(A) WinBUGS Program A WinBUGS program to fit a Corrected Ordinal Logistic Model to the Signal Tandmobiel® study. There are two models arkov chain:- - Main Data Model : Sampling a Markov chain pertaining to the regression parameters using correction term sampled from the calibration model - Calibration Data Model: A Markov chain Sampling the correction terms using the calibration data The Wibugs porgram '.odc' file can be obtained by writing an e-mail to emmanuel.lesaffre@med.kuleuven.ac.be model { # MAIN DATA MODEL for(i in 1:N) { age2[i] <- age[i]-mean(age[]) # center age mu[i] <- beta[1]*xcen[i] + beta[2]*ycen[i] + beta[3]*gender[i] + beta[4]*age2[i] + bs[schocode[i]] # Cumulative piability of response <= r for(r in 1 : Ncut) { logit(F[i, r]) <- (lambda[r] - mu[i] ) } # Probability of response = r Q[i,1]<-F[i, 1] ; Q[i,2]<-F[i, 2]-F[i, 1]; Q[i,3]<-F[i, 3]-F[i, 2]; Q[i,4]<-1- F[i, 3]; # Corrected piability of response <= j for(a in 1:4) { Pr[i,a]<- phi.cut[examiner[i],a,1]*Q[i,1] + phi.cut[examiner[i],a,2]*Q[i,2] + phi.cut[examiner[i],a,3]*Q[i,3] + phi.cut[examiner[i],a,4]*Q[i,4] } dmf_cat[i] ~ dcat(Pr[i, ]) }# end i # random school and examienr effects for(j in 1:Ns) { bs[j] ~ dnorm(0.0 ,tau) } # ordered cut points for underlying continuous latent variable lambda[1] ~ dnorm(0, 1.0E-06)I( ,lambda[2]) lambda[2] ~ dnorm(0, 1.0E-06)I(lambda[1],lambda[3]) lambda[3] ~ dnorm(0, 1.0E-06)I(lambda[2],) # vague prior on regression and precision parameters for(k in 1:4) { beta[k ]~ dnorm(0, 1.0E-06) } tau ~ dgamma(0.01, 0.01) sigma2 <- 1 / tau # Bayesian p-values # if mean(paramater)< 0 then pvalue=1-pvalue else pvalue=pvalue pvalue[1]<- 1-step(lambda[1]); pvalue[2]<- 1-step(lambda[2]); pvalue[3]<- 1-step(lambda[3]); pvalue[4]<- 1-step(beta[1]) ; pvalue[5]<- 1-step(beta[2]) ; pvalue[6]<- 1-step(beta[3]) ; pvalue[7]<- 1-step(beta[4]) ; pvalue[8]<- 1-step(sigma2) ; # CALIBRATION DATA # Loop over cabibration exercise for(j in 1:16){ for(a in 1:4){ M[j,a,1:4] ~ dmulti(tphi[j,a,1:4], m[j,a]) m[j,a] <- sum(M[j,a,1:4]) for(b in 1:4){ tphi[j,a,b] <- w[j]*equals(a,b)+ (1-w[j])*pi[a,b] phi[j,a,b] <- tphi[j,b,a] }}} # gold standard for(a in 1:4) { for(b in 1:4) { phi[17,a,b] <- 1*equals(a,b) }} # prior for w for(j in 1:16){ w[j] ~ dbeta(1,1) } # a ddirch prior for pi using ratio of gamma trick for(a in 1:4) { for(b in 1:4) { pi[a,b] <- delta[a,b]/sum(delta[a,]) delta[a,b] ~ dgamma(1,1) }} # use of 'cut' to ensure indepence of phi from main study parms for(j in 1:17){D for(a in 1:4) { for(b in 