rmflight/presentations.bib

## presentations.bib
@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 Disability: psychology,Interview,Male,Mothers,Mothers: psychology,Personality Assessment,Personality Assessment: statistics \& numerical data,Preschool,Psychological,Psychometrics,Reproducibility of Results},
				 month = oct,
				 number = {5},
				 pages = {659--85},
				 pmid = {7814313},
				 title = {{Autism Diagnostic Interview-Revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders.}},
				 url = {http://www.ncbi.nlm.nih.gov/pubmed/7814313},
				 volume = {24},
				 year = {1994}
}
@article{Lord1989,
				 abstract = {The Autism Diagnostic Observation Schedule (ADOS), a standardized protocol for observation of social and communicative behavior associated with autism, is described. The instrument consists of a series of structured and semistructured presses for interaction, accompanied by coding of specific target behaviors associated with particular tasks and by general ratings of the quality of behaviors. Interrater reliability for five raters exceeded weighted kappas of .55 for each item and each pair of raters for matched samples of 15 to 40 autistic and nonautistic, mildly mentally handicapped children (M IQ = 59) between the ages of 6 and 18 years. Test-retest reliability was adequate. Further analyses compared these groups to two additional samples of autistic and nonautistic subjects with normal intelligence (M IQ = 95), matched for sex and chronological age. Analyses yielded clear diagnostic differences in general ratings of social behavior, specific aspects of communication, and restricted or stereotypic behaviors and interests. Clinical guidelines for the diagnosis of autism in the draft version of ICD-10 were operationalized in terms of abnormalities on specific ADOS items. An algorithm based on these items was shown to have high reliability and discriminant validity.},
				 author = {Lord, C and Rutter, M and Goode, S and Heemsbergen, J and Jordan, H and Mawhood, L and Schopler, E},
				 issn = {0162-3257},
				 journal = {Journal of autism and developmental disorders},
				 keywords = {Adolescent,Adult,Algorithms,Autistic Disorder,Autistic Disorder: diagnosis,Child,Communication,Diagnosis,Differential,Female,Humans,Intellectual Disability,Intellectual Disability: diagnosis,Male,Psychiatric Status Rating Scales,Social Behavior},
				 month = jun,
				 number = {2},
				 pages = {185--212},
				 pmid = {2745388},
				 title = {{Autism diagnostic observation schedule: a standardized observation of communicative and social behavior.}},
				 url = {http://www.ncbi.nlm.nih.gov/pubmed/2745388},
				 volume = {19},
				 year = {1989}
}
@article{Schopler1980,
				 author = {Schopler, E and Reichler, R J and DeVellis, R F and Daly, K},
				 issn = {0162-3257},
				 journal = {Journal of autism and developmental disorders},
				 keywords = {Autistic Disorder,Autistic Disorder: classification,Autistic Disorder: diagnosis,Child,Female,Humans,Male,Preschool,Psychological Tests,Psychometrics,Referral and Consultation},
				 month = mar,
				 number = {1},
				 pages = {91--103},
				 pmid = {6927682},
				 title = {{Toward objective classification of childhood autism: Childhood Autism Rating Scale (CARS).}},
				 url = {http://www.ncbi.nlm.nih.gov/pubmed/6927682},
				 volume = {10},
				 year = {1980}
}
@article{Paul_Perception_2005,
				 author = {Paul, Rhea and Augustyn, Amy and Klin, Ami and Volkmar, Fred R.},
				 doi = {10.1007/s10803-004-1999-1},
				 file = {:C$\backslash$:/Users/jfsantos/Dropbox/Atypical Speech Processing/autism/review/papers/Paul05.pdf:pdf},
				 issn = {0162-3257},
				 journal = {Journal of Autism and Developmental Disorders},
				 month = apr,
				 number = {2},
				 pages = {205--220},
				 title = {{Perception and Production of Prosody by Speakers with Autism Spectrum Disorders}},
				 url = {http://www.springerlink.com/index/10.1007/s10803-004-1999-1},
				 volume = {35},
				 year = {2005}
}

## test.Rmd
# Blah blah blah

```{r,include=FALSE}
library(knitcitations)
bib <- read.bibtex('presentation.bib')
#cleanbib()
```
---

