## ----echo=FALSE------------------------------------------- options(width=60) knitr::knit_hooks$set(document = function(x) {sub('\\usepackage[]{color}', '\\usepackage{xcolor}', x, fixed = TRUE)}) ## ----eval=FALSE------------------------------------------- # source("https://bioconductor.org/biocLite.R") # BiocInstaller::biocLite("semisup") ## --------------------------------------------------------- library(semisup) ## ----eval=FALSE------------------------------------------- # attach(toydata) ## ----echo=FALSE------------------------------------------- names <- names(toydata) for(i in seq_along(names)){ assign(names[i],toydata[[i]]) } rm(names) ## ----eval=FALSE------------------------------------------- # help(semisup) # ?semisup ## ----echo=FALSE,fig.width='\\linewidth',fig.height=3------ par(mar=(c(2,4,1,5))) plot.new() plot.window(xlim=c(1,length(y)),ylim=range(y)) box() axis(side=2) title(ylab="y") mtext(text="labelled",at=25,side=1) mtext(text="unlabelled",at=75,side=1) abline(v=50.5,lty=2) points(y,col=rep(c("blue","black"),each=50)) ## --------------------------------------------------------- fit <- mixtura(y,z) ## ----echo=FALSE------------------------------------------- mean0 <- round(fit$estim1$mean0,0) sd0 <- round(fit$estim1$sd0,0) mean1 <- round(fit$estim1$mean1,0) sd1 <- round(fit$estim1$sd1,0) tau <- round(fit$estim1$p1,2) ## ----results='hide'--------------------------------------- class <- round(fit$posterior) ## ----echo=FALSE,fig.width='\\linewidth',fig.height=3------ par(mar=(c(2,4,1,5))) plot.new() plot.window(xlim=c(1,length(y)),ylim=range(y)) box() axis(side=2) title(ylab="y") mtext(text="labelled",side=1,at=25) mtext(text="unlabelled",side=1,at=75) abline(v=50.5,lty=2) points(y,col=ifelse(class,"red","blue")) # component zero text <- paste("N(",mean0,",",sd0,")",sep="") mtext(text=text,side=4,at=0,line=0.5,las=1,col="blue") # mixing proportion text <- bquote(tau==.(tau)) mtext(text=text,side=4,at=2,line=0.5,las=2) # component one text <- paste("N(",mean1,",",sd1,")",sep="") mtext(text=text,side=4,at=4,line=0.5,las=1,col="red") ## ----results='hide'--------------------------------------- fit$estim1 ## ----results='hide'--------------------------------------- fit$estim0 ## ----echo=FALSE,fig.width='\\linewidth',fig.height=3------ par(mar=(c(2,4,1,5))) plot.new() plot.window(xlim=c(1,length(y)),ylim=range(y)) box() axis(side=2) title(ylab="y") mtext(text="labelled",side=1,at=25) mtext(text="unlabelled",side=1,at=75) abline(v=50.5,lty=2) points(y,col="blue") # estimates mean0 <- round(fit$estim0$mean0,0) sd0 <- round(fit$estim0$sd0,0) # component zero text <- paste("N(",mean0,",",sd0,")",sep="") mtext(text=text,side=4,at=0,line=0.5,las=1,col="blue") # mixing proportion text <- bquote(tau==0) mtext(text=text,side=4,at=2,line=0.5,las=2) # component one text <- paste("N(-,-)",sep="") mtext(text=text,side=4,at=4,line=0.5,las=1,col="red") ## ----eval=FALSE------------------------------------------- # scrutor(y,z) ## ----eval=FALSE------------------------------------------- # n <- length(snp) # # # z <- rep(NA,times=n) # z[snp==0] <- 0 ## ----eval=FALSE------------------------------------------- # n <- nrow(SNPs) # p <- ncol(SNPs) # # Z <- matrix(NA,nrow=n,ncol=p) # Z[SNPs==0] <- 0 ## ----eval=FALSE------------------------------------------- # scrutor(y,z) ## ----eval=FALSE------------------------------------------- # scrutor(y,Z) ## ----eval=FALSE------------------------------------------- # scrutor(Y,z) ## ----eval=FALSE------------------------------------------- # scrutor(Y,Z)