R/paraplot.R In zoib: Bayesian Inference for Beta Regression and Zero-or-One Inflated Beta Regression

Documented in paraplot

```paraplot <- function(para1, para2=NULL, para3=NULL, para4=NULL,
tickx=NULL, jitter=NULL, pch = 1:4, col=1:4,
legpos=NULL, legtext, annotate=FALSE)
{
K <- 4
if(is.null(para4)) K <- K-1
if(is.null(para3)) K <- K-1
if(is.null(para2)) K <- K-1

par(mfrow=c(1,1),mar=c(3,2,1,1))

if(K==1){
p <- nrow(para1)
index <- 1:p
l <- min(para1[,2])
u <- max(para1[,3])
plot(para1[,1], index, xlim=c(l-abs(l)*0.1,u), ylim=c(1,p+1), axes=F,
pch=pch[1], col=col[1], xlab="", ylab="")
segments(para1[,2],index, para1[,3], index, col=col[1])
axis(2, at=NULL, labels=FALSE, tick = FALSE)
if(is.null(tickx)) axis(1,round(seq(l,u,length.out=8),2))
else axis(1,tickx)
if(annotate){
if(is.null(rownames(para1))) stop("Assign row names to the parameter object")
else text(rep(l-abs(l)*0.15,p), 1:p, rownames(para1), cex=1.2)
}
legend(legpos[1], legpos[2], legtext, pch=pch[1], col=pch[1], lty=1, cex=1.2)
}
else if(K>=2){
mesg <- "Assign row names to the parameter object. \n Use the same row name if two parameter \n objects share the same parameter."

if(K==2) {
if(any(c(is.null(rownames(para1)),is.null(rownames(para2))))) stop(mesg)
l <- min(c(min(para1),min(para2)))
u <- max(c(max(para1),max(para2)))

para1 <- data.frame(para1);
para1 <- cbind(rownames(para1), para1);
colnames(para1) <- c("id","e1","l1","u1")

para2 <- data.frame(para2);
para2 <- cbind(rownames(para2), para2);
colnames(para2) <- c("id","e2","l2","u2")

para<- merge(para1, para2, by="id", all.x=TRUE,
all.y=TRUE, suffixes = c(" "," "))
}
if(K==3) {
if(any(c(is.null(rownames(para1)),is.null(rownames(para2)),
is.null(rownames(para3))))) stop(mesg)
l <- min(c(min(para1),min(para2),min(para3)))
u <- max(c(max(para1),max(para2),max(para3)))

para1<- data.frame(para1); id<- rownames(para1);
para1<- cbind(id, para1); colnames(para1) <- c("id","e1","l1","u1")

para2<- data.frame(para2); id<- rownames(para2);
para2<- cbind(id, para2); colnames(para2) <- c("id","e2","l2","u2")

para3<- data.frame(para3); id<- rownames(para3);
para3<- cbind(id, para3); colnames(para3) <- c("id","e3","l3","u3")

para<- merge(para1, para2, by = "id", all.x=TRUE,
all.y=TRUE, suffixes = c(" "," "))
para<- merge(para, para3, by = "id", all.x=TRUE,
all.y=TRUE, suffixes = c(" "," "))
}
if(K==4) {
if(any(c(is.null(rownames(para1)),is.null(rownames(para2)),
is.null(rownames(para3)),is.null(rownames(para4))))) stop(mesg)
l <- min(c(min(para1),min(para2),min(para3),min(para4)))
u <- max(c(max(para1),max(para2),max(para3),max(para4)))

para1<- data.frame(para1); id<- rownames(para1);
para1<- cbind(id, para1); colnames(para1) <- c("id","e1","l1","u1")

para2<- data.frame(para2); id<- rownames(para2);
para2<- cbind(id, para2); colnames(para2) <- c("id","e2","l2","u2")

para3<- data.frame(para3); id<- rownames(para3);
para3<- cbind(id, para3); colnames(para3) <- c("id","e3","l3","u3")

para4<- data.frame(para4); id<- rownames(para4);
para4<- cbind(id, para4); colnames(para4) <- c("id","e4","l4","u4")

para<- merge(para1, para2, by = "id", all.x=TRUE,
all.y=TRUE, suffixes = c(" "," "))
para<- merge(para, para3, by = "id", all.x=TRUE,
all.y=TRUE, suffixes = c(" "," "))
para<- merge(para, para4, by = "id", all.x=TRUE,
all.y=TRUE, suffixes = c(" "," "))
}
p<- nrow(para)
index <- 1:p

for(i in 1:p){
for(j in 1:ncol(para)){
if(is.na(para[i,j])) para[i,j]<- -99999
}}
if(is.null(jitter)) jitter <- p*0.01
plot(para[,2], index, xlim=c(l-abs(l)*0.3,u),
ylim=c(1,p+max(1,jitter*K)),
col=col[1], pch=pch[1], axes=F, xlab="", ylab="")
segments(para[,3], index, para[,4], index, col=col[1])
for(i in 2:K){
points(para[,1+(i-1)*3+1], index+jitter*i, col=col[i], pch=pch[i])
segments(para[,1+(i-1)*3+2], index+jitter*i,
para[,1+(i-1)*3+3], index+jitter*i, col=col[i])
}
axis(2, at=NULL, labels=FALSE, tick=FALSE)
if(is.null(tickx)) axis(1,round(seq(l,u,length.out=8),2))
else axis(1,tickx)
if(annotate) text(rep(l-abs(l)*0.15,p), 1:p, para\$id, cex=1.2)
legend(legpos[1],legpos[2],legtext,
pch=pch[1:K],col=pch[1:K],lty=rep(1,K), cex=1.2)
}
}

```

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zoib documentation built on April 7, 2018, 9:03 a.m.