Nothing
plot.fads<-function (x,opt,cols,lty,main,sub,legend,csize,...) {
NextMethod()
}
plot.fads.kfun<-function (x,opt=c("all","L","K","n","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
ifelse(!is.null(x$call$nsim)&&(x$call$nsim>0),ci<-TRUE,ci<-FALSE)
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
opt<-opt[1]
if(opt=="all")
mylayout<-layout(matrix(c(1,1,1,1,2,2,3,3,2,2,3,3,4,4,5,5,4,4,5,5),ncol=4,byrow=TRUE))
else if(opt%in%c("L","K","n","g"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
else
stopifnot(opt%in%c("all","L","K","n","g"))
if(missing(cols))
cols=c(1,2,3)
else if(length(cols)!=3)
cols=c(cols,cols,cols)
if(missing(lty))
lty=c(1,3,2)
else if(length(lty)!=3)
lty=c(lty,lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-c("pair density function","second-order neighbour density function","Ripley's K-function","L-function : sqrt[K(r)/pi]-r")
if(ci) {
alpha<-x$call[["alpha"]]
p<-ifelse(!is.null(alpha),signif(100*(1-alpha),digits=6),99)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$g$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (CSR)",paste(p,"% CI of CSR")),cex=1.5,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.75*csize,csize))
if(opt%in%c("all","g")) { # g-function
lim<-range(x$g[,1:4])
plot(x$r,x$g$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="g(r)",cex.lab=1.25,...)
lines(x$r,x$g$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$g$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$g$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$g$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","n")) {# n-function
lim<-range(x$n[,1:4])
plot(x$r,x$n$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="n(r)",cex.lab=1.25,...)
lines(x$r,x$n$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$n$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$n$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$n$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","K")) { # K-function
plot(x$r,x$k$obs,ylim=range(x$k[,1:4]),main=paste("\n\n",sub[3]),type="n",xlab="distance (r)",ylab="K(r)",cex.lab=1.25,...)
lines(x$r,x$k$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$k$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$k$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$k$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","L")) { # L-function
lim<-range(x$l[,1:4])
plot(x$r,x$l$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[4]),type="n",xlab="distance (r)",ylab="L(r)",cex.lab=1.25,...)
lines(x$r,x$l$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$l$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$l$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$l$inf,lty=lty[3],col=cols[3],...)
}
}
else {
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$g$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (CSR)"),cex=1.5,lty=lty[1:2],bty="n",horiz=TRUE,title=main,col=cols[1:2],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.75*csize,csize))
if(opt%in%c("all","g")) { # g-function
lim<-range(x$g)
plot(x$r,x$g$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="g(r)",cex.lab=1.25,...)
lines(x$r,x$g$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$g$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","n")) { # n-function
lim<-range(x$n)
plot(x$r,x$n$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="n(r)",cex.lab=1.25,...)
lines(x$r,x$n$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$n$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","K")) { # k-function
plot(x$r,x$k$obs,ylim=range(x$k),main=paste("\n\n",sub[3]),type="n",xlab="distance (r)",ylab="K(r)",cex.lab=1.25,...)
lines(x$r,x$k$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$k$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","L")) { # L-function
lim<-range(x$l)
plot(x$r,x$l$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[4]),type="n",xlab="distance (r)",ylab="L(r)",cex.lab=1.25,...)
lines(x$r,x$l$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$l$theo,lty=lty[2],col=cols[2],...)
