Tags:
create new tag
, view all tags, tagging instructions
Return to Statistical Graphics Home

Please rate the graphic:

  • 5 stars = highest rating
  • 1 star = lowest rating
  • SCORE = average of all votes

Graph Rating
Score: 0, My vote: 0, Total votes: 0

Please add comments and then click on the "Add comment" button.

 

OriginalStatGraphicsForm edit

Image
Lancet Data Graphic
Click to enlarge data.
Title Efficacy of T4N5 The Lancet Data - Code Expands
Graph_Subgroup General Principles
Code Added Yes
Description The cumulative number of AK and BCC lesions for each subject. The y-axis is truncated which hides the fact that Subj. 19 had 193 lesions (detected in alternate views of the data set).
Contributor/Email Mat Soukup (email: Mat.Soukup@fda.hhs.gov)
Background * Data is publicly available on journal website (reference below).
* XP is life-threatening disease occurring in approximately 1 out of 250,000 people in the US. Average age of developing skin cancer is 8 years.
* Study objective is to see if T4N5 reduces number of AK and BCC lesions.
* Study enrolled 30 subjects, 20 randomized to T4N5.
Special Considerations

Date Original
Original Date 2007
Modified Date

Use/Suitability Presentation
Software Program R
Software

R-Code - Attachment Lancet Data - Attached
R-Code More...Close

lan <- read.csv("//cdsnas/oebdbdms/Graphics/DataSets/lancetdata.txt")

c1 <- with(lan, visit1)
c2 <- with(lan, visit1+visit2)
c3 <- with(lan, visit1+visit2+visit3)
c4 <- with(lan, visit1+visit2+visit3+visit4)
c5 <- with(lan, visit1+visit2+visit3+visit4+visit5)
c6 <- with(lan, visit1+visit2+visit3+visit4+visit5+visit6)

csum <- c(lan$base,c1,c2,c3,c4,c5,c6)
ID2 <- paste("subj. ", rep(lan$id, 7),sep="")
age2 <- with(lan, rep(age, 7))
ctry2 <- with(lan, rep(country,7))
trt2 <- with(lan, rep(trt, 7))
month2 <- rep(c(0,3,6,9,12,13,18), each=29)

#BCC data
bat <- read.csv("//cdsnas/oebdbdms/Graphics/DataSets/lancetBCC.txt")

b1 <- with(bat, visit1)
b2 <- with(bat, visit1+visit2)
b3 <- with(bat, visit1+visit2+visit3)
b4 <- with(bat, visit1+visit2+visit3+visit4)
b5 <- with(bat, visit1+visit2+visit3+visit4+visit5)
b6 <- with(bat, visit1+visit2+visit3+visit4+visit5+visit6)

bcc <- c(bat$base,b1,b2,b3,b4,b5,b6)
idb <- paste("subj. ", rep(bat$id, 7), sep="")
trtb <- with(bat, rep(trt, 7))
monthb <- rep(c(0,3,6,9,12,13,18), each=29)

# Combine BCC and AK
lesions <- c(csum, bcc)
trts <- factor(paste(c(rep('AK',203),rep('BCC',203)), c(trt2, trtb), sep="-"),
levels=c('AK-1','AK-2','BCC-1','BCC-2'),
labels=c('Placebo-AK','T4N5-AK','Placebo-BCC',
'T4N5-BCC'))
lesi <- factor(c(rep('AK',203), rep('BCC',203)), labels=c('AK','BCC'))
trti <- factor(c(trt2,trtb), levels=1:2, labels=c('Placebo','T4N5'))

ids <- c(ID2, idb)
amonth <- c(month2, monthb)

aat <- data.frame(id=ids,trt=trts, month=amonth, lesions, trti, lesi)

#png('C:/Research/Graphics/Graphs4Display/webpages/classes/pages/images/lancetdata.png',
# width=700, height=700)

new.back <- trellis.par.get("background")
new.back$col <- "white"
newcol <- trellis.par.get("superpose.symbol")
newcol$col <- c('green4','blue','red','black')
newcol$pch <- c(16,1,4,8)
newline <- trellis.par.get("superpose.line")
newline$col <- c('green4','blue','red','black')
trellis.par.set("background", new.back)
trellis.par.set("superpose.symbol", newcol)
trellis.par.set("superpose.line", newline)
strip <- trellis.par.get("strip.background")
strip$col <- 'gray91'
trellis.par.set("strip.background",strip)

xyplot(lesions~month|id, groups=trt, data=aat, type='s',
xlab='Month',
ylab='Sum of New Lesions',
ylim=c(-5,100),
scales=list(x=list(at=c(0,3,6,9,12,18),
labels=as.character(c(0,3,6,9,12,18)))),
col=c('navy','hotpink4','deepskyblue2','red'),
lty=c(1,1,1,1),
key=list(lines=list(type='l', lty=c(1,1,1,1),
col=c('navy','hotpink4','deepskyblue2','red')),
text=list(lab=c('Placebo-AK','T4N5-AK',
'Placebo-BCC','T4N5-BCC'),
col=c('navy','hotpink4','deepskyblue2','red')),
columns=2, title='Treatment-Lesion'))
#dev.off()

SAS-Code - Attachment

SAS-Code

Stata-Code - Attachment

Stata-Code

Other Code - Attachment

Other Code

Keywords efficacy, orphan indication, XP, Poisson regression
OPTIONAL FIELDS

References Yarosh D, Klein J, O’Connor A, Alas L, et al. Effect of topically applied T4 endonuclease V in liposomes on skin cancer in xero-derma pigmentosum: A randomized study. The Lancet, Vol. 357, Issue 9260, March 2001, pages 926-929.


Datasets

Data

Attached Data

CATEGORIZATIONS

Classification-Evaluation Efficacy
Classification-Graph Type Scatterplot
Graph_Type Scatterplot
Variable Relationship Continuous versus Categorical Conditioned
Data Types Categorical and 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.
Reference Image LancetEfficacy_reference_200.jpg
Topic revision: r13 - 30 Mar 2012 - 13:44:04 - MaryBanach
 

Copyright &© by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding CTSPedia? Send feedback