## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- fig.width = 4, fig.height = 4, fig.show = 'hold'------------------------ library(conf) ballbearing <- c(17.88, 28.92, 33.00, 41.52, 42.12, 45.60, 48.48, 51.84, 51.96, 54.12, 55.56, 67.80, 68.64, 68.64, 68.88, 84.12, 93.12, 98.64, 105.12, 105.84, 127.92, 128.04, 173.40) crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull") ## ---- fig.width = 8, fig.height = 8, fig.show = 'hold'------------------------ par(mfrow = c(3, 3)) crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", animate = TRUE) ## ---- fig.width = 4, fig.height = 4, fig.show = 'hold'------------------------ crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", pts = FALSE, sf = c(2, 4), ylas = 1, origin = TRUE) ## ---- fig.height = 4, fig.width = 4, fig.keep = 'none'------------------------ x <- crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", info = TRUE) str(x) ## ---- fig.height = 4, fig.width = 3.5, fig.show = 'asis'---------------------- # with confidence region data stored in x, it is now available for custom graphics plot(x$kappa, x$lambda, type = 'l', lty = 5, xlim = c(0, 3), ylim = c(0, 0.0163), xlab = expression(kappa), ylab = expression(lambda)) polygon(x$kappa, x$lambda, col = "gray80", border = NA) ## ---- fig.show = 'hold'------------------------------------------------------- # record MLE values (previously output to screen when info = TRUE) & reproduce CR plot kappa.hat <- 2.10206 lambda.hat <- 0.01221 crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", xlab = "shape", ylab = " ", main = paste0("Confidence Region"), pts = FALSE, mlelab = FALSE, sf = c(2, 4), origin = TRUE) par(xpd = TRUE) text(-1.2, 0.007, "scale", srt = 90) # 1st analysis plot: overlay phi angles (as line segments) on the confidence region plot par(xpd = FALSE) segments(rep(kappa.hat, length(x$phi)), rep(lambda.hat, length(x$phi)), x1 = kappa.hat * cos(x$phi) + kappa.hat, y1 = kappa.hat * sin(x$phi) + lambda.hat, lwd = 0.2) # 2nd analysis plot: CDF of phi angles reveals most are very near 0 (2pi) and pi plot.ecdf(x$phi, pch = 20, cex = 0.1, axes = FALSE, xlab = expression(phi), ylab = "", main = "CDF") axis(side = 1, at = round(c(0, pi, 2*pi), 2)) axis(side = 2, at = c(0, 1), las = 2) ## ---- fig.show = 'hold'------------------------------------------------------- crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", ylas = 1, maxdeg = 3, main = "maxdeg = 3", sf = c(5, 5)) crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", ylas = 1, maxdeg = 3, main = "maxdeg = 3 (pts hidden)", sf = c(5, 5), pts = FALSE) crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", ylas = 1, maxdeg = 20, main = "maxdeg = 20", sf = c(5, 5)) crplot(dataset = ballbearing, alpha = 0.05, distn = "weibull", ylas = 1, maxdeg = 20, main = "maxdeg = 20 (pts hidden)", sf = c(5, 5), pts = FALSE) ## ---- fig.show = 'hold'------------------------------------------------------- crplot(dataset = ballbearing, alpha = 0.05, distn = "invgauss", sf = c(2, 2), ylas = 1, main = "default; heuristic = 1") crplot(dataset = ballbearing, alpha = 0.05, distn = "invgauss", sf = c(2, 2), ylas = 1, heuristic = 0, ellipse_n = 100, main = "heuristic = 0") ## ---- fig.show = 'hold'------------------------------------------------------- crplot(dataset = ballbearing, alpha = 0.05, distn = "invgauss", sf = c(2, 2), heuristic = 0, ellipse_n = 40, main = "combination: step 1") crplot(dataset = ballbearing, alpha = 0.05, distn = "invgauss", sf = c(2, 2), maxdeg = 10, ellipse_n = 40, main = "combination: step 2") ## ---- fig.show = 'hold'------------------------------------------------------- crplot(dataset = ballbearing, alpha = 0.05, distn = "invgauss", sf = c(2, 2), maxdeg = 10, main = "default (heuristic = 1)") ## ---- fig.show = 'hold', fig.height = 3.8, fig.width = 4---------------------- mp6_obs <- c(6, 6, 6, 7, 10, 13, 16, 22, 23) # time of cancer remission mp6_cen <- c(6, 9, 10, 11, 17, 19, 20, 25, 32, 32, 34, 35) # right-censored time mp6 <- c(mp6_obs, mp6_cen) cen <- c(rep(1, length(mp6_obs)), rep(0, length(mp6_cen))) crplot(dataset = mp6, alpha = 0.05, distn = "weibull", cen = cen, sf = c(4, 4)) ## ---- fig.show = 'hold', warning = FALSE-------------------------------------- X <- seq(1, 2.5, by = 0.25) crplot(dataset = X, alpha = 0.01, distn = "gamma", sf = c(2, 2), pts = FALSE, repair = FALSE, main = "without repair") x <- crplot(seq(1, 2.5, by = 0.25), 0.01, "gamma", sf = c(2, 2), info = TRUE, repair = FALSE, main = "without repair") index1 <- which(x$kappa == max(x$kappa)) index2 <- which(x$theta == max(x$theta)) lines(c(x$thetahat, x$theta[index1]), c(x$kappahat, x$kappa[index1]), col = "red") lines(c(x$thetahat, x$theta[index2]), c(x$kappahat, x$kappa[index2]), col = "red") ## ---- fig.show = 'hold', warning = FALSE-------------------------------------- crplot(seq(1, 2.5, by = 0.25), 0.01, "gamma", sf = c(2, 2), pts = FALSE, main = "with repair") crplot(seq(1, 2.5, by = 0.25), 0.01, "gamma", sf = c(2, 2), main = "with repair", showjump = TRUE) lines(c(x$thetahat, x$theta[index1]), c(x$kappahat, x$kappa[index1]), col = "red") lines(c(x$thetahat, x$theta[index2]), c(x$kappahat, x$kappa[index2]), col = "red") ## ---- fig.show = 'hold', warning = FALSE-------------------------------------- crplot(seq(1, 2.5, by = 0.25), 0.01, "gamma", sf = c(2, 2), pts = TRUE, main = "max(theta) zoom", xlim = c(1.25, 1.5), ylim = c(1.4, 2.4)) crplot(seq(1, 2.5, by = 0.25), 0.01, "gamma", sf = c(2, 2), pts = TRUE, main = "max(kappa) zoom", xlim = c(0.04, 0.05), ylim = c(37, 41)) ## ---- fig.show = 'hold', warning = FALSE-------------------------------------- x <- crplot(c(2, 2.5), 0.01, "llogis", sf = c(2, 2), info = TRUE, pts = FALSE, main = "llogis") x <- crplot(c(2, 2.5), 0.01, "weibull", sf = c(2, 2), info = TRUE, pts = FALSE, main = "weibull") x <- crplot(c(2, 2.5), 0.01, "norm", sf = c(2, 2), info = TRUE, pts = FALSE, main = "norm")