}
}
}
plot.fads.k12fun<-function(x,opt=c("all","L","K","n","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
#ifelse(!is.null(x$call[["nsim"]]),ci<-TRUE,ci<-FALSE)
ifelse(!is.null(x$call$nsim)&&(x$call$nsim>0),ci<-TRUE,ci<-FALSE)
if(is.null(x$call[["H0"]])||(x$call[["H0"]]=="pitor")) h0<-"PI-tor"
else if(x$call[["H0"]]=="pimim") h0<-"PI-mim"
else h0<-"RL"
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
opt<-opt[1]
if(opt=="all")
mylayout<-layout(matrix(c(1,1,1,1,2,2,3,3,2,2,3,3,4,4,5,5,4,4,5,5),ncol=4,byrow=TRUE))
else if(opt%in%c("L","K","n","g"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
else
stopifnot(opt%in%c("all","L","K","n","g"))
if(missing(cols))
cols=c(1,2,3)
else if(length(cols)!=3)
cols=c(cols,cols,cols)
if(missing(lty))
lty=c(1,3,2)
else if(length(lty)!=3)
lty=c(lty,lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-c("pair density function","second-order neighbour density function","intertype function","modified intertype function : sqrt[K12(r)/pi]-r")
if(ci) {
alpha<-x$call[["alpha"]]
p<-ifelse(!is.null(alpha),signif(100*(1-alpha),digits=6),99)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$g12$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs",paste("theo (",h0,")",sep=""),paste(p,"% CI of",h0)),cex=1.5,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.75*csize,csize))
if(opt%in%c("all","g")) { # g12-function
lim<-range(x$g12[,1:4])
plot(x$r,x$g12$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="g12(r)",cex.lab=1.25)
lines(x$r,x$g12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$g12$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$g12$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$g12$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","n")) { # n12-function
lim<-range(x$n12[,1:4])
plot(x$r,x$n12$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="n12(r)",cex.lab=1.25)
lines(x$r,x$n12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$n12$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$n12$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$n12$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","K")) { # K-function
plot(x$r,x$k12$obs,ylim=range(x$k12[,1:4]),main=paste("\n\n",sub[3]),type="n",xlab="distance (r)",ylab="K12(r)",cex.lab=1.25)
lines(x$r,x$k12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$k12$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$k12$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$k12$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","L")) { # L-function
lim<-range(x$l12[,1:4])
plot(x$r,x$l12$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[4]),type="n",xlab="distance (r)",ylab="L12(r)",cex.lab=1.25)
lines(x$r,x$l12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$l12$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$l12$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$l12$inf,lty=lty[3],col=cols[3],...)
}
}
else {
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$g12$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs",paste("theo (",h0,")",sep="")),cex=1.5,lty=lty[1:2],bty="n",horiz=TRUE,title=main,col=cols[1:2],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.75*csize,csize))
if(opt%in%c("all","g")) { # g-function
lim<-range(x$g12)
plot(x$r,x$g12$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance step (r)",ylab="g12(r)",cex.lab=1.25,...)
lines(x$r,x$g12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$g12$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","n")) { # n-function
lim<-range(x$n12)
plot(x$r,x$n12$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[2]),type="n",xlab="distance step (r)",ylab="n12(r)",cex.lab=1.25,...)
lines(x$r,x$n12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$n12$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","K")) { # k-function
plot(x$r,x$k12$obs,ylim=range(x$k),main=paste("\n\n",sub[3]),type="n",xlab="distance step (r)",ylab="K12(r)",cex.lab=1.25,...)
lines(x$r,x$k12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$k12$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","L")) { # L-function
lim<-range(x$l12)
plot(x$r,x$l12$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[4]),type="n",xlab="distance step (r)",ylab="L12(r)",cex.lab=1.25,...)
lines(x$r,x$l12$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$l12$theo,lty=lty[2],col=cols[2],...)
}
}
}
plot.fads.kpqfun<-function (x,opt=c("L","K","n","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
na<-length(x$labpq)
nf<-ceiling(sqrt(na))
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
opt<-opt[1]
if(opt=="g") {
val<-x$gpq
theo<-matrix(rep(rep(1,na),each=length(x$r)),ncol=na)
ylab=paste("gpq(r)",sep="")
}
if(opt=="n") {
val<-x$npq
theo<-matrix(rep(rep(x$intensity,nf),each=length(x$r)),ncol=na)
ylab=paste("npq(r)",sep="")
}
if(opt=="K") {
val<-x$kpq
theo<-matrix(rep(pi*x$r^2,na),ncol=na)
ylab=paste("Kpq(r)",sep="")
}
if(opt=="L") {
val<-x$lpq
theo<-matrix(rep(rep(0,na),each=length(x$r)),ncol=na)
ylab=paste("Lpq(r)",sep="")
}
if(missing(cols))
cols=c(1,2)
else if(length(cols)!=2)
cols=c(cols,cols)
if(missing(lty))
lty=c(1,3)
else if(length(lty)!=2)
lty=c(lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-x$labpq
lim<-range(val)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot.default(val[,1],val[,2]/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (CSR/PI)"),cex=1.5,lty=lty[1:2],bty="n",horiz=TRUE,title=main,col=cols[1:2],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=0.66*csize)
for(i in 1:na) {
plot(x$r,val[,i],ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[i]),type="n",xlab="distance (r)",ylab=ylab,cex.lab=1.25,...)
lines(x$r,val[,i],lty=lty[1],col=cols[1],...)
lines(x$r,theo[,i],lty=lty[2],col=cols[2],...)
