Nothing
MillerCalib <- function(model = NULL, obs = NULL, pred = NULL, plot = TRUE, line.col = "black", diag = TRUE, diag.col = "grey", plot.values = TRUE, digits = 2, xlab = "", ylab = "", main = "Miller calibration", na.rm = TRUE, rm.dup = FALSE, ...) {
# version 1.8 (6 May 2022)
obspred <- inputMunch(model, obs, pred, na.rm = na.rm, rm.dup = rm.dup)
obs <- obspred[ , "obs"]
pred <- obspred[ , "pred"]
stopifnot(
obs %in% c(0, 1)#,
#pred >= 0,
#pred <= 1
)
if (any(pred < 0) | any(pred > 1)) warning("Some of your predicted values are outside the [0, 1] interval; are you sure these represent probabilities?")
pred[pred == 0] <- 2e-16 # avoid NaN in log below
pred[pred == 1] <- 1 - 2e-16 # avoid NaN in log below
logit <- log(pred / (1 - pred))
mod <- glm(obs ~ logit, family = binomial)
intercept <- mod$coef[[1]]
slope <- mod$coef[[2]]
#std.err <- summary(mod)$coefficients["logit", "Std. Error"]
#slope.p <- abs((slope - 1) / sqrt(std.err^2 + 0)) # Paternoster 98; http://stats.stackexchange.com/questions/55501/test-a-significant-difference-between-two-slope-values
#slope.t <- (slope - 1) / std.err
#slope.p <- pt(slope.t, df = mod$df.residual) # http://stats.stackexchange.com/questions/111559/test-model-coefficient-regression-slope-against-some-value
# both values look wrong...
if (plot) {
ymin <- min(0, intercept)
ymax <- max(1, intercept + 0.3)
plot(c(0, 1), c(ymin, ymax), type = "n", xlab = xlab, ylab = ylab, main = main, ...)
if (diag) abline(0, 1, col = diag.col, lty = 2)
abline(intercept, slope, col = line.col)
if (plot.values) {
# plotext <- paste("intercept =" , round(intercept, digits), "\nslope =", round(slope, digits), "\nslope p-value =", round(slope.p, digits))
plotext <- paste0("slope = " , round(slope, digits), "\nintercept = ", round(intercept, digits))
text(x = 1, y = ymin + 0.15 * (ymax - ymin), adj = 1, labels = plotext)
} # end if plot.values
} # end if plot
# return(list(intercept = intercept, slope = slope, slope.pvalue = slope.p))
list(intercept = intercept, slope = slope)
} # end MillerCalib function
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.