Tag Archive | taxonomy

Taxonomy in R

Hi there,
here is a r-snippet which i wrote to get new data out of a species list.
I have a species-list of insect-pollinated european grassland plants, which is a little to detailed for me.
Through filtering i want to get a subset list with only small herbs.
First i consulted the PESI-Portal for a taxamatch only to find out, that only 75% of my species are currently in the database (Acer campestre is not found?)
After that i searched for a smart solution in r and i found taxize, a newly package which queries different databases and has nice functions for taxonomic data management.
First i want to get familynames for each genus-species combination. My species list contains two columns with the genus and the species name.
See below my solution how to get a family name for each species.

# Load in the source package taxize and get familynames for taxa in splist
install.packages("devtools")
require(devtools)
install_github("taxize_", "ropensci")
require(taxize)

splist <- paste(data$Genus,data$Species,sep="_")
mat <- matrix(nrow=length(splist),ncol=2)
mat[,2] <- splist
for(i in seq(1:length(splist))){
 # I had to use a try, because some entries produce strange errors.
res <- try(expr=get_tsn(splist[i],"sciname", by_="name"),silent=T)
if(is.vector(res)) {
fam <- get_familyname(res)
mat[i,1] <- fam
print(paste(fam,splist[i],sep=" - "))
}
}

It’s kind of rough, but it works. Currently it runs through my plant-species list with over 1500 entries.
The output looks like this…


[1] "Asteraceae - Artemisia_scoparia"

[1] "Asteraceae - Artemisia_vulgaris"

[1] "Araceae - Arum_maculatum"

[1] "Rosaceae - Aruncus_dioicus"

[1] "Asclepiadaceae - Asclepias_syriaca"

[1] "Asparagaceae - Asparagus_officinalis"

Iam still looking for a solution how to get specific traits for every species, such as “Perennial or Annual” or “Grow height”.
Will report back, if i find something.

Taxonomy in Crisis

Just a short comment, because i am short-timed lately.  I want to put a spotlight on this excellent article in wired:

http://www.wired.com/wiredscience/2011/01/extinction-of-taxonomists/

Taxonomy as a discipline is really dying out. We spend millions of euros/dollars in the development of databases and conservation programs while the actual knowledge about how to update these databases in the future is more and more dying out. Mostly because of the horrific job perspectives due to the changes in today’s universities structure. In our scientific world nowadays only the number of grants, publications and your impact factor matters. One of the leaders from the entomological groups at Senckenberg said to me that it is a huge mistake that many scientists only rely on meta-data from species gathered in databases. He is one of the last expert in his field and during his scientific career he corrected several huge mistakes, errors and other misconception from the lepidoptera-literature available. Who will do this as he retires?  We definitely need active biodiversity research and experts!

I am researching myself on many different pollinator-species in temperate european woodlands (apoidea, syrphidae, …) and its sometimes really hard to get in contact with adequate literature. Quite often you have to rely on some observations/books from the 50s or earlier which certainly need a revision in times of molecular biology and dna barcoding. Some universities don’t even teach basic zoology knowledge anymore or how to address species in the field. I am pessimistic that this trend will change, but i really want to see a future coming where those people who research on species taxonomies are adequately honored.

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