This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) (format=latex 2007.12.21) 26 JAN 2008 10:50 entering extended mode %&-line parsing enabled. **ryu-stochastic-code (./ryu-stochastic-code.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, croatian, bulgarian, russian, ukrainian, czech, slovak, danish, dut ch, finnish, finnish, french, basque, french, german, ngerman, german, ngerman, greek, monogreek, ancientgreek, ibycus, hungarian, hungarian, italian, italian , latin, latin, mongolian, mongolian, norsk, norsk, coptic, esperanto, estonian , icelandic, indonesian, interlingua, romanian, serbian, slovenian, turkish, up persorbian, welsh, polish, polish, portuguese, portuguese, spanish, catalan, ga lician, spanish, catalan, galician, swedish, swedish, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk11.clo File: bk11.clo 2005/09/16 v1.4f Standard LaTeX file (size option) ) \c@part=\count79 \c@chapter=\count80 \c@section=\count81 \c@subsection=\count82 \c@subsubsection=\count83 \c@paragraph=\count84 \c@subparagraph=\count85 \c@figure=\count86 \c@table=\count87 \abovecaptionskip=\skip41 \belowcaptionskip=\skip42 \bibindent=\dimen102 ) (./ryu-stochastic-code.aux) \openout1 = `ryu-stochastic-code.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 ######################################################### #######################[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 # : Modeling and inference for an ordinal effect size mea sure #[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 # : Authors: Euijung Ryu and Alan Agresti #[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 # : Statistics in Medicine (2008) #[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 ######################################################### #######################[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [1 ] Overfull \hbox (128.92996pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 A12[i]<-pi.hat[i]*( (1-lambda.hat[i]) * sum(lambda.hat[ (i+1):c]) - (sum(lambda.hat[(i+1):c]) )^2 )[] [] Overfull \hbox (174.91946pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 A1<-A11-(1/(n2-1))*sum(A12)-(1/(4*(n2-1)))*(s um(A13)+pi.hat[c]*lambda.hat[c]*(1-lambda.hat[c]) )[] [] Overfull \hbox (65.6944pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 B12[j-1]<-lambda.hat[j]*( (1-pi.hat[j])*sum(pi.hat[1:(j- 1)]) - (sum(pi.hat[1:(j-1)]))^2 )[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [2] Overfull \hbox (111.6839pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 B1<-B11-(1/(n1-1))*sum(B12)-(1/(4*(n1-1)))*(sum(B13)+ lambda.hat[1]*pi.hat[1]*(1-pi.hat[1]) )[] [] Overfull \hbox (123.18127pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 theta.fn<-( (n1*n2-n1-n2+2)*theta.hat-n1*n2*theta.hat ^2 )/((n1-1)*(n2-1) )+A1/(n1-1)+B1/(n2-1)[] [] Overfull \hbox (31.20227pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 epsilon.hat<- ( (n1+n2-2)*theta.hat-(n2-1)*A1-(n1-1) *B1 )/((n1+n2-2)*theta.fn)[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 L.H<-(CCC+2*theta.hat-sqrt(CCC^2+4*CCC*theta.hat*(1-t heta.hat)))/(2*(CCC+1))[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 U.H<-(CCC+2*theta.hat+sqrt(CCC^2+4*CCC*theta.hat*(1-t heta.hat)))/(2*(CCC+1))[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [3] Underfull \vbox (badness 10000) has occurred while \output is active [] [4] Overfull \hbox (220.90897pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 V.1<-((n2-1)*(CC-theta.hat^2)+(n1-1)*(DD-theta.hat^2) +theta.hat*(1-theta.hat)-.25*t(pi.hat)%*%lambda.hat)/(n1*n2)[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [5] Overfull \hbox (77.19177pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 ########## Unrestricted LRT, Score, and Pseudo-score conf idence intervals ##################[] [] Overfull \hbox (8.20752pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 ## We can change "starting.boundaries" inside the followi ng function if you want[] [] Overfull \hbox (36.95096pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 theta.set<-seq(starting.boundaries[1]-0.02, starting.boun daries[2]+0.02, length=1000)[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [6] Overfull \hbox (71.44308pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 LRT.interval<-Score.interval<-Pseudo.Score.interval<-c(re p(1e+5, length=length(theta.set)))[] [] Overfull \hbox (88.68915pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 a<-mph.fit(yy,Z,ZF,h.fct=h.fct, norm.diff.conv=10 , maxiter=200, norm.score.conv=1e-5)[] [] Overfull \hbox (146.17603pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 a<-mph.fit(yy,Z,ZF,h.fct=h.fct, norm.diff.conv=10 , maxiter=200, norm.score.conv=1e-5, y.eps=.1)[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [7] Overfull \hbox (140.42734pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 a<-mph.fit(yy,Z,ZF,h.fct=h.fct, norm.diff.conv=10, maxiter=200, norm.score.conv=1e-5, y.eps=.1)[] [] Overfull \hbox (146.17603pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 a<-mph.fit(yy,Z,ZF,h.fct=h.fct, norm.diff.conv=10 , maxiter=200, norm.score.conv=1e-5, y.eps=.1)[] [] Overfull \hbox (381.87222pt too wide) in paragraph at lines 371--371 [] \OT1/cmtt/m/n/10.95 var.theta.final<-((n2-1)*(CC-theta.null^2)+(n 1-1)*(DD-theta.null^2)+theta.null*(1-theta.null)-.25*t(pi.final)%*%lambda.final )/(n1*n2)[] [] Overfull \hbox (36.95096pt too wide) in paragraph at lines 371--371 []\OT1/cmtt/m/n/10.95 cat("LRT.stat=", lrt, "Score.stat=", score, "Pseudo.Score .stat=", pseudo.score, "\n")[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [8] [9] (./ryu-stochastic-code.aux) ) Here is how much of TeX's memory you used: 224 strings out of 93946 2492 string characters out of 1162065 51047 words of memory out of 1500000 3588 multiletter control sequences out of 10000+50000 4108 words of font info for 16 fonts, out of 1200000 for 2000 743 hyphenation exceptions out of 8191 21i,4n,19p,167b,239s stack positions out of 5000i,500n,6000p,200000b,5000s Output written on ryu-stochastic-code.dvi (9 pages, 10628 bytes).