}
}
plot.fads.kp.fun<-function (x,opt=c("L","K","n","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
na<-length(x$labp)
nf<-ceiling(sqrt(na))
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
mylayout<-layout(matrix(c(rep(1,nf),seq(2,((nf*nf)+1),1)),(nf+1),nf,byrow=TRUE))
opt<-opt[1]
if(opt=="g") {
val<-x$gp.
theo<-matrix(rep(rep(1,na),each=length(x$r)),ncol=na)
ylab=paste("gp.(r)",sep="")
}
if(opt=="n") {
val<-x$np.
intensity<-sum(x$intensity)-x$intensity
theo<-matrix(rep(intensity,each=length(x$r)),ncol=na)
ylab=paste("np.(r)",sep="")
}
if(opt=="K") {
val<-x$kp.
theo<-matrix(rep(pi*x$r^2,na),ncol=na)
ylab=paste("Kp.(r)",sep="")
}
if(opt=="L") {
val<-x$lp.
theo<-matrix(rep(rep(0,na),each=length(x$r)),ncol=na)
ylab=paste("Lp.(r)",sep="")
}
if(missing(cols))
cols=c(1,2)
else if(length(cols)!=2)
cols=c(cols,cols)
if(missing(lty))
lty=c(1,3)
else if(length(lty)!=2)
lty=c(lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-paste(x$labp,"-all others",sep="")
lim<-range(val)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot.default(val[,1],val[,2]/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (PI)"),cex=1.5,lty=lty[1:2],bty="n",horiz=TRUE,title=main,col=cols[1:2],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=0.66*csize)
for(i in 1:na) {
plot(x$r,val[,i],ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[i]),type="n",xlab="distance (r)",ylab=ylab,cex.lab=1.25,...)
lines(x$r,val[,i],lty=lty[1],col=cols[1],...)
lines(x$r,theo[,i],lty=lty[2],col=cols[2],...)
}
}
plot.fads.kmfun<-function (x,opt=c("all","K","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
ifelse(!is.null(x$call$nsim)&&(x$call$nsim>0),ci<-TRUE,ci<-FALSE)
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
opt<-opt[1]
if(opt=="all")
mylayout<-layout(matrix(c(1,1,1,1,rep(2,8),rep(3,8)),ncol=4,byrow=TRUE))
else if(opt%in%c("K","g"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
else
stopifnot(opt%in%c("all","K","g"))
if(missing(cols))
cols=c(1,2,3)
else if(length(cols)!=3)
cols=c(cols,cols,cols)
if(missing(lty))
lty=c(1,3,2)
else if(length(lty)!=3)
lty=c(lty,lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-c("pair correlation function","mark correlation function")
if(ci) {
alpha<-x$call[["alpha"]]
p<-ifelse(!is.null(alpha),signif(100*(1-alpha),digits=6),99)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gm$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (IM)",paste(p,"% CI of IM")),cex=1.5,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gm-function
lim<-range(x$gm[,1:4])
plot(x$r,x$gm$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gm(r)",cex.lab=1.25,...)
lines(x$r,x$gm$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gm$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$gm$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$gm$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","K")) { # K-function
plot(x$r,x$km$obs,ylim=range(x$km[,1:4]),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Km(r)",cex.lab=1.25,...)
lines(x$r,x$km$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$km$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$km$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$km$inf,lty=lty[3],col=cols[3],...)
}
}
else {
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gm$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (IM)"),cex=1.5,lty=lty[1:2],bty="n",horiz=TRUE,title=main,col=cols[1:2],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # g-function
lim<-range(x$gm)
plot(x$r,x$gm$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gm(r)",cex.lab=1.25,...)
lines(x$r,x$gm$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gm$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","K")) { # k-function
plot(x$r,x$km$obs,ylim=range(x$km),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Km(r)",cex.lab=1.25,...)
lines(x$r,x$km$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$km$theo,lty=lty[2],col=cols[2],...)
