My workspace objects: http://www.filedropper.com/workspace1_1
Hello everyone. I need help calculating FD as stated in Petchey & Gaston 2002 in R. I have a series of communities with present/absent kind of species data (object name: comm) and traits data (object name: zscores) which have been standardized. I'm trying to follow "http://rfunctions.blogspot.com/2012/05/functional-diversity-fd-petchey-gaston.html" to calculate FD index but I always fail and get the error message "Error in rep(NA, nEdges) : invalid 'times' argument. In addition: Warning message: In drop.tip(tree, treeabsent) : drop all tips of the tree: returning NULL". I made sure that my data has no NA's and I really have no idea about what else to do to calculate FD by using the method outlined in the link below (uses phylogenetic diversity approach to calculate FD actually). I really need some expert help here. By the way, I'm using the packages "picante" and "ade4" as advised in the source above. I should add that FD package doesn't offer a tool to calculate FD (it has functions to calculate Fric, Fdiv, Feve etc. but not FD index) as far as I know. I mean I couldn't see it on the manual. Thanks in advance!
Hi Kaan,
Could you attach some example data here rather than the link? My agency's firewall doesn't like that site.
Best wishes
Malcolm
Hi Malcolm,
Thanks for your reply. I've just added the file that. If you also have some experience with FD Package and its dbFD function, please let me know as I'm also having some problems with it.
Cheers,
Kaan
Hi Kaan,
My apologies - I misread initially, I have edited my answer:
Hopefully I have resolved your problem. Your comm dataset had names with dots between species and genus, while the zscores had a space. R wasn't smart enough to realise these are the same species. This code should work for you:
library(picante)
row.names(zscores)
Dear Malcolm,
Yes, it worked! How could I miss that? This resolved my problem. Thank you so much for taking your time to help. One more thing. Do you have any idea how can I include the weights of the traits into this? By the way, I solved my problem with FD package. Thank you once again for offering help.
Cheers,
Kaan
Great, glad that worked.
Not sure re weights, perhaps someone else can help.
Best
Malcolm
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