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Topic revision: 30 Mar 2012, MaryBanach
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| Image | %LIGHTBOX{ image="efficacybysite.jpg" thumbnail="tn_efficacybysite.jpg" caption="Efficacy by Site"}% Click on image to enlarge.. |
| Title | Efficacy Across Sites |
| Graph_Subgroup | General Principles |
| Code Added | Yes |
| Description | Treatment Effects and the corresponding sample sizes are plotted for each site in a multi-center trial in addition to the overall treatment effect (horizontal lines). |
| Contributor/Email | Mat Soukup (email: Mat.Soukup@fda.hhs.gov) |
| Background | The endpoint is binary with higher proportions corresponding to increased efficacy. The data set is from a randomly generated data set located on the OB network drive. |
| Special Considerations | |
| Date | Original |
| Original Date | 2007 |
| Modified Date | |
| Use/Suitability | Exploration |
| Software Program | R |
| Software | |
| R-Code - Attachment | Efficacy by Site - Attached |
| R-Code | library(Hmisc) dat <- read.csv('C:/RGraphicsTutorial/Datasets/CleanTrial.csv')<br /> base <- subset(dat, visit%in%2)<br />eot <- subset(dat, visit%in%6)<br /> # binary endpoint is success if at least 2 grade improvement eot$binep <- ifelse(base$catvar-eot$catvar >= 2, 1, 0) # Also create a site id (25 total sites) set.seed(42) eot$site <- sample(1:25, 1500, replace=TRUE)<br /> ss <- with(eot, summarize(binep, llist(site, trtf), mean))<br /> n <- with(eot, summarize(binep, llist(site, trtf), length))<br /> sdat <- data.frame(ss, n[,3])<br /> names(sdat) <- c("Site", "Trt", "Mean", "N")<br /> so <- with(eot, summarize(binep, llist(trtf), mean))<br /> nsn <- length(unique(sdat$Site))<br /> ut <- unique(sdat$Trt)<br /> rnx <- tabulate(as.factor(sdat$Site))<br /> sdat$plotx <- rep(1:nsn, rnx[rnx>0]) # Creation of the figure. #png('C:/Research/Graphics/Graphs4Display/webpages/classes/pages/images/efficacybysite.png', # width=670, height=500) plot(c(.5, nsn+.5), c(min(sdat$Mean)-.05, max(sdat$Mean)+.05), type="n", ylab='Response Rate', xlab='', axes=FALSE) axis(1, at=1:nsn, labels=as.character(unique(sdat$Site)), cex.axis=1, las=3) axis(2) box() sdat$plotx <- sdat$plotx + rep(c(-.05,.05), length(sdat[,1])/2)<br /> coluers <- c('seagreen2','grey60')<br /> pchs <- c(1,16)<br /> for(k in 1:length(ut)){ subdat <- subset(sdat, sdat$Trt==ut[k])<br /> points(subdat$plotx, subdat$Mean, pch=pchs[k], col=coluers[k]) # Add overall means as horizontal lines abline(h=so[k,2], col=coluers[k], lty=3, lwd=2) for(j in 1:length(subdat$N)){ text(subdat$plotx[j]+.4, subdat$Mean[j], labels=subdat$N[j], col=coluers[k], cex=1) } } for(i in 1:nsn){ subdat <- subset(sdat, sdat$Site==unique(sdat$Site)[i])<br /> lines(c(i,i), c(min(subdat$Mean), max(subdat$Mean)), lty=2,col='gray60') } legend("topleft", legend=as.character(sort(unique(eot$trtf))), pch=pchs, col=coluers, cex=1.25, xjust=0) #dev.off() |
| SAS-Code - Attachment | |
| SAS-Code | |
| Stata-Code - Attachment | |
| Stata-Code | |
| Other Code - Attachment | |
| Other Code | |
| Keywords | treatment effects, multi-centered clinical trial, efficacy |
| OPTIONAL FIELDS | |
| References | |
| Datasets | |
| Data | |
| Attached Data | |
| CATEGORIZATIONS | |
| Classification-Evaluation | Efficacy |
| Classification-Graph Type | Scatterplot |
| Graph_Type | Scatterplot |
| Variable Relationship | Continuous versus Categorical |
| 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 |  |
Topic revision: 30 Mar 2012, MaryBanach
Copyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors. Ideas, requests, problems regarding Foswiki? Send feedback