### * <HEADER>
###
attach(NULL, name = "CheckExEnv")
assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
## add some hooks to label plot pages for base and grid graphics
setHook("plot.new", ".newplot.hook")
setHook("persp", ".newplot.hook")
setHook("grid.newpage", ".gridplot.hook")

assign("cleanEx",
       function(env = .GlobalEnv) {
	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
           RNGkind("default", "default")
	   set.seed(1)
   	   options(warn = 1)
	   assign("T", delay(stop("T used instead of TRUE")),
		  pos = .CheckExEnv)
	   assign("F", delay(stop("F used instead of FALSE")),
		  pos = .CheckExEnv)
	   sch <- search()
	   newitems <- sch[! sch %in% .oldSearch]
	   for(item in rev(newitems))
               eval(substitute(detach(item), list(item=item)))
	   missitems <- .oldSearch[! .oldSearch %in% sch]
	   if(length(missitems))
	       warning("items ", paste(missitems, collapse=", "),
		       " have been removed from the search path")
       },
       env = .CheckExEnv)
assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
assign("ptime", proc.time(), env = .CheckExEnv)
grDevices::postscript("NPBayes-Examples.ps")
assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
library('NPBayes')

assign(".oldSearch", search(), env = .CheckExEnv)
assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
cleanEx(); ..nameEx <- "Lemma1"

### * Lemma1

flush(stderr()); flush(stdout())

### Name: Lemma1
### Title: Conditional expectation with respect to a Dirichlet process
###   prior, given right censored data.
### Aliases: Lemma1
### Keywords: nonparametric survival

### ** Examples

uncensored <- c(1,5,9)
rightcensored <- c(4,7)
NPBayes(B=12, theta=0.2, u=3.2, uncen=uncensored, rightcen=rightcensored)

leftpt <- 0
rightpt <- 3
NPBayes(B=12, theta=0.2, u=3.2, uncen=uncensored, rightcen=rightcensored, 
lefts = leftpt, rights = rightpt)



cleanEx(); ..nameEx <- "NPBayes"

### * NPBayes

flush(stderr()); flush(stdout())

### Name: NPBayes
### Title: Nonparametric Bayes estimate of CDF from arbitrary censored data
### Aliases: NPBayes
### Keywords: nonparametric survival

### ** Examples

uncensored <- c(1,5,9)
rightcensored <- c(4,7)
NPBayes(B=12, theta=0.2, u=3.2, uncen=uncensored, rightcen=rightcensored)

leftpt <- 0
rightpt <- 3
NPBayes(B=12, theta=0.2, u=3.2, uncen=uncensored, rightcen=rightcensored, 
lefts = leftpt, rights = rightpt)



cleanEx(); ..nameEx <- "NPBayesT"

### * NPBayesT

flush(stderr()); flush(stdout())

### Name: NPBayesT
### Title: Nonparametric Bayes estimate of CDF from left truncated, right
###   censored data
### Aliases: NPBayesT
### Keywords: nonparametric survival

### ** Examples

trunc <- c(2,4,10)
xtime <- c(9,13,15)
d <- c(1,0,0) 
NPBayesT(B=8, theta=0.12, u=3.2, y=trunc, x=xtime, status=d)
#you should get 0.6955968 as the Bayes estimator

ui <- seq(0.1, 20, 0.1)
fui <- ui
for(i in 1:200) 
   fui[i] <- NPBayesT(B=8, theta=0.12, u=ui[i],y=trunc, x=xtime, status=d)
#plot(ui, fui)

ypsy <- c(51, 58, 55, 28, 25, 48, 47, 25, 31, 30, 33, 43, 45, 35, 36)
xpsy <- c(52, 59, 57, 50, 57, 59, 61, 61, 62, 67, 68, 69, 69, 65, 76)
dpsy <- c(1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1 ) 
NPBayesT(B=8,theta=0.02,u=56,y=ypsy,x=xpsy,status=dpsy)



cleanEx(); ..nameEx <- "NPBayesT2"

### * NPBayesT2

flush(stderr()); flush(stdout())

### Name: NPBayesT2
### Title: Nonparametric Bayes estimate of CDF from left truncated, right
###   censored data
### Aliases: NPBayesT2
### Keywords: nonparametric survival

### ** Examples

trunc <- c(2,4,10)
xtime <- c(9,13,15)
d <- c(1,0,0) 
NPBayesT(B=8, theta=0.12, u=3.2, y=trunc, x=xtime, status=d)

ui <- seq(0.1, 20, 0.1)
fui <- ui
for(i in 1:200) 
   fui[i] <- NPBayesT(B=8, theta=0.12, u=ui[i],y=trunc, x=xtime, status=d)
#plot(ui, fui)

ypsy <- c(51, 58, 55, 28, 25, 48, 47, 25, 31, 30, 33, 43, 45, 35, 36)
xpsy <- c(52, 59, 57, 50, 57, 59, 61, 61, 62, 67, 68, 69, 69, 65, 76)
dpsy <- c(1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1 ) 
NPBayesT(B=8,theta=0.02,u=56,y=ypsy,x=xpsy,status=dpsy)



cleanEx(); ..nameEx <- "NewLemma1"

### * NewLemma1

flush(stderr()); flush(stdout())

### Name: NewLemma1
### Title: Compute the Conditional Expectation given left truncated and
###   right censored observations
### Aliases: NewLemma1
### Keywords: nonparametric survival

### ** Examples

uncensored <- c(1,5,9)
rightcensored <- c(4,7)
NPBayes(B=12, theta=0.2, u=3.2, uncen=uncensored, rightcen=rightcensored)

leftpt <- 0
rightpt <- 3
NPBayes(B=12, theta=0.2, u=3.2, uncen=uncensored, rightcen=rightcensored, 
lefts = leftpt, rights = rightpt)



### * <FOOTER>
###
cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')