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DESCRIPTION

A function to plot confidential interval for such as ‘htest’, ‘glm’ (logistic regression only!) and ‘posthocTGH’ {userfriendlyscience} objects.

Usage

‘htest’ object

CIplot(x,
       log = FALSE,
       xlim = NULL, xlab = NULL, main = NULL,
       pch = 21, pcol = "black", pcolbg = "white", pcex = 1,
       cilty = 1, cilwd = 1, cicol = "black",
       v = NULL, vlty = 2, vlwd = 1,  vcol = "black",
       ...)

‘glm’ object (logistic regression only!)

CIplot(x,
       conf.level = 0.95,
       xlim = NULL, xlab = "Odds Ratio",
       main = NULL,
       pch = 21, pcol = "black",
       pcolbg = "white", pcex = 1, cilty = 1, cilwd = 1,
       cicol = "black", vlty = 2, vlwd = 1,  vcol = "black",
       las = NULL,
       ...)

‘posthocTGH’ object (Tukey or Games-Howell method)

CIplot(x,
       xlim = NULL, xlab = "Differences in mean", main = NULL,
       pch = 21, pcol = "black", pcolbg = "white", pcex = 1,
       cilty = 1, cilwd = 1, cicol = "black",
       vlty = 2, vlwd = 1,  vcol = "black",
       las = NULL,
       ...)

Arguments

• x:
  • ‘htest’ object, typically result of ‘t.test’, ‘binom.test’, or ‘prop.test’.
  • ‘glm’ object (logistic regression only)
  • ‘posthocTGH’ object, result of ‘posthocTGH’ {userfriendlyscience}
• log: (logical) if log is TRUE, the x axis is drawn logarithmically. ‘htest’ object only. Default is FALSE.
• options of plot
  • xlim: the x limits (x1, x2) of the plot.
  • xlab: a title for the x axis: see ‘title’.
  • main: a main title for the plot.
  • …: other options for x-axis.
• options of point
  • pch: plotting ‘character’, i.e., symbol to use.
  • pcol: color code or name.
  • pcolgb: background (fill) color for the open plot symbols given by ‘pch = 21:25’.
  • pcex: character (or symbol) expansion.
• options of confidence interval line
  • cilty: line types.
  • cilwd: line width.
  • cicol: color code or name.
• options of an additional line
  • v: the x-value(s) for vertical line. ‘htest’ object only.
  • lty: line types.
  • lwd: line width.
  • lcol: color code or name.
• …: other options for x-axis.

Examples

‘htest’ object

Difference [log = FALSE (default)]

set.seed(1234)
x <- rnorm(10, 10, 2); y <- rnorm(10, 8, 2)
res <- t.test(x, y)
CIplot(res)

x <- binom.test(20, 100, 0.3)
CIplot(x)

x <- matrix(c(10, 7, 8, 9), 2, 2, byrow = TRUE)
res <- prop.test(x)
CIplot(res)

res <- chisq.test(x)
CIplot(x)                  ## Warning and no plot

set.seed(1234)
x <- cor.test(rnorm(10), rnorm(10))
CIplot(x, xlim = c(-1, 1))

Ratio (log = TRUE)

x <- var.test(1:10, (1:10)*1.5)
CIplot(x, log = TRUE)

x <- matrix(c(10, 7, 8, 9), 2, 2, byrow = TRUE)
res <- fisher.test(x)
CIplot(res, log = TRUE)

library(exact2x2)
x <- mcnemar.exact(dat)
CIplot(x, log = TRUE)

‘glm’ object

library(MASS)
data(birthwt)
x <- glm(low ~  age + lwt + smoke + ptl + ht + ui, data = birthwt,
         family = binomial)
CIplot(x, las = 1)

OR1 <- ORci(x)
CIplot(OR1, las = 1)

‘posthocTGH’ object

library(userfriendlyscience)
x <- posthocTGH(warpbreaks$breaks, warpbreaks$tension)
CIplot(x, las = 1)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.