R/plotPredIntNparDesign.R

In EnvStats: Package for Environmental Statistics, Including US EPA Guidance

plotPredIntNparDesign <-
function (x.var = "n", y.var = "conf.level", range.x.var = NULL, 
    n = max(25, lpl.rank + n.plus.one.minus.upl.rank + 1), k = 1, 
    m = ifelse(x.var == "k", ceiling(max.x), 1), conf.level = 0.95, 
    pi.type = "two.sided", lpl.rank = ifelse(pi.type == "upper", 
        0, 1), n.plus.one.minus.upl.rank = ifelse(pi.type == 
        "lower", 0, 1), n.max = 5000, maxiter = 1000, plot.it = TRUE, 
    add = FALSE, n.points = 100, plot.col = "black", plot.lwd = 3 * 
        par("cex"), plot.lty = 1, digits = .Options$digits, cex.main = par("cex"), 
    ..., main = NULL, xlab = NULL, ylab = NULL, type = "l") 
{
    x.var <- match.arg(x.var, c("n", "conf.level", "k", "m"))
    y.var <- match.arg(y.var, c("conf.level", "n"))
    pi.type <- match.arg(pi.type, c("two.sided", "lower", "upper"))
    if (x.var == y.var) 
        stop("'x.var' and 'y.var' cannot denote the same quantity")
    if (missing(range.x.var)) {
        range.x.var <- switch(x.var, n = {
            c(if (pi.type == "two.sided") lpl.rank + n.plus.one.minus.upl.rank + 
                1 else if (pi.type == "lower") lpl.rank + 1 else n.plus.one.minus.upl.rank + 
                1, 50)
        }, conf.level = c(0.5, 0.99), k = c(1, 20), m = c(1, 
            20))
    }
    else {
        if (is.null(range.x.var) || !all(is.finite(range.x.var)) || 
            !is.vector(range.x.var, mode = "numeric") || length(range.x.var) != 
            2) 
            stop(paste("'range.x.var' must be a numeric vector of length 2", 
                "with no missing (NA), infinite(-Inf, Inf), or undefined(NaN) values"))
    }
    min.x <- range.x.var[1]
    max.x <- range.x.var[2]
    if (min.x >= max.x) 
        stop("The second element of 'range.x.var' must be larger than the first")
    if (!is.vector(n.points, mode = "numeric") || length(n.points) != 
        1 || n.points != trunc(n.points) || n.points < 2) 
        stop("'n.points' must be an integer larger than 1")
    switch(x.var, n = {
        if (min.x < 2 || min.x != trunc(min.x)) stop(paste("When x.var=\"n\" the first element of", 
            "range.x.var must be an integer greater than 1"))
        if (max.x != trunc(max.x)) stop(paste("When x.var=\"n\" the second element of", 
            "range.x.var must be an integer greater than", "the first element of range.x.var"))
    }, conf.level = {
        if (min.x < .Machine$double.eps || min.x > 1 - .Machine$double.eps) stop(paste("When x.var=\"conf.level\" the first element of range.x.var", 
            "must be a positive number between 0 and 1"))
        if (max.x > 1 - .Machine$double.eps) stop(paste("When x.var=\"conf.level\" the second element of", 
            "range.x.var must be an positive number between 0 and 1", 
            "and greater than the first element of range.x.var"))
    }, k = {
        if (min.x < 1 || min.x != trunc(min.x)) stop(paste("When x.var=\"k\" the first element of", 
            "range.x.var must be an integer greater than 0"))
        if (max.x != trunc(max.x)) stop(paste("When x.var=\"k\" the second element of", 
            "range.x.var must be an integer greater than", "the first element of range.x.var"))
    }, m = {
        if (min.x < 1 || min.x != trunc(min.x)) stop(paste("When x.var=\"m\" the first element of", 
            "range.x.var must be an integer greater than 0"))
        if (max.x != trunc(max.x)) stop(paste("When x.var=\"m\" the second element of", 
            "range.x.var must be an integer greater than", "the first element of range.x.var"))
    })
    if (pi.type == "upper") 
        lpl.rank <- 0
    else if (pi.type == "lower") 
        n.plus.one.minus.upl.rank <- 0
    if (length(lpl.rank) != 1 || !is.vector(lpl.rank, mode = "numeric") || 
        !is.finite(lpl.rank) || lpl.rank != trunc(lpl.rank) || 
        lpl.rank < 0) 
        stop("'lpl.rank' must be a non-negative integer")
    if (pi.type %in% c("two.sided", "lower") & lpl.rank < 1) 
        stop("When pi.type='two.sided' or pi.type='lower', 'lpl.rank' must be a positive integer")
    if (length(n.plus.one.minus.upl.rank) != 1 || !is.vector(n.plus.one.minus.upl.rank, 
        mode = "numeric") || !is.finite(n.plus.one.minus.upl.rank) || 
        n.plus.one.minus.upl.rank != trunc(n.plus.one.minus.upl.rank) || 
        n.plus.one.minus.upl.rank < 0) 
