generateReport: Generates report

In microbiomeExplorer: Microbiome Exploration App

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.

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.