Table of Contents

• 1. DESCRIPTION
  • 1.1. Usage
    • 1.1.1. 'htest' object
    • 1.1.2. 'glm' object (logistic regression only!)
    • 1.1.3. 'posthocTGH' object (Tukey or Games-Howell method)
    • 1.1.4. Arguments
• 2. Examples
  • 2.1. 'htest' object
    • 2.1.1. Difference [log = FALSE (default)]
    • 2.1.2. Ratio (log = TRUE)
  • 2.2. 'glm' object
  • 2.3. 'posthocTGH' object

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)