phyloseq: distanceMethodList – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

distanceMethodList

List of distance method keys supported in distance

Description

Distance methods should be specified by exact string match. Cannot do partial matching for all options, because too many similar options in downstream method dispatch.

Usage

distanceMethodList

Format

A list of character vectors. Every entry specifies a supported distance method. Names in the list indicate which downstream function is being utilized for further details. Same functions are linked in the itemized list below.

unifrac: UniFrac
wunifrac: UniFrac
dpcoa: DPCoA
jsd: JSD
manhattan: vegdist
euclidean: vegdist
canberra: vegdist
bray: vegdist
kulczynski: vegdist
jaccard: vegdist
gower: vegdist
altGower: vegdist
morisita: vegdist
horn: vegdist
mountford: vegdist
raup: vegdist
binomial: vegdist
chao: vegdist
cao: vegdist
w: betadiver
-: betadiver
c: betadiver
wb: betadiver
r: betadiver
I: betadiver
e: betadiver
t: betadiver
me: betadiver
j: betadiver
sor: betadiver
m: betadiver
-: betadiver
co: betadiver
cc: betadiver
g: betadiver
-: betadiver
l: betadiver
hk: betadiver
rlb: betadiver
sim: betadiver
gl: betadiver
z: betadiver
maximum: dist
binary: dist
minkowski: dist
ANY: designdist

Examples

distanceMethodList

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23