## 2007-07-12

Categories: Blog post Tags: Diagnostic testing

I have made some minor changes to my likelihood ratio slide. The original code was lost somewhere, so I wrote some new code and added documentation. I also changed the orientation of the slide rule so it can be held horizontally and shaded the regions that need to be cut out or away. This program runs in R. I've inserted images of the new slide rule on my tutorial page

The new version of the slide rule in PDF format has been placed on the web (SlideRule.pdf), and I am keepting the old version as well (SlideRuleOldVersion.pdf).

Here is the code.

##################### # special functions # ##################### hline <- function(x1,x2,y0) {segments(x1,y0,x2,y0)} vline <- function(x0,y1,y2) {segments(x0,y1,x0,y2)} rectangle <- function(x1,y1,x2,y2) {  x0 <- c(x1,x1,x2,x2)  y0 <- c(y1,y2,y2,y1)  polygon(x=x0,y=y0,density=-1,border=NA,col="gray90") } triangle <- function(x1,y1,x2,y2,x3,y3) {  x0 <- c(x1,x2,x3)  y0 <- c(y1,y2,y3)  polygon(x=x0,y=y0,density=-1,border=NA,col="gray90") }

##################################### # location of tick marks and labels # ##################################### # where to draw probability tick marks pr1 <- c(  0.1,0.2,0.3,0.4,  0.5,0.6,0.7,0.8,0.9,  1,1.5,2,2.5,3,4,  5,6,7,8,9,  10,15,20,25,30,40,  50,60,70,75,80,85,  90,91,92,93,94,  95,96,97,98,99) # where to print probability labels pr2 <- c(  0.1,0.2,0.3,  0.5,0.7,  1,2,3,  5,7,  10,20,30,40,  50,60,70,80,  90,93,  95,97,98,99) # physical location of probability ticks and labels pr3 <- 60+15*log(pr1/(100-pr1))/log(10) pr4 <- 60+15*log(pr2/(100-pr2))/log(10) n1 <- sort(c(1:9,1.5,2.5)) n2 <- c(1:3,5,7) # where to draw likelihood ratio tick marks pr5 <- c(n1/100,n1/10,n1,n1*10,100) # where to print likelihood ratio labels pr6 <- c(n2/100,n2/10,n2,n2*10,100) # physical location of likelihood ratio ticks and labels pr7 <- 50-15*log(pr5)/log(10) pr8 <- 50-15*log(pr6)/log(10) # odd and even probability labels od2 <- paste(pr2[seq(1,length(pr2),by=2)],"%",sep="") ev2 <- paste(pr2[seq(2,length(pr2),by=2)],"%",sep="") # odd and even likelihood ratio labels od4 <- pr4[seq(1,length(pr4),by=2)] ev4 <- pr4[seq(2,length(pr2),by=2)] # physical locations of odd/even labels od6 <- pr6[seq(1,length(pr6),by=2)] ev6 <- pr6[seq(2,length(pr6),by=2)] od8 <- pr8[seq(1,length(pr8),by=2)] ev8 <- pr8[seq(2,length(pr8),by=2)] draw.frame <- function() {  ################################  # outline sleeve of slide rule #  ################################  hline( 5, 95, 0) # bottom edge  hline( 0,100, 20) # fold line  hline( 0,100, 50) # fold line  hline( 5, 95, 70) # top edge  vline( 0, 12, 28) # left edge  vline( 0, 42, 58) # left edge  vline(100, 12, 28) # right edge  vline(100, 42, 58) # right edge  ################  # left notches #  ################  vline( 5, 0, 10)  segments( 5, 10, 0, 12)  segments( 0, 28, 5, 30)  vline( 5, 30, 40)  segments( 5, 40, 0, 42)  vline( 5, 60, 70)  segments( 0, 58, 5, 60)  #################  # right notches #  #################  vline( 95, 0, 10)  segments( 95, 10,100, 12)  segments(100, 28, 95, 30)  vline( 95, 30, 40)  segments( 95, 40,100, 42)  vline( 95, 60, 70)  segments(100, 58, 95, 60)  ################################  # outline insert of slide rule #  ################################  hline( 0,100, 71) # bottom edge  hline( 0,100,100) # top