        stop("'n.plus.one.minus.upl.rank' must be a non-negative integer")
    if (pi.type %in% c("two.sided", "upper") & n.plus.one.minus.upl.rank < 
        1) 
        stop("When pi.type='two.sided' or pi.type='upper', 'n.plus.one.minus.upl.rank' must be a positive integer")
    if (x.var != "n" && y.var != "n") {
        if (is.null(n) || !is.finite(n) || !is.vector(n, mode = "numeric") || 
            length(n) != 1 || n < 2 || n != trunc(n)) 
            stop("'n' must be an integer greater than 1")
        if (pi.type == "two.sided" || pi.type == "lower") {
            if (lpl.rank >= n) 
                stop("'lpl.rank' must be less than 'n'")
        }
        if (pi.type == "two.sided" || pi.type == "upper") {
            if (n.plus.one.minus.upl.rank >= n) 
                stop("'n.plus.one.minus.upl.rank' must be less than 'n'")
        }
        if (pi.type == "two.sided") {
            upl.rank <- n + 1 - n.plus.one.minus.upl.rank
            if (lpl.rank >= upl.rank) 
                stop(paste("Illegal values for 'lpl.rank' and 'n.plus.one.minus.upl.rank'.", 
                  "Make one or both of them smaller"))
        }
    }
    if (x.var != "conf.level" && y.var != "conf.level") {
        if (is.null(conf.level) || !is.finite(conf.level) || 
            !is.vector(conf.level, mode = "numeric") || length(conf.level) != 
            1 || conf.level <= .Machine$double.eps || conf.level >= 
            1 - .Machine$double.eps) {
            stop("'conf.level' must be a scalar between 0 and 1")
        }
    }
    if (x.var != "m") {
        if (is.null(m) || !is.finite(m) || !is.vector(m, mode = "numeric") || 
            length(m) != 1 || m < 1 || m != trunc(m)) 
            stop("'m' must be a positive integer")
    }
    if (x.var != "k") {
        if (is.null(k) || !is.finite(k) || !is.vector(k, mode = "numeric") || 
            length(k) != 1 || k < 1 || k != trunc(k)) 
            stop("'k' must be a positive integer")
    }
    if (x.var != "k" && x.var != "m" && k > m) 
        stop("'k' must be less than or equal to 'm'")
    if (x.var == "k" && max.x > m) 
        stop(paste("When x.var=\"k\" 'max.x' must be", "less than or equal to 'm'"))
    if (x.var == "m" && min.x < k) 
        stop(paste("When x.var=\"m\" 'min.x' must be", "greater than or equal to 'k'"))
    if (!is.vector(maxiter, mode = "numeric") || length(maxiter) != 
        1 || !is.finite(maxiter) || maxiter != trunc(maxiter) || 
        maxiter < 1) 
        stop("'maxiter' must be a positive integer")
    pi.string <- switch(pi.type, two.sided = "(Two-Sided PI)", 
        lower = "(One-Sided Lower PI)", upper = "(One-Sided Upper PI)")
    n.string <- paste("n =", n)
    conf.string <- paste("Confidence Level = ", format(100 * 
        conf.level, digits = digits), "%", sep = "")
    k.string <- paste("k =", k)
    m.string <- paste("m =", m)
    if (x.var != "n" & y.var != "n") {
        upl.rank <- n + 1 - n.plus.one.minus.upl.rank
        rank.string <- switch(pi.type, two.sided = paste("Rank(LPL) =", 
            lpl.rank, "and Rank(UPL) =", upl.rank), lower = paste("Rank(LPL) =", 
            lpl.rank), upper = paste("Rank(UPL) =", upl.rank))
    }
    else {
        rank.string <- switch(pi.type, two.sided = paste("Rank(LPL) =", 
            lpl.rank, "and Rank(UPL) =", ifelse(n.plus.one.minus.upl.rank == 
                1, "n", paste("n -", n.plus.one.minus.upl.rank - 
                1))), lower = paste("Rank(LPL) =", lpl.rank), 
            upper = paste("Rank(UPL) =", ifelse(n.plus.one.minus.upl.rank == 
                1, "n", paste("n -", n.plus.one.minus.upl.rank - 
                1))))
    }
    if (plot.it) 
        gen.gp.list <- checkGraphicsPars(...)$gen.gp.list
    combo <- paste(c(x.var, y.var), collapse = " & ")
    switch(combo, `n & conf.level` = {
        x <- seq(min.x, max.x, by = ceiling((max.x - min.x + 
            1)/n.points))
        if (is.null(xlab)) xlab <- "Sample Size (n)"
        y <- predIntNparConfLevel(n = x, k = k, m = m, lpl.rank = lpl.rank, 
            n.plus.one.minus.upl.rank = n.plus.one.minus.upl.rank, 
            pi.type = pi.type)
        if (is.null(ylab)) ylab <- "Confidence Level"
        line1 <- paste("Confidence Level vs. Sample Size for", 
            "Nonparametric Prediction Interval")
        line2 <- paste("for ", k.string, ", ", m.string, " ", 
            pi.string, sep = "")
        line3 <- rank.string
    }, `conf.level & n` = {