### Introduction

ASD is usually diagnosed by the age of 36 months, based on diagnostic instruments such as the ADOS `r citep(bib["Lord1989"])`,

```{r o1}
options()$works_cited
```

ADI-R `r citep(bib["Lord1994"])`

```{r o2}
options()$works_cited
```

and CARS `r citep(bib[c("Schopler1980", "Paul_Perception_2005")])`; however, symptoms may become apparent early at childhood `r citep(bib["Paul_Perception_2005"])`.


```{r lookOptions1}
options()$works_cited
```

### Plots

```{r,include=FALSE}
data(iris)
```


```{r lookOptions2}

```


### References

```{r results="asis", echo=FALSE}
bibliography()
```

```{r t1}
sessionInfo()
```

## test_knit2html.md

      
    Raw
  

              test_knit2html.md
            
          
    Blah blah blah


Introduction

ASD is usually diagnosed by the age of 36 months, based on diagnostic instruments such as the ADOS (Lord et. al. 1989),
options()$works_cited
## Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and
## Schopler E (1989). "Autism diagnostic observation schedule: a
## standardized observation of communicative and social behavior."
## _Journal of autism and developmental disorders_, *19*(2), pp.
## 185-212. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/2745388>.

ADI-R (Lord et. al. 1994)
options()$works_cited
## Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and
## Schopler E (1989). "Autism diagnostic observation schedule: a
## standardized observation of communicative and social behavior."
## _Journal of autism and developmental disorders_, *19*(2), pp.
## 185-212. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/2745388>.

and CARS (Schopler et. al. 1980; Paul et. al. 2005); however, symptoms may become apparent early at childhood (Paul et. al. 2005).
options()$works_cited
## Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and
## Schopler E (1989). "Autism diagnostic observation schedule: a
## standardized observation of communicative and social behavior."
## _Journal of autism and developmental disorders_, *19*(2), pp.
## 185-212. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/2745388>.

Plots

References

Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and Schopler E (1989).
“Autism diagnostic observation schedule: a standardized observation of communicative and social behavior.”
Journal of autism and developmental disorders, 19(2), pp. 185–212.
ISSN 0162-3257, http://www.ncbi.nlm.nih.gov/pubmed/2745388.
sessionInfo()
## R version 2.15.0 (2012-03-30)
## Platform: x86_64-pc-mingw32/x64 (64-bit)
## 
## locale:
## [1] LC_COLLATE=English_United States.1252 
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitcitations_0.1-0 bibtex_0.3-3        knitr_0.8          
## 
## loaded via a namespace (and not attached):
##  [1] codetools_0.2-8 digest_0.5.2    evaluate_0.4.2  formatR_0.6    
##  [5] pkgmaker_0.8.5  plyr_1.7.1      RCurl_1.91-1.1  stringr_0.6.1  
##  [9] tools_2.15.0    XML_3.9-4.1     xtable_1.7-0


## test_knitr.md

      
    Raw
  

              test_knitr.md
            
          
    Blah blah blah


Introduction

ASD is usually diagnosed by the age of 36 months, based on diagnostic instruments such as the ADOS (Lord et. al. 1989),
options()$works_cited
## Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and
## Schopler E (1989). "Autism diagnostic observation schedule: a
## standardized observation of communicative and social behavior."
## _Journal of autism and developmental disorders_, *19*(2), pp.
## 185-212. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/2745388>.

ADI-R (Lord et. al. 1994)
options()$works_cited
## Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and
## Schopler E (1989). "Autism diagnostic observation schedule: a
## standardized observation of communicative and social behavior."
## _Journal of autism and developmental disorders_, *19*(2), pp.
## 185-212. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/2745388>.
## 
## Lord C, Rutter M and Le Couteur A (1994). "Autism Diagnostic
## Interview-Revised: a revised version of a diagnostic interview for
## caregivers of individuals with possible pervasive developmental
## disorders." _Journal of autism and developmental disorders_,
## *24*(5), pp. 659-85. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/7814313>.