}
}
}
plot.fads.ksfun<-function (x,opt=c("all","K","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
ifelse(!is.null(x$call$nsim)&&(x$call$nsim>0),ci<-TRUE,ci<-FALSE)
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
opt<-opt[1]
if(opt=="all")
mylayout<-layout(matrix(c(1,1,1,1,rep(2,8),rep(3,8)),ncol=4,byrow=TRUE))
else if(opt%in%c("K","g"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
else
stopifnot(opt%in%c("all","K","g"))
# opt<-opt[1]
# if(opt=="all")
# mylayout<-layout(matrix(c(1,1,1,1,2,2,3,3,2,2,3,3,4,4,4,4,4,4,4,4),ncol=4,byrow=TRUE))
# else if(opt%in%c("K","P","g"))
# mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
# else
# stopifnot(opt%in%c("all","K","P","g"))
if(missing(cols))
cols=c(1,2,3)
else if(length(cols)!=3)
cols=c(cols,cols,cols)
if(missing(lty))
lty=c(1,3,2)
else if(length(lty)!=3)
lty=c(lty,lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-c("Standardized Shimatani non-cumulative (beta) function","Standardized Shimatani cumulative (alpha) function")
if(ci) {
alpha<-x$call[["alpha"]]
p<-ifelse(!is.null(alpha),signif(100*(1-alpha),digits=6),99)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gs$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (RL)",paste(p,"% CI of RL",sep="")),cex=1.3,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gs-function
lim<-range(x$gs[,1:4])
plot(x$r,x$gs$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gs(r)",cex.lab=1.25,...)
lines(x$r,x$gs$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gs$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$gs$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$gs$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","K")) { # Ks-function
plot(x$r,x$ks$obs,ylim=range(x$ks[,1:4]),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Ks(r)",cex.lab=1.25,...)
lines(x$r,x$ks$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$ks$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$ks$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$ks$inf,lty=lty[3],col=cols[3],...)
}
}
else {
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gs$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (RL)"),cex=1.3,lty=lty[1:2],bty="n",horiz=TRUE,title=main,col=cols[1:2],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gs-function
lim<-range(x$gs)
plot(x$r,x$gs$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gs(r)",cex.lab=1.25,...)
lines(x$r,x$gs$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gs$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","K")) { # ks-function
plot(x$r,x$ks$obs,ylim=range(x$ks),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Ks(r)",cex.lab=1.25,...)
lines(x$r,x$ks$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$ks$theo,lty=lty[2],col=cols[2],...)
}
}
}
plot.fads.krfun<-function (x,opt=c("all","K","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
ifelse(!is.null(x$call$nsim)&&(x$call$nsim>0),ci<-TRUE,ci<-FALSE)
ifelse((is.null(x$call[["H0"]])||(x$call[["H0"]]=="rl")),h0<-"RL",h0<-"SE")
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
opt<-opt[1]
if(opt%in%c("all"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,8),rep(3,8)),ncol=4,byrow=TRUE))
else if(opt%in%c("K","g"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
else
stopifnot(opt%in%c("all","K","g"))
if(missing(cols))
cols=c(1,2,3)
else if(length(cols)!=3)
cols=c(cols,cols,cols)
if(missing(lty))
lty=c(1,3,2)
else if(length(lty)!=3)
lty=c(lty,lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-c("Standardized Rao non-cumulative function","Standardized Rao cumulative function")
if(ci) {
alpha<-x$call[["alpha"]]
p<-ifelse(!is.null(alpha),signif(100*(1-alpha),digits=6),99)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gr$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs",paste("theo (",h0,")",sep=""),paste(p,"% CI of",h0)),cex=1.3,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gr-function
lim<-range(x$gr[,1:4])
plot(x$r,x$gr$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gr(r)",cex.lab=1.25,...)
lines(x$r,x$gr$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gr$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$gr$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$gr$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","K")) { # Kr-function
plot(x$r,x$kr$obs,ylim=range(x$kr[,1:4]),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Kr(r)",cex.lab=1.25,...)
lines(x$r,x$kr$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$kr$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$kr$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$kr$inf,lty=lty[3],col=cols[3],...)
}
}
else {
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gr$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs",paste("theo (",h0,")",sep="")),cex=1.3,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gr-function
lim<-range(x$gr)
plot(x$r,x$gr$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gr(r)",cex.lab=1.25,...)
lines(x$r,x$gr$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gr$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","K")) { # kr-function
plot(x$r,x$kr$obs,ylim=range(x$kr),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Kr(r)",cex.lab=1.25,...)
lines(x$r,x$kr$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$kr$theo,lty=lty[2],col=cols[2],...)
