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"read.yesno" <-
function (string, default=TRUE)
{
wrd <- ifelse(default, " (Y/n)?\n:", " (y/N)?\n:")
cat("\n", string, wrd, sep = "")
ans <- readline()
val <- if (default)
pmatch(ans, c("no","NO"), nomatch=0) == 0
else
pmatch(ans, c("yes","YES"), nomatch=0) != 0
return(val)
}
"change.tfoption" <-
function (string, option)
{
current.value <- coda.options(option)
if (!is.logical(current.value))
stop("Invalid option: must take logical values")
new.value <- read.yesno(string, current.value)
if (new.value != current.value) {
arg <- list(new.value)
names(arg) <- option
coda.options(arg)
}
return()
}
"coda.options" <-
function (...)
{
## Set and display coda options
single <- FALSE
copt <- if (exists(".Coda.Options", frame = 1)) {
if (is.R())
get(".Coda.Options", pos=1)
else
get(".Coda.Options")
}
else {
.Coda.Options.Default
}
if (nargs() == 0) {
return(copt)
}
else {
args <- list(...)
if (length(args) == 1) {
if (is.list(args[[1]]))
args <- args[[1]]
else if (is.null(names(args)))
single <- TRUE
}
}
if (is.null(names(args))) {
## Display options
args <- unlist(args)
value <- vector("list", length(args))
names(value) <- args
for (v in args) if (any(v == names(copt)))
value[v] <- copt[v]
if (single)
return(value[[1]])
else return(value)
}
else {
## Set options
oldvalue <- vector("list", length(args))
names(oldvalue) <- names(args)
if (any(names(args) == "default") && args$default ==
TRUE)
copt <- .Coda.Options.Default
for (v in names(args)) if (any(v == names(copt))) {
oldvalue[v] <- copt[v]
if (is.null(args[[v]]))
copt[v] <- list(NULL)
else if (mode(copt[[v]]) == mode(args[[v]]))
copt[v] <- args[v]
}
if (is.R())
assign(".Coda.Options", copt, pos=1)
else
assign(".Coda.Options", copt)
invisible(oldvalue)
}
}
"multi.menu" <- function (choices, title, header, allow.zero = TRUE)
{
## Select more than one value from a menu
##
if (!missing(title))
cat(title, "\n\n")
mat <- matrix(c(1:length(choices), choices), ncol = 2)
if (!missing(header)) {
if (length(header) == 2)
mat <- rbind(header, mat)
else stop("header is wrong length")
}
cat(paste(format(mat[, 1]), format(mat[, 2])), sep = "\n")
repeat {
cat("\nEnter relevant number(s), separated by commas",
"Ranges such as 3:7 may be specified)", sep = "\n")
if (allow.zero)
cat("(Enter 0 for none)\n")
ans <- scan(what = character(), sep = ",", strip.white = TRUE,
nlines = 1, quiet = TRUE)
if (length(ans) > 0) {
out <- numeric(0)
for (i in 1:length(ans)) {
nc <- nchar(ans[i])
wrd <- substring(ans[i], 1:nc, 1:nc)
colons <- wrd == ":"
err <- any(is.na(as.numeric(wrd[!colons]))) |
sum(colons) > 1 | colons[1] | colons[nc]
if (err) {
cat("Error: you have specified a non-numeric value!\n")
break
}
else {
out <- c(out, eval(parse(text = ans[i])))
if (min(out) < ifelse(allow.zero, 0, 1) | max(out) >
length(choices) | (any(out == 0) & length(out) >
1)) {
err <- TRUE
cat("Error: you have specified variable number(s) out of range!\n")
break
}
}
}
if (!err)
break
}
}
return(out)
}
"read.and.check" <-
function (message = "", what = numeric(), lower, upper, answer.in, default)
{
## Read data from the command line and check that it satisfies
## certain conditions. The function will loop until it gets
## and answer satisfying the conditions. This entails extensive
## checking of the conditions to make sure they are consistent
## so we don't end up in an infinite loop.
have.lower <- !missing(lower)
have.upper <- !missing(upper)
have.ans.in <- !missing(answer.in)
have.default <- !missing(default)
if (have.lower | have.upper) {
if (!is.numeric(what))
stop("Can't have upper or lower limits with non numeric input")
if (have.lower && !is.numeric(lower))
stop("lower limit not numeric")
if (have.upper && !is.numeric(upper))
stop("upper limit not numeric")
if ((have.upper & have.lower) && upper < lower)
stop("lower limit greater than upper limit")
}
if (have.ans.in) {
if (mode(answer.in) != mode(what))
stop("inconsistent values of what and answer.in")
if (have.lower)
answer.in <- answer.in[answer.in >= lower]
if (have.upper)
answer.in <- answer.in[answer.in <= upper]
if (length(answer.in) == 0)
stop("No possible response matches conditions")
}
if (have.default) {
if (mode(default) != mode(what))
stop("inconsistent values of what and default")
if (have.lower && default < lower)
stop("default value below lower limit")
if (have.upper && default > upper)
stop("default value above upper limit")
if (have.ans.in && !any(answer.in == default))
stop("default value does not satisfy conditions")
}
err <- TRUE
while (err) {
if (nchar(message) > 0) {
cat("\n", message, "\n", sep = "")
if (have.default)
cat("(Default = ", default, ")\n", sep = "")
}
repeat {
cat("1:")
ans <- readline()
if (length(ans) == 1 && nchar(ans) > 0)
break
else if (have.default) {
ans <- default
break
}
}
if (is.numeric(what)) {
err1 <- TRUE
ans <- as.numeric(ans)
message <- "You must enter a number"
if (is.na(ans))
NULL
else if ((have.lower & have.upper) && (ans < lower |
ans > upper))
message <- paste(message, "between", lower, "and",
upper)
else if (have.lower && ans < lower)
message <- paste(message, ">=", lower)
else if (have.upper && ans > upper)
message <- paste(message, "<=", upper)
else err1 <- FALSE
}
else err1 <- FALSE
if (have.ans.in) {
if (!is.na(ans) && !any(ans == answer.in)) {
message <- paste("You must enter one of the following:",
paste(answer.in, collapse = ","))
err2 <- TRUE
}
else err2 <- FALSE
}
else err2 <- FALSE
err <- err1 | err2
}
return(ans)
}
".Coda.Options.Default" <-
list(trace = TRUE,
densplot = TRUE,
lowess = FALSE,
combine.plots = TRUE,
bandwidth = function (x)
{
x <- x[!is.na(x)]
1.06 * min(sd(x), IQR(x)/1.34) * length(x)^-0.2
},
digits = 3,
quantiles = c(0.025, 0.25, 0.5, 0.75, 0.975),
frac1 = 0.1,
frac2 = 0.5,
q = 0.025,
r = 0.005,
s = 0.95,
combine.stats = FALSE,
combine.corr = FALSE,
halfwidth = 0.1,
user.layout = FALSE,
gr.bin = 10,
geweke.nbin = 20,
gr.max = 50,
data.saved = TRUE
)
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