Description Usage Arguments Value Examples
Calculate pairwise site PCD, users can specify expected values from pcd_pred()
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1 2 |
comm |
site by species data frame or matrix, sites as rows. |
tree |
a phylogeny for species |
expectation |
nsp_pool, psv_bar, psv_pool, and nsr calculated from |
cpp |
whether to use loops written with c++, default is TRUE |
unif_dim |
the number of cells (nrow * ncol) of the comm, if it is less than unif_dim, then calculate unifrac and phylosor; these functions are very slow. |
verbose |
do you want to see the progress? |
a list of a variety of pairwise dissimilarities.
1 2 3 4 5 6 | x1 = pcd_pred(comm_old = read.csv('data/li_2015_old.csv', row.names = 1, check.names = F),
comm_new = read.csv('data/li_2015_new.csv', row.names = 1, check.names = F),
tree = ape::read.tree('data/phy.tre'), reps = 100)
pcd2(comm = read.csv('data/li_2015_old.csv', row.names = 1, check.names = F),
tree = ape::read.tree('data/phy.tre'),
expectation = x1)
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