}
}
}
plot.fads.kdfun<-function (x,opt=c("all","K","g"),cols,lty,main,sub,legend=TRUE,csize=1,...) {
ifelse(!is.null(x$call$nsim)&&(x$call$nsim>0),ci<-TRUE,ci<-FALSE)
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
#if(options()$device=="windows")
# csize<-0.75*csize
opt<-opt[1]
if(opt%in%c("all"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,8),rep(3,8)),ncol=4,byrow=TRUE))
else if(opt%in%c("K","g"))
mylayout<-layout(matrix(c(1,1,1,1,rep(2,16)),ncol=4,byrow=TRUE))
else
stopifnot(opt%in%c("all","K","g"))
if(missing(cols))
cols=c(1,2,3)
else if(length(cols)!=3)
cols=c(cols,cols,cols)
if(missing(lty))
lty=c(1,3,2)
else if(length(lty)!=3)
lty=c(lty,lty,lty)
if(missing(main))
main<-deparse(x$call,width.cutoff=100)
if(missing(sub))
sub<-c("Standardized Shen non-cumulative function","Standardized Shen cumulative function")
if(ci) {
alpha<-x$call[["alpha"]]
p<-ifelse(!is.null(alpha),signif(100*(1-alpha),digits=6),99)
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gd$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (SE)",paste(p,"% CI of SE")),cex=1.3,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gd-function
lim<-range(x$gd[,1:4])
plot(x$r,x$gd$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gd(r)",cex.lab=1.25,...)
lines(x$r,x$gd$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gd$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$gd$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$gd$inf,lty=lty[3],col=cols[3],...)
}
if(opt%in%c("all","K")) { # Kd-function
plot(x$r,x$kd$obs,ylim=range(x$kd[,1:4]),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Kd(r)",cex.lab=1.25,...)
lines(x$r,x$kd$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$kd$theo,lty=lty[2],col=cols[2],...)
lines(x$r,x$kd$sup,lty=lty[3],col=cols[3],...)
lines(x$r,x$kd$inf,lty=lty[3],col=cols[3],...)
}
}
else {
par(mar=c(0.1,0.1,0.1,0.1),cex=csize)
plot(x$r,x$gd$obs/2,type="n",axes=FALSE,xlab="",ylab="")
if(legend)
legend("center",c("obs","theo (SE)"),cex=1.3,lty=lty[1:3],bty="n",horiz=TRUE,title=main,col=cols[1:3],...)
else
legend("center","",cex=1.5,bty="n",horiz=TRUE,title=main,...)
par(mar=c(5,5,0.1,2),cex=ifelse(opt%in%c("all"),0.85*csize,csize))
if(opt%in%c("all","g")) { # gd-function
lim<-range(x$gd)
plot(x$r,x$gd$obs,ylim=c(lim[1],lim[2]+0.1*diff(lim)),main=paste("\n\n",sub[1]),type="n",xlab="distance (r)",ylab="gd(r)",cex.lab=1.25,...)
lines(x$r,x$gd$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$gd$theo,lty=lty[2],col=cols[2],...)
}
if(opt%in%c("all","K")) { # Kd-function
plot(x$r,x$kd$obs,ylim=range(x$kd),main=paste("\n\n",sub[2]),type="n",xlab="distance (r)",ylab="Kd(r)",cex.lab=1.25,...)
lines(x$r,x$kd$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$kd$theo,lty=lty[2],col=cols[2],...)
}
}
}
plot.fads.mimetic<-function (x,opt=NULL,cols,lty,main,sub,legend=TRUE,csize=1,cex.main=1.5,pos,...) {
if(missing(cols))
cols=c(1,2)
else if(length(cols)!=2)
cols=c(cols,cols)
if(missing(lty))
lty=c(1,1)
else if(length(lty)!=2)
lty=c(lty,lty)
if(missing(main)) {
call<-match.call()
main<-deparse(eval(eval(expression(call))[[2]][[2]])$call,width.cutoff=100)
}
plot(x$r,x$l$obs,ylim=range(rbind(x$l$obs,x$l$sim)),main=main,type="n",xlab="distance (r)",ylab="L(r)",cex.lab=1.25,cex.main=cex.main,...)
lines(x$r,x$l$obs,lty=lty[1],col=cols[1],...)
lines(x$r,x$l$sim,lty=lty[2],col=cols[2],...)
if(legend)
legend(pos,c("obs","sim"),cex=1.5,lty=lty[1:2],bty="n",horiz=TRUE,col=cols[1:2],...)
}
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