% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/1.calculate.R

\name{c_net_calculate}

\alias{c_net_calculate}

\alias{c_net_cal}

\title{Calculate correlation for one or two t(otutab), or distance for one t(otutab).}

\usage{

c_net_calculate(

  totu,

  totu2 = NULL,

  method = "spearman",

  filename = FALSE,

  p.adjust.method = NULL,

  p.adjust.mode = "all",

  threads = 1,

  verbose = TRUE

)

}

\arguments{

\item{totu}{t(otutab), row are samples, column are features.}

\item{totu2}{t(otutab2) or NULL, row are samples, column are features.}

\item{method}{"spearman" (default), "pearson", "sparcc", or distance index from \code{\link[vegan]{vegdist}}.}

\item{filename}{the prefix of saved .corr file or FALSE.}

\item{p.adjust.method}{see \code{\link[stats]{p.adjust}}}

\item{p.adjust.mode}{see \code{\link{p.adjust.table}}}

\item{threads}{threads, default: 1.}

\item{verbose}{verbose, default: TRUE.}

}

\value{

a corr object with 3 elements:

\item{r}{default: spearman correlation}

\item{p.value}{default: p-value of spearman correlation}

\item{p.adjust}{default p.adjust.method = NULL}

}

\description{

Calculate correlation for one or two t(otutab), or distance for one t(otutab).

}

\examples{

data("otutab", package = "pcutils")

t(otutab) -> totu

c_net_calculate(totu) -> corr

metadata[, 3:10] -> env

c_net_calculate(totu, env) -> corr2

}

\seealso{

Other calculate: 

\code{\link{cal_sim}()},

\code{\link{fast_cor}()},

\code{\link{p.adjust.table}()},

\code{\link{read_corr}()}

}

\concept{calculate}