> Dear Jeff,
> thank you for your email and advice. I found a previous thread from 2010 > which mentioned that as a workaround when using categorical data and > calculating FD indices: > > https://stat.ethz.ch/pipermail/r-sig-ecology/2010-November/001642.html > > Within the thread, it doesn't give all the steps to take i.e. > > library(FD) > df<-gowdist(traits) > df<-dudi.pco(df) > df_traits<-df$tab (not sure if this is correct but gives me a df with numbers > for all eight traits) > > As I am not sure how to take the result from the gowdis and then use it with > the dbFD function in the FD package, or even after I use the dudi.pco. > > I have tried many ways and I don't really have an example to base it on, so I > am not totally sure if what I have done is correct. > > Thanks > Mark > > ---------- Forwarded message ---------- > From: <r-sig-ecology-requ...@r-project.org> > Date: Sat, Aug 11, 2018 at 11:00 AM > Subject: R-sig-ecology Digest, Vol 125, Issue 2 > To: r-sig-ecology@r-project.org > > > Send R-sig-ecology mailing list submissions to > r-sig-ecology@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > or, via email, send a message with subject or body 'help' to > r-sig-ecology-requ...@r-project.org > > You can reach the person managing the list at > r-sig-ecology-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-ecology digest..." > > > Today's Topics: > > 1. Functional Diversity help! (Mark Thomas) > 2. FW: Functional Diversity help! (Holland, Jeffrey D) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Aug 2018 12:06:50 +0100 > From: Mark Thomas <travelmar...@gmail.com> > To: r-sig-ecology@r-project.org > Subject: [R-sig-eco] Functional Diversity help! > Message-ID: > <CABdKAsn+dP+TPo+x_nhb2UXnaTEkq=4CJgYyDGbQc=58jkb...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear r-sig-ecology, > Please forgive me if this question has already been answered, I have > perused the web and due to me being fairly new to R, I have had trouble > interpreting the answers. > > I wish to calculate the functional diversity indices (Functional Richness, > divergence, evenness, Rao-quadratic). > > My dataset consists of 14 species, 25 sites, and 8 categorical traits. > > I have been using the FD package but from what I have read I need to > convert the categorical data using the gowdist function and then run pcoa > to generate continuous data? > > However, when I run the gowdist and pcoa I thought I'd get a number to > replace the categorical data so I could then run the dbFD function in the > FD package to calculate the FD indices, but this isn't happening, and I am > not sure how to take the output from the pcoa and run in dbFD. > > Any help would be greatly appreciated (apologies for the beginner question) > thanks > > [[alternative HTML version deleted]] > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Aug 2018 12:37:36 +0000 > From: "Holland, Jeffrey D" <jdhol...@purdue.edu> > To: "r-sig-ecology@r-project.org" <r-sig-ecology@r-project.org> > Subject: [R-sig-eco] FW: Functional Diversity help! > Message-ID: <cc68207f0f7743f085c31d148ab78...@wppexc08.purdue.lcl> > Content-Type: text/plain; charset="us-ascii" > > Dear Mark, > Gower does seem to the correct dissimilarity metric based upon your > variables. This will return a dissimilarity matrix that I believe you can > use to calculate the functional diversity indices, by base code and likely by > FD package as well. Using this matrix will ensure that you are actually > calculating the indices based upon the functional differences of the actual > replicates, and will give you a continuous dissimilarity measure. However, I > am unsure why you want to insert PCoA into this before using FD? This will > output a reduced dimensionality object with replicate scores on the PCo > axes---is this what you are after? In any case, you will not get a number to > replace the classes of your categorical data---you will get a dissimilarity > measure between all pairs of replicates. > Hope this helps, > Jeff Holland > > -----Original Message----- > From: R-sig-ecology <r-sig-ecology-boun...@r-project.org> On Behalf Of Mark > Thomas > Sent: Friday, August 10, 2018 7:07 AM > To: r-sig-ecology@r-project.org > Subject: [R-sig-eco] Functional Diversity help! > > Dear r-sig-ecology, > Please forgive me if this question has already been answered, I have perused > the web and due to me being fairly new to R, I have had trouble interpreting > the answers. > > I wish to calculate the functional diversity indices (Functional Richness, > divergence, evenness, Rao-quadratic). > > My dataset consists of 14 species, 25 sites, and 8 categorical traits. > > I have been using the FD package but from what I have read I need to convert > the categorical data using the gowdist function and then run pcoa to generate > continuous data? > > However, when I run the gowdist and pcoa I thought I'd get a number to > replace the categorical data so I could then run the dbFD function in the FD > package to calculate the FD indices, but this isn't happening, and I am not > sure how to take the output from the pcoa and run in dbFD. > > Any help would be greatly appreciated (apologies for the beginner question) > thanks > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > ------------------------------ > > End of R-sig-ecology Digest, Vol 125, Issue 2 > ********************************************* > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
