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

rmflight

# 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

rmflight

```{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)
```

rmflight

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.

rmflight

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

rmflight

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')

rmflight

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

rmflight

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

rmflight

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;
}

rmflight

@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