and CARS (Schopler et. al. 1980; Paul et. al. 2005); however, symptoms may become apparent early at childhood (Paul et. al. 2005).
options()$works_cited
## Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and
## Schopler E (1989). "Autism diagnostic observation schedule: a
## standardized observation of communicative and social behavior."
## _Journal of autism and developmental disorders_, *19*(2), pp.
## 185-212. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/2745388>.
## 
## Lord C, Rutter M and Le Couteur A (1994). "Autism Diagnostic
## Interview-Revised: a revised version of a diagnostic interview for
## caregivers of individuals with possible pervasive developmental
## disorders." _Journal of autism and developmental disorders_,
## *24*(5), pp. 659-85. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/7814313>.
## 
## Schopler E, Reichler RJ, DeVellis RF and Daly K (1980). "Toward
## objective classification of childhood autism: Childhood Autism
## Rating Scale (CARS)." _Journal of autism and developmental
## disorders_, *10*(1), pp. 91-103. ISSN 0162-3257, <URL:
## http://www.ncbi.nlm.nih.gov/pubmed/6927682>.
## 
## Paul R, Augustyn A, Klin A and Volkmar FR (2005). "Perception and
## Production of Prosody by Speakers with Autism Spectrum Disorders."
## _Journal of Autism and Developmental Disorders_, *35*(2), pp.
## 205-220. ISSN 0162-3257, <URL:
## http://dx.doi.org/10.1007/s10803-004-1999-1>, <URL:
## http://www.springerlink.com/index/10.1007/s10803-004-1999-1>.
## 
## Paul R, Augustyn A, Klin A and Volkmar FR (2005). "Perception and
## Production of Prosody by Speakers with Autism Spectrum Disorders."
## _Journal of Autism and Developmental Disorders_, *35*(2), pp.
## 205-220. ISSN 0162-3257, <URL:
## http://dx.doi.org/10.1007/s10803-004-1999-1>, <URL:
## http://www.springerlink.com/index/10.1007/s10803-004-1999-1>.

