query_nemaplex: Query NEMAPLEX to retrieve information about nematode taxa

In amynang/marcel: Calculates nematode community indices

Query NEMAPLEX to retrieve information about nematode taxa

Usage

name_check(taxa)
query_nemaplex(taxa, complete = FALSE)

Arguments

taxa	A vector with the taxa for which the database will be queried.
complete	Logical. Default returns a subset of all the information provided by nemaplex. This does not make the query faster, it just makes the output less messy.

Details

If the input contains taxa not present in Nemaplex, these will appear on the console.

name_check() can be used to examine if taxa in the input are not present in the database, before running the entire query. These can be false absences, due to nomenclature differences (eg. "Thornematidae" vs "Thornenematidae").

query_nemaplex() currently uses Firefox, so the browser needs to be installed in your computer. It also requires JAVA. For 64bit(32bit) R you need 64bit(32bit) JAVA.

Value

A dataframe with Ecophysiological Parameters for the genera and families in 'taxa'.

Note

My experience is that the first time you will call the function, RSelenium will do some setup procedure. It is a good idea to start with a small number of taxa (1 or 2 are fine) to make sure everything runs ok before you input the complete list of taxa you want to retrieve information for.

If any error occurs that breaks the process, you will need to call system("taskkill /im java.exe /f", intern=FALSE, ignore.stdout=FALSE) to kill java manually, before you try calling the function again.

Author(s)

Angelos Amyntas

References

Ferris, Howard. "Nemaplex". UC-Davis <http://nemaplex.ucdavis.edu/>

Examples

# the input can contain genera and/or families

query_nemaplex("Actinolaimidae", 
               "Alaimidae", 
               "Acrobeles", 
               "Acrobeloides")

amynang/marcel documentation built on June 24, 2024, 10 p.m.