1:4) { phi.cut[j,a,b] <- cut(phi[j,a,b]) }}} }# end model (B) DATA SET A subset of 435 children, about 10% of the complete dataset. The complete dataset can be obtained by writing an e-mail to emmanuel.lesaffre@med.kuleuven.ac.be The dataset is given in LIST format, a common format of WinBUGS input dataset. list( N=435, Ns=150, Ncut=3, examiner=c(12, 7, 9, 15, 13, 5, 4, 14, 6, 6, 8, 15, 2, 7, 2, 1, 9, 7, 6, 5, 15, 14, 13, 12, 5, 2, 6, 4, 15, 6, 6, 14, 1, 6, 10, 15, 1, 9, 11, 15, 3, 9, 9, 8, 6, 6, 7, 9, 6, 10, 11, 4, 7, 15, 15, 12, 15, 16, 2, 4, 1, 15, 11, 2, 6, 16, 11, 15, 7, 2, 2, 13, 15, 12, 10, 15, 9, 4, 16, 15, 10, 6, 4, 10, 8, 7, 2, 2, 15, 2, 5, 4, 16, 9, 7, 2, 2, 9, 1, 5, 15, 6, 1, 10, 6, 15, 13, 1, 11, 10, 15, 10, 16, 16, 1, 2, 13, 14, 5, 8, 16, 15, 8, 14, 13, 15, 6, 6, 6, 2, 1, 5, 14, 7, 13, 15, 12, 6, 11, 15, 2, 6, 10, 7, 1, 9, 6, 16, 5, 16, 1, 15, 1, 15, 2, 8, 15, 15, 13, 5, 15, 16, 11, 16, 4, 11, 11, 15, 10, 9, 1, 15, 3, 7, 6, 2, 6, 2, 4, 16, 7, 6, 6, 12, 14, 5, 6, 16, 2, 6, 8, 4, 13, 8, 15, 15, 14, 15, 2, 4, 12, 11, 2, 5, 15, 3, 8, 5, 7, 14, 12, 1, 13, 6, 7, 13, 13, 14, 2, 6, 16, 5, 3, 4, 15, 2, 16, 6, 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22, 114, 79, 12, 143, 95, 137, 10, 28, 93, 41, 119, 75, 77, 48, 62, 80, 92, 131, 110, 5, 133, 72, 52, 5, 143, 122, 121, 46, 143, 143, 48, 136, 43, 114, 139, 131, 50, 51, 57, 118, 28, 69, 124, 42, 40, 71, 45, 4, 74, 134, 77, 133, 33, 96, 59, 123, 71, 87, 38, 90, 100, 72, 42, 143, 15, 55, 31, 49, 48, 15, 46, 101, 99, 66, 82, 142, 22, 58, 15, 34, 3, 114, 73, 78, 37, 18, 66, 47, 48, 8, 50, 130, 67, 32, 12, 144, 50, 52, 50, 63, 39, 61, 84, 44, 110, 58, 150, 39, 69, 147, 148, 38, 90, 92, 137, 136, 73, 18, 66, 107, 116, 14, 69, 103, 128, 97, 128, 87, 140, 26, 98, 18, 3, 131, 40, 58, 55, 18, 74, 18, 69, 83, 91, 74, 90, 32, 58, 65, 35, 125, 39, 62, 112, 96, 128, 46, 143, 8, 28, 131, 106, 140, 86, 131, 84, 45, 33, 115, 92, 109, 97, 110, 75, 43, 54, 86, 131, 138, 17, 38, 138, 81, 69, 127, 47, 82, 15, 111, 125, 71, 66, 69, 24, 101, 75, 99, 148, 119, 12, 20, 43, 115, 32, 32, 149, 83, 133, 33, 75, 135, 16, 42, 68, 54, 131, 48, 74, 67, 7, 145, 62, 68, 128, 137, 65, 37, 43, 4, 43, 136, 78, 111, 38, 21, 136, 92, 131, 41, 117, 9, 89, 59, 17, 97, 135, 122, 46, 15, 110, 9, 2, 18, 90, 58, 77, 64, 78, 25, 30, 55, 81, 29, 108, 42, 59, 97, 78, 150, 142, 136, 64, 96, 14, 147, 65, 37, 47, 15, 20, 120, 138, 6, 43, 64, 80, 18, 143, 65, 26, 8, 13, 76, 96, 17, 65, 105, 41, 105, 28, 86, 135, 75, 100, 40, 92, 102, 60, 85, 112, 16, 48, 69, 37, 27, 69, 84, 