library(devtools)
install_github("Russel88/MicEco")
With unrooted phylogenies UniFrac sets the root randomly on the tree. The position of the root affects the results. This function runs UniFrac multiple times in parallel, with different roots, and takes the average to smooth potential bias.
Calculate the average 16S rRNA copy number of the OTUs in a community/sample
Combines rarefaction with 16S rRNA copy number correction. It rarefies counts with a probability of the inverse 16S rRNA copy number, such that besides rarefying the read counts the otu-table will be corrected for the varying 16S rRNA copy numbers of the OTUs.
Fit neutral model developed by Sloan et al. (2006, Environ Microbiol 8(4):732-740) and implemented by Burns et al. (2015, ISME J 10(3):655-664).
Fit neutral model developed by Sloan et al. (2006, Environ Microbiol 8(4):732-740) and implemented by Burns et al. (2015, ISME J 10(3):655-664) several times on ramdomly picked samples and with 16S rRNA gene copy number corrected rarefaction (rarefy_rrna).
Calculate proportionality on a phyloseq object or otu-table. Proposed by Lovell et al. 2016 Proportionality: a valid alternative to correlation for relative data (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004075)
Standardized effect size of UniFrac, based on null models created with permatfull/permatswap from the vegan package, or simple shuffling of phylogenetic tree.
Standardized effect size of MPD (mean pairwise distance) separating taxa in two communities, a measure of phylogenetic beta diversity (also called betaNRI and betaMPD). This is a combination of ses.mpd (Standardized effect size of MPD in single communities) and comdist (MPD between two communities) from the picante package.
Standardized effect size of MNTD (mean nearest taxon distance) separating taxa in two communities, a measure of phylogenetic beta diversity (also called betaNTI and betaMNTD). This is a combination of ses.mntd (Standardized effect size of MNTD in single communities) and comdistnt (MNTD between two communities) from the picante package.
As ses.comdist
, but null models are created with permatfull/permatswap
from the vegan package
As ses.comdistnt
, but null models are created with
permatfull/permatswap from the vegan package
A parallel version of the comdist function from the picante package for significant speedup
A parallel version of the comdistnt function from the picante package for significant speedup
Permutation test of z-matrix from ses.comdist
, ses.comdist2
, ses.comdistnt
, ses.comdistnt2
and ses.UniFrac
.
rarefy_rrna
: Some code is from vegan licensed under GPL-2
(https://github.com/vegandevs/vegan)
comdist.par
, comdistnt.par
, ses.comdist
, ses.comdist2
, ses.comdistnt
and ses.comdistnt2
: Some
code is from picante licensed under GPL-2
(https://github.com/skembel/picante)
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