/worrms
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