Robert M Flight rmflight

This code block goes at the top of every Rmd file that I create for eventual conversion by knitr

# sets output for inline results nicely
knit_hooks$set(inline = identity) 

# kills knitr if there is an error, therefore we don't waste time generating error messages
knit_hooks$set(error = function(x, options) stop(x)) 

# these are extremely useful options for working in R

How to host a blog using github

http://mbmccormick.com/2011/10/ditching-wordpress-for-jekyll-and-github/

How to do figure captions in knitr / markdown

yihui/knitr#81

use \caption{} and \label{} in latex; use in HTML; use in markdown

From the options manual: eval.after: (NULL) a character vector of option names; these options will be evaluated after a chunk is evaluated, and all other options will be evaluated before a chunk (e.g. for chunk option fig.cap=paste('p-value is', t.test(x)$p.value), it will be evaluated after the chunk according to the value of x if eval.after='fig.cap')

	# Creating custom CDF for Affy chips in R / Bioconductor

	```{r knitrOpts, echo=FALSE}
	knit_hooks$set(inline = identity) # sets output for inline resutls nicely
	knit_hooks$set(error = function(x, options) stop(x)) # kills knitr if there
	# is an error, therefore we don't waste time generating error messages
	options(save.defaults=list(compress="xz"), stringsAsFactors=FALSE)
	# set up the default compression, and do NOT allow strings in data frames to become factors.
	# That one is really important, and continually messes me up.
	startTime <- Sys.time() # when did we start

	```{r showLink, results='asis'}
	var1 <- "672"
	var2 <- "12189"
	srchVar <- paste(var1, var2, collapse=",", sep=",")
	tmp1 <- paste('<a href="http://www.ncbi.nlm.nih.gov/gene?term=', srchVar, '">Results</a>', sep="")
	cat(tmp1)
	```

	If you want to display time elapsed nicely in an Rmd object generated by knitr, here is my suggesion:

	```{r diffT}
	t1 <- Sys.time()
	Sys.sleep(5)
	t2 <- Sys.time()
	tDiff <- difftime(t2, t1, units="hours")
	```

	This process took `r format(tDiff)`. Note that units above can be whatever unit you want, see ?difftime.

	options(rstudio.markdownToHTML =
	function(inputFile, outputFile) {
	require(markdown)
	htmlOptions <- markdownHTMLOptions(defaults=TRUE)
	htmlOptions <- htmlOptions[htmlOptions != "hard_wrap"]
	markdownToHTML(inputFile, outputFile, options = htmlOptions)
	}
	)

	pasteLabel <- function(preText, inObj, objName, insLink=TRUE){
	objNum <- inObj[objName]

	useText <- paste(preText, objNum, sep=" ")
	if (insLink){
	useText <- paste("[", useText, "](#", objName, ")", sep="")
	}
	useText
	}

	http://stackoverflow.com/questions/5328452/overlaid-histograms-in-r-ggplot2-preferred
	http://stackoverflow.com/questions/6939136/how-to-overlay-density-plots-in-r

	body {
	box-sizing: border-box;
	font-size: 16px;
	font-family: 'Myriad Pro', Calibri, Helvetica, Arial, sans-serif;
	line-height: 1.5;
	-webkit-font-smoothing: antialiased;
	width:800px;
	margin: auto;
	}

	@article{Lord1994,
	abstract = {Describes the Autism Diagnostic Interview-Revised (ADI-R), a revision of the Autism Diagnostic Interview, a semistructured, investigator-based interview for caregivers of children and adults for whom autism or pervasive developmental disorders is a possible diagnosis. The revised interview has been reorganized, shortened, modified to be appropriate for children with mental ages from about 18 months into adulthood and linked to ICD-10 and DSM-IV criteria. Psychometric data are presented for a sample of preschool children.},
	author = {Lord, C and Rutter, M and {Le Couteur}, A},
	issn = {0162-3257},
	journal = {Journal of autism and developmental disorders},
	keywords = {Algorithms,Autistic Disorder,Autistic Disorder: classification,Autistic Disorder: diagnosis,Autistic Disorder: psychology,Caregivers,Caregivers: psychology,Child,Female,Humans,Intellectual Disability,Intellectual Disability: classification,Intellectual Disability: diagnosis,Intellectual Disabi