ba_plot: Bland-Altman plot

In raredd/ragree: Rater agreement

Description

Creates a scatter plot using the method of Bland and Altman where the x- and y-axes are the means of and differences between x and y, respectively. Lines for the mean and +/-1.96 times the standard deviation of the difference between x and y are shown.

Usage

ba_plot(x, y, trend = c("loess", "gam", "none"), span = 0.5,
  trend.n = 1000L, alpha = 0.05, xlab = "", ylab = "",
  xlim = NULL, ylim = NULL, panel.first = NULL, panel.last = NULL,
  ..., line_pars = list(col = 1:2, lty = c(2, 1, 2)))

Arguments

x, y	measurements
trend	character string giving the type of trend line, one of "loess" (default), "gam" (requires the mgcv package), or "none" where no curve is drawn
span	if trend = "loess", a numeric value that controls the degree of smoothing (see loess)
trend.n	integer value for the number of data points to be used by predict.loess
alpha	confidence level affecting the critical values and trend confidence bands
xlab, ylab	x- and y-axis labels
xlim, ylim	x- and y-axis limits
panel.first	an expression to be evaluated after the plot axes are set up but before any plotting takes place (default is just a grid); see plot.default
panel.last	an expression to be evaluated after plotting has taken place but before the axes, title, and box are added; see comments about panel.first
...	additional parameters passed to plot
line_pars	additional graphical parameters passed to text or abline; all parameters will be passed as-is except col which should be a vector of length one, two, or three to color the lines and text accordingly; see examples

References

Altman DG, Bland JM (1983). Measurement in medicine: the analysis of method comparison studies. The Statistician 32: 307-317.

Examples

set.seed(1)
x <- rnorm(100)
y <- rnorm(100, 0.5)

## basic usage
ba_plot(x, y)
ba_plot(x, y, trend = 'gam')
ba_plot(x, y, trend = 'none', alpha = 0.1)


## use line_pars to set graphical parameters of individual lines
ba_plot(x, y, col = c('black', 'green')[(abs(x - y) > 2) + 1L],
        pch = '.', cex = 5, line_pars = list(col = c('yellow', 'red')))
        
## panel.first/panel.last is used as in plot.default
ba_plot(x, y, cex = 2, las = 1,
        col = as.numeric(cut(x - y, c(-Inf, -2, 2, Inf))) + 2,
        panel.first = {
          p <- par('usr')
          rect(p[1L], p[3L], p[2L], p[4L], col = 'cornsilk')
          grid(col = 'grey90', lty = 1)
        },
        line_pars = list(col = 3:5, family = 'HersheySerif'))

raredd/ragree documentation built on March 25, 2021, 1:42 p.m.