        x <- seq(min.x, max.x, length = n.points)
        if (is.null(xlab)) xlab <- "Confidence Level"
        y <- predIntNparN(k = k, m = m, lpl.rank = lpl.rank, 
            n.plus.one.minus.upl.rank = n.plus.one.minus.upl.rank, 
            pi.type = pi.type, conf.level = x, n.max = n.max, 
            maxiter = maxiter)
        if (is.null(ylab)) ylab <- "Sample Size (n)"
        line1 <- paste("Sample Size vs. Confidence Level for", 
            "Nonparametric Prediction Interval")
        line2 <- paste("for ", k.string, ", ", m.string, " ", 
            pi.string, sep = "")
        line3 <- rank.string
    }, `k & conf.level` = {
        x <- seq(min.x, max.x, by = ceiling((max.x - min.x + 
            1)/n.points))
        if (is.null(xlab)) xlab <- "Min # Future Obs PI Should Contain (k)"
        y <- predIntNparConfLevel(n = n, k = x, m = m, lpl.rank = lpl.rank, 
            n.plus.one.minus.upl.rank = n.plus.one.minus.upl.rank, 
            pi.type = pi.type)
        if (is.null(ylab)) ylab <- "Confidence Level"
        line1 <- paste("Confidence Level vs. Min # Future Obs for", 
            "Nonparametric Prediction Interval")
        line2 <- paste("for ", n.string, ", ", m.string, " ", 
            pi.string, sep = "")
        line3 <- rank.string
    }, `k & n` = {
        x <- seq(min.x, max.x, by = ceiling((max.x - min.x + 
            1)/n.points))
        if (is.null(xlab)) xlab <- "Min # Future Obs PI Should Contain (k)"
        y <- predIntNparN(k = x, m = m, lpl.rank = lpl.rank, 
            n.plus.one.minus.upl.rank = n.plus.one.minus.upl.rank, 
            pi.type = pi.type, conf.level = conf.level, n.max = n.max, 
            maxiter = maxiter)
        if (is.null(ylab)) ylab <- "Sample Size (n)"
        line1 <- paste("Sample Size vs. Min # Future Obs for", 
            "Nonparametric Prediction Interval")
        line2 <- paste("for ", m.string, ", ", conf.string, " ", 
            pi.string, sep = "")
        line3 <- rank.string
    }, `m & conf.level` = {
        x <- seq(min.x, max.x, by = ceiling((max.x - min.x + 
            1)/n.points))
        if (is.null(xlab)) xlab <- "# Future Obs (m)"
        y <- predIntNparConfLevel(n = n, k = k, m = x, lpl.rank = lpl.rank, 
            n.plus.one.minus.upl.rank = n.plus.one.minus.upl.rank, 
            pi.type = pi.type)
        if (is.null(ylab)) ylab <- "Confidence Level"
        line1 <- paste("Confidence Level vs. # Future Obs for", 
            "Nonparametric Prediction Interval")
        line2 <- paste("for ", n.string, ", ", k.string, " ", 
            pi.string, sep = "")
        line3 <- rank.string
    }, `m & n` = {
        x <- seq(min.x, max.x, by = ceiling((max.x - min.x + 
            1)/n.points))
        if (is.null(xlab)) xlab <- "# Future Obs (m)"
        y <- predIntNparN(k = k, m = x, lpl.rank = lpl.rank, 
            n.plus.one.minus.upl.rank = n.plus.one.minus.upl.rank, 
            pi.type = pi.type, conf.level = conf.level, n.max = n.max, 
            maxiter = maxiter)
        if (is.null(ylab)) ylab <- "Sample Size (n)"
        line1 <- paste("Sample Size vs. # Future Obs for", "Nonparametric Prediction Interval")
        line2 <- paste("for ", k.string, ", ", conf.string, " ", 
            pi.string, sep = "")
        line3 <- rank.string
    })
    if (plot.it) {
        if (!add) {
            plot(x, y, type = "n", main = "", sub = "", ..., 
                xlab = xlab, ylab = ylab)
            if (is.null(main)) {
                mtext(text = line1, side = 3, line = 3, cex = 1.25 * 
                  cex.main)
                mtext(text = line2, side = 3, line = 1.75, cex = 1.25 * 
                  cex.main)
                mtext(text = line3, side = 3, line = 0.5, cex = cex.main)
            }
            else {
                arg.list <- c(list(main = main), gen.gp.list, 
                  list(cex = cex.main))
                do.call("title", arg.list)
            }
            arg.list <- c(list(x = x, y = y), gen.gp.list, list(type = type, 
                col = plot.col, lwd = plot.lwd, lty = plot.lty))
            do.call("lines", arg.list)
        }
        else {
            arg.list <- c(list(x = x, y = y), gen.gp.list, list(type = type, 
                col = plot.col, lwd = plot.lwd, lty = plot.lty))
            do.call("lines", arg.list)
        }
    }
    ret.list <- list(x, y)
    names(ret.list) <- c(x.var, y.var)
    invisible(ret.list)
}