% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pairMicroTest.R
\name{pairMicroTest}
\alias{pairMicroTest}
\title{Beta diversity statistics by adonis/anosim/MRPP in pair}
\usage{
pairMicroTest(ps = ps, Micromet = "anosim", dist = "bray")
}
\arguments{
\item{ps}{alternative input;}

\item{Micromet}{statistics default by adonis, alternative anosim or MRPP;}

\item{dist}{distance type, including "unifrac" "wunifrac" "dpcoa" "jsd" "manhattan" "euclidean"   "canberra" "bray" "kulczynski"  "jaccard" "gower" "altGower" "morisita" "horn" "mountford"  "raup" "binomial"  "chao"  "cao" "w"  "-1"  "c" "wb"  "r"   "I"  "e" "t" "me"   "j"  "sor"  "m"   "-2"  "co";}

\item{otu}{OTU/ASV table;}

\item{map}{Sample metadata;}

\item{tree}{tree/nwk file;}

\item{group}{group ID;}

\item{method}{DCA, CCA, RDA, NMDS, MDS, PCoA, PCA, LDA;}

\item{pvalue.cutoff}{Pvalue threshold, default in 0.05;}
}
\value{
stat table
}
\description{
Input phyloseq object, test method and distance type
}
\details{
By default, input phyloseq object include metadata and otutab
The available diversity indices include the following:
\itemize{
\item{most used indices: bray unifrac wunifrac}
\item{other used indices: dpcoa jsd manhattan euclidean canberra kulczynski jaccard gower altGower morisita horn mountford raup binomial chao cao w -1 c wb r I e t me j sor m -2 co}
}
}
\examples{
# Input phyloseq format input, and options group, method and distance
# 鐢熸垚phyloseq瀵硅薄
ps=phyloseq(otu_table(otutab_rare, taxa_are_rows=TRUE), sample_data(metadata))
pairMicroTest (ps=ps, Micromet="anosim", dist="bray")
}
\references{
Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai.
A practical guide to amplicon and metagenomic analysis of microbiome data.
Protein Cell, 2020(41), 1-16, DOI: \url{https://doi.org/10.1007/s13238-020-00724-8}

Jingying Zhang, Yong-Xin Liu, Na Zhang, Bin Hu, Tao Jin, Haoran Xu, Yuan Qin, Pengxu Yan, Xiaoning Zhang, Xiaoxuan Guo, Jing Hui, Shouyun Cao, Xin Wang, Chao Wang, Hui Wang, Baoyuan Qu, Guangyi Fan, Lixing Yuan, Ruben Garrido-Oter, Chengcai Chu & Yang Bai.
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.
Nature Biotechnology, 2019(37), 6:676-684, DOI: \url{https://doi.org/10.1038/s41587-019-0104-4}
}
\seealso{
BetaDiv beta_pcoa beta_cpcoa
}
\author{
Contact: Tao Wen \email{2018203048@njau.edu.cn}, Yong-Xin Liu \email{yxliu@genetics.ac.cn}
}
