StatGraphTopic002 < CTSpedia

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Image	%LIGHTBOX{ image="HPAaxis.jpg" thumbnail="tn_HPAaxis.jpg" caption="HPA Axis Suppression" }% Click on image to enlarge.
Title	HPA Axis Suppression
Graph_Subgroup	General Principles
Code Added	Yes
Description	* Method of assessing immune system function * Serum cortisol levels below 18 mg/dL at 30 minutes post-stimulation are considered suppressed. * Expectation that younger children are more at risk of HPA axis suppression due to larger ratio of skin surface area to body mass.
Contributor/Email	Mat Soukup (email: Mat.Soukup@fda.hhs.gov)
Background	Rather than look at tabular information or rates of suppression, this shows each subjects' baseline and end of treatment cortisol level. Shift in the whole distribution suggests a trend towards suppression which would not be captured in a table.
Special Considerations
Date	Original
Original Date	2006
Modified Date
Use/Suitability	Publication
Software Program	R
Software	R version 2.10
R-Code - Attachment	HPA Axis code attached
R-Code	set.seed(147) id <- 1:160<br />hpab <- rnorm(160, 35, 4)<br />trt <- rep(rep(c('Low','High'), each=20),4)<br />cohort <- rep(c('6 mo. - 2 y.','2 y. - 6 y.',<br />'6 y. - 12 y.', '12 y. - 18 y.'), each=40) hpae <- c(rnorm(20, 27, 4), rnorm(20, 23, 4),<br />rnorm(20, 29, 4), rnorm(20, 25, 4), rnorm(20, 31, 4), rnorm(20, 27, 4), rnorm(20, 33, 4), rnorm(20, 29, 4)) #png('C:/Research/Graphics/Graphs4Display/webpages/classes/pages/images/HPAaxis.png', # width=700, height=700) new.line <- trellis.par.get('superpose.line')<br />new.line$col <- c('black','seagreen2')<br />new.line$lty <- c(1,1,1,1)<br />new.symbol <- trellis.par.get('superpose.symbol')<br />new.symbol$col <- c('black', 'seagreen2')<br />new.symbol$pch <- c(1, 4, 16, 8)<br />trellis.par.set('superpose.line', new.line) trellis.par.set('superpose.symbol', new.symbol) xyplot(hpae~hpab \| cohort, groups=trt, panel=function(x, y, ...){ panel.plsmo(x, y, ...) llines(c(-100,100),c(18,18), lty=2, col='grey60') panel.abline(v=18, lty=2, col='grey60') llines(c(-100,100),c(-100,100), lty=2, col='grey60') }, xlab='Screening Post-Stimulation', xlim=c(15, max(hpab)+2), ylab='End of Treatment Post Stimulation', index.cond=list(c(3,2,4,1)), label.curves=FALSE, strip=strip.custom(bg='grey80'), aspect=1, key=list(type='p', points=list(pch=trellis.par.get('superpose.symbol')$pch[1:2], col=trellis.par.get('superpose.symbol')$col[1:2]), text=list(c('High','Low'), col=trellis.par.get('superpose.symbol')$col[1:2]), columns=2, cex=1.25, title='Treatment')) ww <- which(hpae < 18)<br />ww trellis.focus('panel', 1, 1, highlight=FALSE) ltext(x=hpab[c(9,35,40)]-.5, y=hpae[c(9,35,40)], c('9','35','40'), col=c('seagreen2','black','black'), adj=c(1,1)) trellis.unfocus() trellis.focus('panel', 2, 2, highlight=FALSE) ltext(x=hpab[c(153)]-.5, y=hpae[c(153)], c('153'), col=c('black'), adj=c(1,1)) trellis.unfocus() trellis.focus('strip', 1, 1, highlight=FALSE) ltext(x=0.025, y=.5, 'N=20', col=c('black'), adj=c(0,NA), cex=.9) ltext(x=.975, y=.5, 'N=20', col=c('seagreen2'), adj=c(1,NA), cex=.9) trellis.unfocus() trellis.focus('strip', 1, 2, highlight=FALSE) ltext(x=0.025, y=.5, 'N=20', col=c('black'), adj=c(0,NA), cex=.9) ltext(x=.975, y=.5, 'N=20', col=c('seagreen2'), adj=c(1,NA), cex=.9) trellis.unfocus() trellis.focus('strip', 2, 1, highlight=FALSE) ltext(x=0.025, y=.5, 'N=20', col=c('black'), adj=c(0,NA), cex=.9) ltext(x=.975, y=.5, 'N=20', col=c('seagreen2'), adj=c(1,NA), cex=.9) trellis.unfocus() trellis.focus('strip', 2, 2, highlight=FALSE) ltext(x=0.025, y=.5, 'N=20', col=c('black'), adj=c(0,NA), cex=.9) ltext(x=.975, y=.5, 'N=20', col=c('seagreen2'), adj=c(1,NA), cex=.9) trellis.unfocus() #dev.off()
SAS-Code - Attachment
SAS-Code
Stata-Code - Attachment
Stata-Code
Other Code - Attachment
Other Code
Keywords	baseline, end of treatment
OPTIONAL FIELDS
References
Datasets
Data	Simulated dataset
Attached Data
CATEGORIZATIONS
Classification-Evaluation	Safety
Classification-Graph Type	Scatterplot
Graph_Type	Scatterplot
Variable Relationship	Continuous versus Continuous
Data Types	Continuous
Special Cases
Disclaimer	The views expressed within CTSpedia are those of the author and must not be taken to represent policy or guidance on the behalf of any organization or institution with which the author is affiliated.
Permission	Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT OLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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This topic: CTSpedia > WebHome > StatGraphHome > ContributeGraphics > StatGraphTopic002
Topic revision: 30 Mar 2012, MaryBanach

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