70, 128, 150, 146, 62, 107, 128, 66, 35, 94, 38, 125, 23, 12, 72, 19, 83, 97, 22, 56, 123, 113, 53, 53, 128, 126, 124, 82, 12, 16, 96, 11, 38, 90, 47, 62, 43, 38, 88, 5, 149, 32, 17, 145, 62, 19, 96, 59, 8, 110, 90, 53, 86, 92, 49, 24, 74, 47, 36, 58, 82, 52, 77, 105, 1, 118, 142, 28, 146, 120, 56, 104, 48, 46, 132, 91, 144, 18, 96, 74, 25, 143, 112, 60, 62, 147, 130, 44, 35, 7, 137, 129, 97, 38, 129, 128, 49, 119, 66, 98, 42, 121, 43, 35, 97, 121), M = structure(.Data= c(17, 0, 2, 0, 2, 3, 1, 0, 0, 0, 6, 1, 0, 0, 0, 1, 18, 0, 0, 0, 2, 4, 0, 0, 0, 1, 7, 0, 0, 0, 1, 2, 19, 1, 1, 0, 1, 0, 1, 0, 0, 0, 5, 0, 0, 0, 0, 0, 10, 0, 0, 0, 2, 4, 0, 0, 0, 2, 4, 1, 0, 0, 0, 1, 15, 0, 1, 0, 2, 2, 0, 0, 0, 1, 8, 2, 0, 0, 0, 2, 16, 0, 0, 0, 2, 6, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 8, 0, 0, 0, 1, 2, 0, 0, 0, 0, 6, 0, 0, 0, 0, 3, 17, 1, 0, 0, 1, 5, 1, 0, 0, 0, 6, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 2, 0, 0, 0, 0, 3, 21, 0, 0, 0, 0, 5, 0, 0, 0, 0, 7, 0, 0, 0, 0, 2, 10, 0, 0, 0, 1, 1, 1, 0, 0, 0, 3, 0, 0, 0, 0, 3, 15, 1, 0, 0, 1, 2, 2, 0, 0, 0, 6, 0, 0, 0, 0, 3, 16, 0, 1, 0, 2, 3, 1, 0, 0, 0, 5, 3, 0, 0, 0, 1, 15, 1, 1, 0, 2, 1, 1, 0, 0, 0, 5, 0, 0, 0, 0, 3, 20, 1, 1, 0, 0, 1, 0, 0, 0, 0, 5, 0, 0, 0, 0, 0, 17, 0, 0, 0, 0, 2, 0, 0, 0, 0, 8, 0, 0, 0, 0, 3), .Dim=c(16, 4, 4)) ) (C) INITIAL VALUES A list of initial values to the WinBUGS program list(lambda=c(-0.64,0.00,2.00), beta=c(0.02,-0.06, 0.03,0.23), tau=4.0, delta = structure(.Data = c(3.02821186716995,0.08332666428735359,0.07419299262029873,0.008059025597196226,0.7220556849562841, 0.535181555851886,0.4604990696278605,0.02300617205313604,0.1444148934672606,0.505300612432072, 4.08670909051092,0.04405808326675045,0.3454558299063502,0.2997270407843201,0.4014285598400601, 3.049869944592438),.Dim = c(4,4)), w = c(0.1938879064367082,0.3082251959080907,0.3976174116771475,0.08803732369193379,0.04404709753187268, 0.7224843158451535,0.7511736191436543,0.8425815826480191,0.5713319062379999,0.9232168427893085, 0.2207114915961449,0.2477630078349058,0.254143242785686,0.6155134597936252,0.4490437400861457, 0.8766236239575043)) list(lambda=c(-0.04,0.20,1.00), beta=c(0.42, 0.02,-0.02,0.03), tau=1.0, delta = structure(.Data = c(5.025892470151376,0.376189965677409,0.4314906083776112,0.00326785186492139,3.160783182533284, 0.5063280453618199,1.36410224272391,0.1066890874495908,0.016694366165325,1.212781473025998, 3.228517042341537,0.2261396219807522,0.6316849356275059,0.2196589664263533,0.1841762274831587, 1.502734413651113),.Dim = c(4,4)), w = c(0.4985185265202123,0.6581138639600906,0.6240230599843403,0.4697872739311377,0.3428314759711447, 0.815977876004412,0.858073598010187,0.6040675245139917,0.4149944014559592,0.9846918331418342, 0.871645053323193,0.4790513618482073,0.2616102726971218,0.3574161309620325,0.8216315685705765, 0.9753200882349632)) list(lambda=c(-0.44,0.06,1.17), beta=c(0.22,-0.02,-0.07,0.33), tau=5.3, delta = structure(.Data = c(2.285148823675355,0.09358238777369159,0.1126720137121962,0.02843057175894592,1.205595754773291, 0.4570333392383865,0.4370342509521121,0.02378615541406277,0.03362382019392043,0.7881903297515734, 2.566635391723692,0.04360489385041454,0.5727426798702359,0.2208080290320477,0.2969754497226734, 4.50249848710502),.Dim = c(4,4)), w = c(0.2194472284196692,0.4669587345272758,0.1674732044719388,0.4719642461236636,0.5094061981439, 0.7826550957161017,0.950215327064607,0.8271033902778772,0.5516384156111833,0.7957318113967325, 0.207499036196386,0.1683697445012838,0.08134174117836253,0.5456163601696568,0.6592878055103532, 0.9010012474486458)) list(lambda=c(-0.24,0.12,1.70), beta=c(0.32,-0.10,-0.17,0.53), tau=8.3, delta = structure(.Data = c(4.0935753812725,0.1509334779970691,0.1330368924059832,0.001031601470504925,3.075085918164132, 3.102663945243298,0.7528712199315544,0.1236791778530205,0.05575985523939865,0.3101724069194222, 3.046931251802173,0.08375677084698101,0.8602051445145789,0.1950645318840977,0.2504292840862828, 1.827707768288177),.Dim = c(4,4)), w = c(0.1275987155392187,0.4763820197584091,0.2507908691459491,0.2796531754919482,0.4590527265030838, 0.5751109018218692,0.8096215713606422,0.3230787149272294,0.2653744048515348,0.9414511150025765, 0.5598714718508113,0.2319782474409413,0.196813457435786,0.4025155050195529,0.02986182100218052, 0.9415792778862027)) list(lambda=c(-0.84,0.30,0.80), beta=c(0.12,-0.00,-0.10,0.13), tau=2.0, delta = structure(.Data = c(3.644660263619611,0.2921465193140186,0.143121075010806,0.02672675190279807,3.047116998301678, 1.005666957393303,1.765414241011373,0.01758744104180956,0.1906951467334762,1.169252232359629, 4.019310981455396,0.3546820317386415,0.4117793955590412,0.05536981624253349,0.235458657741816, 1.385260554300138),.Dim = c(4,4)), w = c(0.3906343965181638,0.5998877795018537,0.1957001887772123,0.6168053089730058,0.6955712922913762, 0.803210346565939,0.519534466760316,0.7181739677229961,0.4220322456283374,0.897622765075753, 0.3206344229730937,0.7195821381770769,0.2000724265924498,0.5950497149466768,0.3968543724142268, 0.8872930336629012))