reconcile_categories {phyloseq} | R Documentation

## Cleans absent levels in sample_data/data.frame.

### Description

This is used internally by the builder method, `sample_data`, to ensure that the factors describing categorical variables in a data.frame or sample_data object are free of extra levels that can plague downstream plots analysis.

### Usage

    reconcile_categories(DFSM)

### Arguments

`DFSM` | (Required). A `data.frame` or `sample_data` object that needs to be cleaned.

### Value

A single `data.frame` object. Even if the input argument is a `sample_data`, the return is a `data.frame`. Because this is intended to be used internally by the builder method, it cannot also call the builder function to re-build the cleaned `sample_data`.

### Examples

    # # # data(GlobalPatterns)
    # # # SM <- sample_data(GlobalPatterns)
    # # # DF <- data.frame(SM)
    # # # DF <- data.frame(DF, col1=1:nrow(DF), col2=paste(1:nrow(DF), "t", sep=""))
    # # # DF <- reconcile_categories(DF)
    # # # SM <- sample_data(reconcile_categories(SM))
    # # # sapply(DF, class)
    # # # sapply(SM, class)

[Package phyloseq version 1.26.1 Index]