edge  vline( 0, 71,100) # left edge  vline(100, 71,100) # right edge  ####################################  # cut-out for pre-test probability #  ####################################  h <- 29  hline( 17, 83,h+0) # bottom edge  hline( 17, 83,h+7) # top edge  vline( 17,h+0,h+7) # left edge  vline( 83,h+0,h+7) # right edge  #####################################  # cut-out for post-test probability #  #####################################  h <- 46  v <- 50  hline(v-3,v+3,h+0) # top edge  hline(v-3,v+3,h-6) # bottom edge  vline(v-3,h+0,h-6) # left edge  vline(v+3,h+0,h-6) # right edge  vline(v+0,h+0,h+1) # top tick  vline(v+0,h-6,h-7) # bottom tick } draw.ticks <- function() {  ####################  # Likelihood ratio #  ####################  h <- 29  segments(pr7,h+0,pr7,h-1) # all ticks  segments(od8,h-2,od8,h-1) # extend odd ticks  segments(ev8,h-4,ev8,h-1) # extend even ticks  text(od8,h-3,od6) # label odd ticks  text(ev8,h-5,ev6) # label even ticks  ########################  # Pre-test probability #  ########################  h <- 79  segments(pr3,h-1,pr3,h+1) # all ticks  segments(od4,h+2,od4,h+1) # extend odd ticks  segments(ev4,h+4,ev4,h+1) # extend even ticks  text(od4,h+3,od2) # label odd ticks  text(ev4,h+5,ev2) # label even ticks  #########################  # Post-test probability #  #########################  h <- 97  segments(pr3,h+1,pr3,h-1) # all ticks  segments(od4,h-2,od4,h-1) # extend odd ticks  segments(ev4,h-4,ev4,h-1) # extend even ticks  text(od4,h-3,od2) # label odd ticks  text(ev4,h-5,ev2) # label even ticks } draw.shade <- function() {  xlo <- -999  ylo <- -999  xhi <- 999  yhi <- 999  #########################  # shade extreme regions #  #########################  rectangle(xlo,ylo,xhi, 0) # bottom  rectangle(xlo,100,xhi,yhi) # top  rectangle(xlo,ylo, 0,yhi) # left  rectangle(100,ylo,xhi,yhi) # right  rectangle( 0, 70,100, 71) # between sleeve and insert  ################  # left notches #  ################  rectangle( 0, 0, 5, 10)  triangle ( 0, 10, 5, 10, 0, 12)  triangle ( 0, 30, 5, 30, 0, 28)  rectangle( 0, 30, 5, 40)  triangle ( 0, 40, 5, 40, 0, 42)  triangle ( 0, 60, 5, 60, 0, 58)  rectangle( 0, 60, 5, 70)  #################  # right notches #  #################  rectangle(100, 0, 95, 10)  triangle (100, 10, 95, 10,100, 12)  triangle (100, 40, 95, 40,100, 42)  rectangle(100, 30, 95, 40)  triangle (100, 30, 95, 30,100, 28)  triangle (100, 60, 95, 60,100, 58)  rectangle(100, 60, 95, 70)  ########################  # Pre-test probability #  ########################  h <- 29  rectangle( 17,h+0, 83,h+7)  #########################  # Post-test probability #  #########################  h <- 46  v <- 50  rectangle(v-3,h-6,v+3,h+0) } draw.notes <- function() {  m0 <- paste(   "Line up the pre-test probability",   "with the likelihood ratio, and read",   "the post-test probability here."   ,sep="\n")  m1 <- paste(   "(C) The Children's Mercy Hospital.",   "For more information, please go to",   "www.childrensmercy.org/sliderule.asp",   sep="\n")  text(45,43,m0,adj=1)  text(55,43,m1,adj=0)  text(15,33,"Pre-test\nprobability",adj=1)  text(15,25,"Likelihood\nratio",adj=1) } pdf(file="sliderule.pdf",width=8,height=10)  par(mar=rep(0.1,4),cex=0.75,adj=0.5)  plot(c(0,100),c(0,100),axes=F,type="n",xlab=" ",ylab=" ")  draw.notes()  draw.shade()  draw.frame()  draw.ticks() dev.off()