Plots

References

Lord C, Rutter M, Goode S, Heemsbergen J, Jordan H, Mawhood L and Schopler E (1989).
“Autism diagnostic observation schedule: a standardized observation of communicative and social behavior.”
Journal of autism and developmental disorders, 19(2), pp. 185–212.
ISSN 0162-3257, http://www.ncbi.nlm.nih.gov/pubmed/2745388.
Lord C, Rutter M and Le Couteur A (1994).
“Autism Diagnostic Interview-Revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders.”
Journal of autism and developmental disorders, 24(5), pp. 659–85.
ISSN 0162-3257, http://www.ncbi.nlm.nih.gov/pubmed/7814313.
Schopler E, Reichler RJ, DeVellis RF and Daly K (1980).
“Toward objective classification of childhood autism: Childhood Autism Rating Scale (CARS).”
Journal of autism and developmental disorders, 10(1), pp. 91–103.
ISSN 0162-3257, http://www.ncbi.nlm.nih.gov/pubmed/6927682.
Paul R, Augustyn A, Klin A and Volkmar FR (2005).
“Perception and Production of Prosody by Speakers with Autism Spectrum Disorders.”
Journal of Autism and Developmental Disorders, 35(2), pp. 205–220.
ISSN 0162-3257, http://dx.doi.org/10.1007/s10803-004-1999-1, http://www.springerlink.com/index/10.1007/s10803-004-1999-1.
sessionInfo()
## R version 2.15.0 (2012-03-30)
## Platform: x86_64-pc-mingw32/x64 (64-bit)
## 
## locale:
## [1] LC_COLLATE=English_United States.1252 
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitcitations_0.1-0 bibtex_0.3-3        knitr_0.8          
## 
## loaded via a namespace (and not attached):
##  [1] codetools_0.2-8 digest_0.5.2    evaluate_0.4.2  formatR_0.6    
##  [5] pkgmaker_0.8.5  plyr_1.7.1      RCurl_1.91-1.1  stringr_0.6.1  
##  [9] tools_2.15.0    XML_3.9-4.1     xtable_1.7-0
	@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 Disability: psychology,Interview,Male,Mothers,Mothers: psychology,Personality Assessment,Personality Assessment: statistics \& numerical data,Preschool,Psychological,Psychometrics,Reproducibility of Results},
	month = oct,
	number = {5},
	pages = {659--85},
	pmid = {7814313},
	title = {{Autism Diagnostic Interview-Revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders.}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7814313},
	volume = {24},
	year = {1994}
	}
	@article{Lord1989,
	abstract = {The Autism Diagnostic Observation Schedule (ADOS), a standardized protocol for observation of social and communicative behavior associated with autism, is described. The instrument consists of a series of structured and semistructured presses for interaction, accompanied by coding of specific target behaviors associated with particular tasks and by general ratings of the quality of behaviors. Interrater reliability for five raters exceeded weighted kappas of .55 for each item and each pair of raters for matched samples of 15 to 40 autistic and nonautistic, mildly mentally handicapped children (M IQ = 59) between the ages of 6 and 18 years. Test-retest reliability was adequate. Further analyses compared these groups to two additional samples of autistic and nonautistic subjects with normal intelligence (M IQ = 95), matched for sex and chronological age. Analyses yielded clear diagnostic differences in general ratings of social behavior, specific aspects of communication, and restricted or stereotypic behaviors and interests. Clinical guidelines for the diagnosis of autism in the draft version of ICD-10 were operationalized in terms of abnormalities on specific ADOS items. An algorithm based on these items was shown to have high reliability and discriminant validity.},
	author = {Lord, C and Rutter, M and Goode, S and Heemsbergen, J and Jordan, H and Mawhood, L and Schopler, E},
	issn = {0162-3257},
	journal = {Journal of autism and developmental disorders},
	keywords = {Adolescent,Adult,Algorithms,Autistic Disorder,Autistic Disorder: diagnosis,Child,Communication,Diagnosis,Differential,Female,Humans,Intellectual Disability,Intellectual Disability: diagnosis,Male,Psychiatric Status Rating Scales,Social Behavior},
	month = jun,
	number = {2},
	pages = {185--212},
	pmid = {2745388},
	title = {{Autism diagnostic observation schedule: a standardized observation of communicative and social behavior.}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/2745388},
	volume = {19},
	year = {1989}
	}
	@article{Schopler1980,
	author = {Schopler, E and Reichler, R J and DeVellis, R F and Daly, K},
	issn = {0162-3257},
	journal = {Journal of autism and developmental disorders},
	keywords = {Autistic Disorder,Autistic Disorder: classification,Autistic Disorder: diagnosis,Child,Female,Humans,Male,Preschool,Psychological Tests,Psychometrics,Referral and Consultation},
	month = mar,
	number = {1},
	pages = {91--103},
	pmid = {6927682},
	title = {{Toward objective classification of childhood autism: Childhood Autism Rating Scale (CARS).}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/6927682},
	volume = {10},
	year = {1980}
	}
	@article{Paul_Perception_2005,
	author = {Paul, Rhea and Augustyn, Amy and Klin, Ami and Volkmar, Fred R.},
	doi = {10.1007/s10803-004-1999-1},
	file = {:C$\backslash$:/Users/jfsantos/Dropbox/Atypical Speech Processing/autism/review/papers/Paul05.pdf:pdf},
	issn = {0162-3257},
	journal = {Journal of Autism and Developmental Disorders},
	month = apr,
	number = {2},
	pages = {205--220},
	title = {{Perception and Production of Prosody by Speakers with Autism Spectrum Disorders}},
	url = {http://www.springerlink.com/index/10.1007/s10803-004-1999-1},
	volume = {35},
	year = {2005}
	}
	# Blah blah blah

	```{r,include=FALSE}
	library(knitcitations)
	bib <- read.bibtex('presentation.bib')
	#cleanbib()
	```
	---

	### Introduction

	ASD is usually diagnosed by the age of 36 months, based on diagnostic instruments such as the ADOS `r citep(bib["Lord1989"])`,

	```{r o1}
	options()$works_cited
	```

	ADI-R `r citep(bib["Lord1994"])`

	```{r o2}
	options()$works_cited
	```

	and CARS `r citep(bib[c("Schopler1980", "Paul_Perception_2005")])`; however, symptoms may become apparent early at childhood `r citep(bib["Paul_Perception_2005"])`.


	```{r lookOptions1}
	options()$works_cited
	```

	### Plots

	```{r,include=FALSE}
	data(iris)
	```




	```{r lookOptions2}

	```


	### References

	```{r results="asis", echo=FALSE}
	bibliography()
	```

	```{r t1}
	sessionInfo()
	```