get_alphaindex {MicrobiotaProcess} | R Documentation

## alpha index

### Description

calculate the alpha index (Obseve,Chao1,Shannon,Simpson) of sample with `diversity`

### Usage

    get_alphaindex(obj, ...)

    ## S4 method for signature 'matrix'
    get_alphaindex(obj, mindepth, sampleda, force = FALSE, ...)

    ## S4 method for signature 'data.frame'
    get_alphaindex(obj, ...)

    ## S4 method for signature 'integer'
    get_alphaindex(obj, ...)

    ## S4 method for signature 'numeric'
    get_alphaindex(obj, ...)

    ## S4 method for signature 'phyloseq'
    get_alphaindex(obj, ...)

### Arguments

`obj` | object, data.frame of (nrow sample * ncol taxonomy(feature)) or phyloseq.
`...` | additional arguments.
`mindepth` | numeric, Subsample size for rarefying community.
`sampleda` | data.frame,sample information, row sample * column factors.
`force` | logical whether calculate the alpha index even the count of otu is not rarefied, default is FALSE. If it is TRUE, meaning the rarefaction is not be performed automatically.

### Value

data.frame contained alpha Index.

### Author(s)

Shuangbin Xu

### Examples

    ## Not run:
    otudafile <- system.file("extdata", "otu_tax_table.txt",
                            package="MicrobiotaProcess")
    otuda <- read.table(otudafile, sep="\t",
                 header=TRUE, row.names=1,
                 check.names=FALSE, skip=1, comment.char="")
    otuda <- otuda[sapply(otuda, is.numeric)] %>% t() %>%
              data.frame(check.names=FALSE)
    set.seed(1024)
    alphatab <- get_alphaindex(otuda)
    head(as.data.frame(alphatab))
    data(test_otu_data)
    class(test_otu_data)
    set.seed(1024)
    alphatab2 <- get_alphaindex(test_otu_data)
    head(as.data.frame(alphatab2))

    ## End(Not run)

[Package MicrobiotaProcess version 1.4.4 Index]