Note.md

In Junzheshao5959/ssmimputedemo: SSM Imputation DEMO(Title Case)

R package developement

Junzhe Shao 10/21/2021

Credit to John Muschelli

Where to start

check your name is available on CRAN, Bioconductor or GitHub

library(available)
available("ssmimputedemo")

Basic file Introduction in R package:

\~/man/xx.Rd …… R documentation \~/DESCRIPTION ……. sample description file: Package: ssmimputedemo Type: Package Title: SSM Imputation DEMO(Title Case) Version: 0.1.0 Author: Junzhe Shao Maintainer: The package maintainer [e-mail] Description: More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description. A demo for SSM Imputation License: GPL-3 Encoding: UTF-8 LazyData: true

Build -> install and restart

library(ssmimputedemo)

## Loading required package: tibble

?hello

Roxygen

Build -> Configure Build Tools -> Build Tools Configure Roxygen -> Check everything cran check : –as-cran to be more stable

roxygen file automatically create .Rd file any time we recompile the package

Code ->insert roxygen skeleton

#' @title 
#' @description 
#' My hello world function
#' @param x The name of person to say hi to
#'
#' @return The output from  \code{\link{print}}    
#' @export
#'
#' @examples
#' hello("Steve")
#' \dontrun{
#' hello("Steve")}

tab auto completion for @__, will create title and description exactly the same. can link you to outside, examples and function

Build -> clean and rebuild

ℹ Loading ssmimputedemo Warning: The existing ‘hello.Rd’ file was not generated by roxygen2, and will not be overwritten. Warning: The existing ‘NAMESPACE’ file was not generated by roxygen2, and will not be overwritten.

delete these files with default setup Build -> clean and rebuild

export(hello), let the users using hello

check package

creater a new printer funtion, you can add multiple files

R package usethis

library(usethis)
#automaticlly create a readme file
use_readme_rmd()
#push to github, set github remote repository
use_git(message = "")
use_github(protocol = "https")

really nice to add these RoxygenNote: 7.1.2 URL: https://github.com/Junzheshao5959/ssmimputedemo BugReports: https://github.com/Junzheshao5959/ssmimputedemo/issues

Importing and Exporting funcitons

using vignette https://r-pkgs.org/vignettes.html

use_vignette("SSM_vignette")

Suggests: knitr, rmarkdown VignetteBuilder: knitr importFrom(tibble,as_data_frame)

automatically add

use_package("tibble")

Depends: tibble

You can use check package to see if there is any function not imported.

Travis and Continuous Integration

Check changes from timeline

use_github_actions()
codecov()

https://app.travis-ci.com/github/Junzheshao5959/ssmimputedemo/builds

Unit Tests and Local Package Coverage

Let’s do some test

usethis::use_testthat()

## ✓ Setting active project to '/Users/junzheshao/Documents/ssmimputedemo'

## • Call `use_test()` to initialize a basic test file and open it for editing.

library(testthat)

create a file under \~/test/testthat, like this:

test_that("test test",{
  set.seed(123)
  res = printer(x = rnorm(5), r = rnorm(5))
  expect_that(nrow(res) ,equals(5) )
})

Addins: calculate packge coverage or you can

covr::package_coverage(type = 'all')

## ssmimputedemo Coverage: 100.00%

## R/hello.R: 100.00%

## R/printer.R: 100.00%

Add some data to our package

use_data_raw()

set.seed(123)

library(dplyr)
x = rnorm(100)
y = rnorm(100)
sample_data = tibble(x = x, y = y)

usethis::use_data(sample_data, compress = "xz")

You will have sampe_data.rda under the \~/data folder

library(ssmimputedemo)
head(sample_data)

## # A tibble: 6 × 2
##         x       y
##     <dbl>   <dbl>
## 1 -0.560  -0.710 
## 2 -0.230   0.257 
## 3  1.56   -0.247 
## 4  0.0705 -0.348 
## 5  0.129  -0.952 
## 6  1.72   -0.0450

?sample_data

you can also create a website by package down.

Junzheshao5959/ssmimputedemo documentation built on Aug. 27, 2022, 8:49 a.m.