generateReport {microbiomeExplorer} | R Documentation

## Generates report

### Description

This function generates the pieces of the report, which includes the R script, Rmarkdown file, and any Rmarkdown outputs.

### Usage

    generateReport(
      rcode,
      filename = "report",
      dir = "out",
      title = "MicrobiomeExplorer Report",
      author = "",
      date = "`r format(Sys.time(), '%d %B, %Y')`",
      data.source = "",
      output = c("html_document"),
      toc = TRUE,
      intro_text = NULL
    )

### Arguments

`rcode` | A named list where each element corresponds to a different analysis (Alpha diversity, Beta diversity). The name of the list is used to denote the first part of the code chunks in each analysis section (alpha, beta). Each element is itself a list of R commands corresponding to a code chunk.
`filename` | Name of output files. Default is "report".
`dir` | Directory of output. Default is "out".
`title` | Title of the report.
`author` | Author of the report.
`date` | Date of the report.
`data.source` | R code used to obtain the dataset
`output` | Output of Rmarkdown file. Options defined in global.R
`toc` | Table of contents. Default is TRUE.
`intro_text` | Introductory text to include with the report (optional)

### Details

Adapted from https://yihui.name/knitr/demo/stitch/

### Value

A character vector where each element is a line in the R script.

[Package microbiomeExplorer version 1.4.0 Index]