#' Plot calibration graphs from univariate linear models #' #' Produce graphics of calibration data, the fitted model as well as #' confidence, and, for unweighted regression, prediction bands. #' #' @aliases calplot calplot.default calplot.lm #' @param object A univariate model object of class \code{\link{lm}} or #' \code{\link[MASS:rlm]{rlm}} with model formula \code{y ~ x} or \code{y ~ x - #' 1}. #' @param xlim The limits of the plot on the x axis. #' @param ylim The limits of the plot on the y axis. #' @param xlab The label of the x axis. #' @param ylab The label of the y axis. #' @param legend_x An optional numeric value for adjusting the x coordinate of #' the legend. #' @param alpha The error tolerance level for the confidence and prediction #' bands. Note that this includes both tails of the Gaussian distribution, #' unlike the alpha and beta parameters used in \code{\link{lod}} (see note #' below). #' @param varfunc The variance function for generating the weights in the #' model. Currently, this argument is ignored (see note below). #' @return A plot of the calibration data, of your fitted model as well as #' lines showing the confidence limits. Prediction limits are only shown for #' models from unweighted regression. #' @note Prediction bands for models from weighted linear regression require #' weights for the data, for which responses should be predicted. Prediction #' intervals using weights e.g. from a variance function are currently not #' supported by the internally used function \code{\link{predict.lm}}, #' therefore, \code{calplot} does not draw prediction bands for such models. #' #' It is possible to compare the \code{\link{calplot}} prediction bands with #' the \code{\link{lod}} values if the \code{lod()} alpha and beta parameters #' are half the value of the \code{calplot()} alpha parameter. #' @author Johannes Ranke #' @importFrom graphics legend matlines plot points #' @examples #' #' data(massart97ex3) #' m <- lm(y ~ x, data = massart97ex3) #' calplot(m) #' #' @export calplot calplot <- function(object, xlim = c("auto", "auto"), ylim = c("auto", "auto"), xlab = "Concentration", ylab = "Response", legend_x = "auto", alpha = 0.05, varfunc = NULL) { UseMethod("calplot") } #' @export calplot.default <- function(object, xlim = c("auto","auto"), ylim = c("auto","auto"), xlab = "Concentration", ylab = "Response", legend_x = "auto", alpha=0.05, varfunc = NULL) { stop("Calibration plots only implemented for univariate lm objects.") } #' @export calplot.lm <- function(object, xlim = c("auto","auto"), ylim = c("auto","auto"), xlab = "Concentration", ylab = "Response", legend_x = "auto", alpha=0.05, varfunc = NULL) { if (length(object$coef) > 2) stop("More than one independent variable in your model - not implemented") if (alpha <= 0 | alpha >= 1) stop("Alpha should be between 0 and 1 (exclusive)") m <- object level <- 1 - alpha y <- m$model[[1]] x <- m$model[[2]] if (xlim[1] == "auto") xlim[1] <- 0 if (xlim[2] == "auto") xlim[2] <- max(x) xlim <- as.numeric(xlim) newdata <- list( x = seq(from = xlim[[1]], to = xlim[[2]], length=250)) names(newdata) <- names(m$model)[[2]] if (is.null(varfunc)) { varfunc <- if (length(m$weights)) { function(variable) mean(m$weights) } else function(variable) rep(1,250) } pred.lim <- predict(m, newdata, interval = "prediction", level=level, weights.newdata = varfunc(m)) conf.lim <- predict(m, newdata, interval = "confidence", level=level) yrange.auto <- range(c(0,pred.lim)) if (ylim[1] == "auto") ylim[1] <- yrange.auto[1] if (ylim[2] == "auto") ylim[2] <- yrange.auto[2] if (legend_x[1] == "auto") legend_x <- min(object$model[[2]]) plot(1, type = "n", xlab = xlab, ylab = ylab, xlim = as.numeric(xlim), ylim = as.numeric(ylim) ) points(x,y, pch = 21, bg = "yellow") matlines(newdata[[1]], pred.lim, lty = c(1, 4, 4), col = c("black", "red", "red")) if (length(object$weights) > 0) { legend(min(x), max(pred.lim, na.rm = TRUE), legend = c("Fitted Line", "Confidence Bands"), lty = c(1, 3), lwd = 2, col = c("black", "green4"), horiz = FALSE, cex = 0.9, bg = "gray95") } else { matlines(newdata[[1]], conf.lim, lty = c(1, 3, 3), col = c("black", "green4", "green4")) legend(legend_x, max(pred.lim, na.rm = TRUE), legend = c("Fitted Line", "Confidence Bands", "Prediction Bands"), lty = c(1, 3, 4), lwd = 2, col = c("black", "green4", "red"), horiz = FALSE, cex = 0.9, bg = "gray95") } }