vignettes/practical3.R

In jr-packages/jrAdvPackage: Course Material for Advanced R / Building an R Package Combo

## ----echo=FALSE----------------------------
library(tufte)
#knitr::opts_chunk$set(results = "hide", echo = FALSE)

## ----setup, include=FALSE, cache=FALSE----------
library(knitr)
options(replace.assign=FALSE,width=50)

opts_chunk$set(fig.path='knitr_figure/graphics-',
               cache.path='knitr_cache/graphics-',
               fig.align='center',
               dev='pdf', fig.width=5, fig.height=5,
               fig.show='hold', cache=FALSE, par=TRUE)
knit_hooks$set(crop=hook_pdfcrop)

knit_hooks$set(par = function(before, options, envir) {
    if (before && options$fig.show!='none') {
        par(mar=c(3,3,2,1),cex.lab=.95,cex.axis=.9,
            mgp=c(2,.7,0),tcl=-.01, las=1)
}}, crop=hook_pdfcrop)

## ---- fig.margin = TRUE, out.width="\\textwidth", echo = FALSE----
knitr::include_graphics("logo.png")

## ----eval=FALSE---------------------------------
#  library("pkg")
#  hello()

## ----eval=FALSE---------------------------------
#  help("hello")

## -----------------------------------------------
#' @export
#' @details
#' @aliases

## ----message=FALSE------------------------------
library("devtools")
library("roxygen2")

## ----eval=FALSE---------------------------------
#  install.packages(c("devtools", "roxygen2"))

## ----eval=FALSE---------------------------------
#  library("roxygen2")
#  roxygenise(".")

## -----------------------------------------------
#' @export

## -----------------------------------------------
#' @export
hello <- function() {
  print("Hello, world!")
}

## ----message=FALSE, eval=FALSE------------------
#  library("pkg")

## ----eval=FALSE---------------------------------
#  hello()

## ----eval=FALSE---------------------------------
#  # Generated by roxygen2: do not edit by hand
#  export(hello)

## -----------------------------------------------
#' @export
add = function(x, y) {
  return(x + y)
}

## ----message=FALSE, eval=FALSE------------------
#  library("pkg")
#  add(1, 2)

## -----------------------------------------------
check_numeric = function(x) all(is.numeric(x))

## -----------------------------------------------
add = function(x, y) {
  if(!check_numeric(c(x, y))) stop("Not numeric")
  x + y
}

## ----results="hide", eval=FALSE-----------------
#  library("pkg")
#  check_numeric(1)

## ----eval=FALSE---------------------------------
#  pkg:::check_numeric(1)

## ----eval=FALSE---------------------------------
#  pkg::add(1, 1)

## ----eval=FALSE---------------------------------
#  #' @title A function for adding
#  #'
#  #' @description A really good adding function.
#  #' Perhaps the best function ever!
#  #'
#  #' A work of pure genius.
#  #' @param x a number
#  #' @param y another number
#  #' @return a number
#  #' @export
#  #' @examples
#  #' add(5, 10)
#  #' ## Can also use negative numbers
#  #' add(-5, 10)
#  add = function(x, y) {
#    if(!check_numeric(c(x, y))) stop("Not numeric")
#    x + y
#  }

## ----results="hide", eval=FALSE-----------------
#  example(add)

## ----eval=FALSE---------------------------------
#  times = function(x, y) multiply(x, y)

## -----------------------------------------------
#' @rdname multiply

## ----eval=FALSE, tidy=FALSE---------------------
#  install.packages("drat")

## ----eval=FALSE, tidy=FALSE---------------------
#  drat::addRepo("jr-packages")

## ----eval=FALSE, tidy=FALSE---------------------
#  install.packages("jrAdvPackage")

## -----------------------------------------------
library("jrAdvPackage")
div(10, 2)

## -----------------------------------------------
#' @importFrom jrAdvPackage div

## -----------------------------------------------
#' add("A", "B")

## ----eval=FALSE, tidy=FALSE---------------------
#  ## Entry in data_help_files.R
#  ## Name is name of the data set.
#  #' @name moby
#  #' @aliases moby_sample
#  #' @title Moby Dick word count
#  #' @description The frequency of occurrence of unique words
#  #' in the novel Moby Dick by Herman Melville.
#  #'
#  #' The data set moby_sample is 2000 values sampled from the
#  #' moby data set.
#  #' @docType data
#  #' @format A vector
#  #' @source M. E. J. Newman, "Power laws, Pareto distributions
#  #' and Zipf's law." Contemporary Physics 46, 323 (2005).
#  NULL

## -----------------------------------------------
example_data = data.frame(x = runif(10), y = runif(10))

## ----eval=FALSE---------------------------------
#  save(example_data, file="data/example_data.RData")

## ----eval=FALSE---------------------------------
#  vignette(package="knitr")

## ----eval=FALSE---------------------------------
#  browseVignettes(package="knitr")

## ----eval=FALSE---------------------------------
#  ---
#  title: "My very first vignette"
#  author: "Colin Gillespie and Robin Lovelace"
#  output: rmarkdown::html_vignette
#  vignette: >
#    %\VignetteIndexEntry{My very first vignette}
#    %\VignetteEngine{knitr::rmarkdown}
#    %\VignetteEncoding{UTF-8}
#  ---
#  
#  ## My first package
#  
#  This is my **first** package vignette.
#  I can include mathematics, such as $x^2$.
#  R code is also nicely formatted and displayed.
#  

## -----------------------------------------------
x = runif(10)
x

## -----------------------------------------------
plot(x)

## ----eval=FALSE, tidy=FALSE---------------------
#  install.packages("pkg_1.0.tar.gz", repos=NULL,
#                   type="source")

## ----eval=FALSE, tidy=FALSE---------------------
#  library("pkg")
#  ?pkg