Merge commit '264376435b8aac47b808a287d13250523df65e9a'

_R-debugging/Makefile

@@ -1,9 +1,23 @@
-vectorisation.pdf: debugging.Rnw
+all:
+	make debugging.pdf
+	make unittesting.md
+	make testing.md
+
+debugging.pdf: debugging.Rnw
 	R --vanilla -e "library(knitr); knit('debugging.Rnw')"
 	pdflatex debugging.tex
 
 unittesting.md: unittesting.Rmd
-		R --vanilla -e "library(knitr); knit2html('unittesting.Rmd')"
+		R --vanilla -e "library(knitr); knit('unittesting.Rmd')"
+
+unittesting.html: unittesting.md
+		R --vanilla -e "markdown::markdownToHTML('unittesting.md', output = 'unittesting.html')"
+
+testing.md: testing.Rmd
+		R --vanilla -e "library(knitr); knit('testing.Rmd')"
+
+testing.html: testing.md
+		R --vanilla -e "markdown::markdownToHTML('testing.md', output = 'testing.html')"
 
 .PHONY: clean
 

_R-debugging/debugging.Rnw

@@ -60,14 +60,15 @@
 
 \author[Stojnic and Gatto]
 {
-  Robert~Stojnic <\url{[email protected]}> \\
-  Laurent~Gatto <\url{[email protected]}> \\
+  Robert~Stojnic \url{[email protected]} \\
+  Laurent~Gatto \url{[email protected]} \\
 }
 
 \institute[CSBC]
 {
 %   \inst{1}%
   University of Cambridge \\
+  \url{DataProgrammers.net}
 }
 
 \begin{document}

_R-debugging/testing.Rmd

@@ -0,0 +1,96 @@
+# Why test?
+
+* Nobody writes buggy code... sure!
+
+* How do you know your code is right unless you test?
+
+* Can act as specification/examples of what the programme should do.
+
+# Inverting some data can have serious consequences ...
+
+http://www.sciencemag.org/content/314/5807/1856.full.pdf
+
+2001 Science paper, and two more Science papers retracted after
+inversion along x axis noted.
+
+# Testing needs to be:
+
+* reliable
+* fast
+* easy to run
+* easy to summarise
+
+# stop() vs warning()
+
+* A warning is softer than an error; if a warning is generated
+your program will still continue, whereas an error will stop the
+program.
+
+```{r eval=FALSE,tidy=FALSE}
+log(c(2, 1, 0, -1, 2)); print('end')  # warning 
+xor( c(TRUE, FALSE));  print ('end')  # error
+```
+
+* If you try to isolate warnings, you can change warnings to
+  errors: `options(warn=2)`
+
+* Add warnings and errors to your code using `warning()`,
+  `stop()`
+
+```{r eval=TRUE}
+x <- -1:1
+y <- -5:-1
+
+if ( any(x<0) ) warning("some elements of x are negative")
+
+if ( all(y<0) ) stop("all elements of x are negative")
+
+stopifnot(all.equal(pi, 3.1415927), 2 < 2, all(1:10 < 12), "a" < "b")
+```
+
+# Catching errors and warnings
+
+```{r eval=FALSE}
+safelog <- function(x) {
+  tryCatch(log(x),
+           error = function(e) "an error",
+           warning = function(e) "a warning")
+}
+
+safelog(3)
+safelog(-5)
+safelog("string")
+```
+
+# Floating point issues to be aware of
+
+R FAQ 7.31? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f
+
+
+```{r}
+a <- sqrt(2)
+a * a == 2
+a * a - 2
+```
+
+```{r,eval=FALSE}
+1.0 + 2.0 == 3.0
+0.1 + 0.2 == 0.3
+```
+
+# Floating point: how to compare
+
+```{r}
+all.equal( 0.1 + 0.2, 0.3)
+all.equal( 0.1 + 0.2, 3.0)
+isTRUE(all.equal(0.1 + 0.2, 3))           # when you just want TRUE/FALSE
+```
+
+# Compile this document.
+
+```{r eval=FALSE, compiling}
+library("knitr")
+knit('testing.Rmd')
+knit2html('testing.Rmd')
+browseURL('testing.html')
+```

_R-debugging/testing.md

@@ -0,0 +1,148 @@
+# Why test?
+
+* Nobody writes buggy code... sure!
+
+* How do you know your code is right unless you test?
+
+* Can act as specification/examples of what the programme should do.
+
+# Inverting some data can have serious consequences ...
+
+http://www.sciencemag.org/content/314/5807/1856.full.pdf
+
+2001 Science paper, and two more Science papers retracted after
+inversion along x axis noted.
+
+# Testing needs to be:
+
+* reliable
+* fast
+* easy to run
+* easy to summarise
+
+# stop() vs warning()
+
+* A warning is softer than an error; if a warning is generated
+your program will still continue, whereas an error will stop the
+program.
+
+
+```r
+log(c(2, 1, 0, -1, 2)); print('end')  # warning 
+xor( c(TRUE, FALSE));  print ('end')  # error
+```
+
+* If you try to isolate warnings, you can change warnings to
+  errors: `options(warn=2)`
+
+* Add warnings and errors to your code using `warning()`,
+  `stop()`
+
+
+```r
+x <- -1:1
+y <- -5:-1
+
+if ( any(x<0) ) warning("some elements of x are negative")
+```
+
+```
+## Warning: some elements of x are negative
+```
+
+```r
+if ( all(y<0) ) stop("all elements of x are negative")
+```
+
+```
+## Error in eval(expr, envir, enclos): all elements of x are negative
+```
+
+```r
+stopifnot(all.equal(pi, 3.1415927), 2 < 2, all(1:10 < 12), "a" < "b")
+```
+
+```
+## Error: 2 < 2 is not TRUE
+```
+
+# Catching errors and warnings
+
+
+```r
+safelog <- function(x) {
+  tryCatch(log(x),
+           error = function(e) "an error",
+           warning = function(e) "a warning")
+}
+
+safelog(3)
+safelog(-5)
+safelog("string")
+```
+
+# Floating point issues to be aware of
+
+R FAQ 7.31? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f
+
+
+
+```r
+a <- sqrt(2)
+a * a == 2
+```
+
+```
+## [1] FALSE
+```
+
+```r
+a * a - 2
+```
+
+```
+## [1] 4.440892e-16
+```
+
+
+```r
+1.0 + 2.0 == 3.0
+0.1 + 0.2 == 0.3
+```
+
+# Floating point: how to compare
+
+
+```r
+all.equal( 0.1 + 0.2, 0.3)
+```
+
+```
+## [1] TRUE
+```
+
+```r
+all.equal( 0.1 + 0.2, 3.0)
+```
+
+```
+## [1] "Mean relative difference: 9"
+```
+
+```r
+isTRUE(all.equal(0.1 + 0.2, 3))           # when you just want TRUE/FALSE
+```
+
+```
+## [1] FALSE
+```
+
+# Compile this document.
+
+
+```r
+library("knitr")
+knit('testing.Rmd')
+knit2html('testing.Rmd')
+browseURL('testing.html')
+```