1. Devtools and package building Phuse Non-clinical Scripts

2. Prerequisites install.packages("roxygen2")
install.packages("devtools")
install.packages("testthat")
Download and install Rtools 3.4 from

3. Devtools workflow for package:
library(devtools)
build()
install()
document()
test()
Will run the “testthat” test case files, from tests subdirect.
To get the pdf manual: check(cleanup = FALSE,manual = TRUE,path = getwd())

4. Rstudio New project – From Build pulldown
Create project from existing directory
From Build pulldown
Build and reload -> does compile,loading
Test -> runs the testthat scripts
Check -> does build, testthat and checks documentation

5. Rstudio

6. Rstudio – check of parsedate
Results:
Undocumented arguments in documentation object 'dur_to_seconds'
'input'
Documented arguments not in \usage in documentation object 'dur_to_seconds':
'date'
checking package dependencies ... NOTE
Package suggested but not available for checking: 'covr'

7. Rstudio – check of parsedate
Remedied:
Changed from:
date The date(s) to format. To
input The date(s) to format.
install.packages("covr")

8. Parsedate – tests directory
“testthat” test case files

9. Testthat test cases “Test” from Build pulldown:
==> devtools::test()
Loading parsedate
Loading required package: testthat
Testing parsedate
Dates and empty strings:
Git dates:
ISO 8601 moment.js:
ISO 8601 Pelago:
ISO 8601 Pelago non-matching:
ISO week dates: ...
DONE ===========================================================================
Warning message:
package 'testthat' was built under R version 3.2.5

10. Testthat test cases in parsedate
Testthat.r:
library(testthat)
library(parsedate)
test_check("parsedate")

11. Testthat test cases in parsedate

12. Testthat documentation
Context – name under which to group tests
test_that(name,code) – create a test
Expect_equal – checks if 2 values are the same
See documentation for other types of equality-expectations
Also see document for “mock” usage for complicated out-of-package function substitution

13. Testthat parsedate example
context("ISO week dates") test_that("Exotic ISO week dates are OK", { tests <- read.table(stringsAsFactors = FALSE, header = FALSE, strip.white = TRUE, row.names = NULL, sep = "|", textConnection(" 2009-W01-1 | T00:00:00+00: W53-7 | T00:00:00+00: W06-5 | T00:00:00+00:00" )) apply(tests, 1, function(x) { d <- format_iso_8601(parse_iso_8601(x[1])) expect_equal(d, unname(x[2])) })
Expected output
Input to parse function

14. Testthat parsedate - boundary checks (corner cases) also done
test_that("Non-sensical input is removed", { date <- "?=)(!$§#$%" expected <- as.POSIXct(NA) actual <- parse_date(date) expect_equal(expected, actual) })

15. Testthat added as a test
context("BJF examples") library(stringr) test_that("Example 1 BJF", { tests <- read.table(stringsAsFactors = FALSE, header = FALSE, strip.white = TRUE, row.names = NULL, sep = "|", textConnection(" T09:30: | T10:30:26+00: T09:30: | T09:30:26+00:00 " )) apply(tests, 1, function(x) { d <- format_iso_8601(parse_iso_8601(x[1])) expect_equal(d, unname(x[2]), info = x[1]) })

16. Testthat added as a test
test_that("Example for BJF", {
tests <- read.table(stringsAsFactors = FALSE, header = FALSE,
strip.white = TRUE, row.names = NULL, sep = "|",
textConnection("
The sky is blue | red
The sky is blue | blue
" ))
apply(tests, 1, function(x) {
d <- (word(x[1],-1))
expect_equal(d, unname(x[2]), info = x[1]) })

17. Testthat added as a test - output
==> devtools::test() Loading parsedate Loading required package: testthat Testing parsedate BJF examples.js: 1.2. Dates and empty strings: Git dates: ISO 8601 moment.js: ISO 8601 Pelago: ISO 8601 Pelago non-matching: ISO week dates: ... Failed Failure: Examples for BJF.js `d` not equal to unname(x[2]). 1/1 mismatches x[1]: " T09:30:26+00:00" y[1]: " T10:30:26+00:00" T09:30: Failure: Examples for BJF.js x[1]: "blue" y[1]: "red" The sky is blue

18. Testthat - describe
describe(function,code) – description of function and its test
(alternative function in test_that package)

19. Testthat – describe added as test
describe("parse_iso_8601()", { it ("can convert fractional hours and time zone offset",{ tests <- read.table(stringsAsFactors = FALSE, header = FALSE, strip.white = TRUE, row.names = NULL, sep = "|", textConnection(" T16: | T10:23:19+00:00 " )) apply(tests, 1, function(x) { d <- format_iso_8601(parse_iso_8601(x[1])) expect_equal(d, unname(x[2]), info = x[1]) })