Faith's Phylogenetic Diversity (PD) index supported on Phyloseq?

[JPBalmonte]

Hi,

Could the Faith's Phylogenetic Diversity (PD) index be one day supported on Phyloseq? It is included in the output of the QIIME alpha diversity function, and would be very informative interpreted by itself as well as alongside the other diversity indices.

Thanks!
JP Balmonte

[spholmes]

JP
I always just call up the picante package's implementation, just to try to
always use things that already exist in R.

Susan

On Tue, Aug 30, 2016 at 1:32 PM, JP Balmonte [email protected]
wrote:

Hi,

Could the Faith's Phylogenetic Diversity (PD) index be one day supported
on Phyloseq? It is included in the output of the QIIME alpha diversity
function, and would be very informative interpreted by itself as well as
alongside the other diversity indices.

Thanks!
JP Balmonte

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[mghanbari]

https://cran.r-project.org/web/packages/picante/picante.pdf
The pd function returns two values for each community, Faith's PD and species richness (SR).
library(picante)

Calculate Faith's PD

comm.pd <- pd(comm, phy)
head(comm.pd)

[colinbrislawn]

This could be easily added to the estimate_richness() function.

  if( "FaithPD" %in% measures){
  	outlist <- c(outlist, list(FaithPD = t(picante::pd(samp = OTU, tree = phy_tree(physeq), include.root = F))[1,] ))
  }

Are you accepting code PRs, or just documentation changes? I could fold this into #575, if folks are interested.

[jjsolano]

The function estimate_pd from btools package you can use the phyloseq object to estimate the Faith's Phylogenetic Diversity (PD) index:

estimate_pd(phyloseq.object)

[kusandeep]

The function estimate_pd from btools package you can use the phyloseq object to estimate the Faith's Phylogenetic Diversity (PD) index:

estimate_pd(phyloseq.object)

Hi, this worked but how can we plot it with treatment..? or perhaps combine it with plot_richness output from phyloseq?