CIplot: Plot Confidential Interval
In toshi-ara/CIplot: Functions to Plot Confidence Interval

Description Usage Arguments Note See Also Examples

A function to plot confidential interval for such as htest, TukeyHSD, glht (multcomp), glm (logistic regression only!) and posthocTGH (userfriendlyscience) objects.

CIplot(x, ...)

## Default S3 method:
CIplot(x, xlog = FALSE, xlim = NULL, xlab = NULL,
  yname = TRUE, las = 0, pch = 21, pcol = 1, pcolbg = "white",
  pcex = 1, conf.level = 0.95, cilty = 1, cilwd = 1, cicol = 1, v,
  vlty = 2, vlwd = 1, vcol = 1, main = NULL, ...)

## S3 method for class 'htest'
CIplot(x, xlog = FALSE, xlim = NULL, xlab = NULL,
  yname = FALSE, v = NULL, ...)

## S3 method for class 'TukeyHSD'
CIplot(x, xlab = "Differences in mean", v = 0, ...)

## S3 method for class 'glht'
CIplot(x, xlab = "Differences in mean", v = 0, ...)

## S3 method for class 'glm'
CIplot(x, conf.level = 0.95, xlog = TRUE,
  xlab = "Odds Ratio", v = 1, ...)

## S3 method for class 'ORci'
CIplot(x, xlog = TRUE, xlab = "Odds Ratio", v = 1, ...)

## S3 method for class 'posthocTGH'
CIplot(x, xlab = "Differences in mean", v = 0, ...)

`x`	`default`: `matrix` or `data.frame` class with 3 columns ('any name', `lwr`, `upr`), or an object: `htest`, `TukeyHSD`, `glht` (multcomp), `glm` (logistic regression only!) or `posthocTGH` (userfriendlyscience).
`...`	other options for x-axis.
`xlog`	(logical) if `log` is `TRUE`, the x axis is drawn logarithmically. Default is `FALSE`.
`xlim`	the x limits (x1, x2) of the plot.
`xlab`	a title for the plot.
`yname`	If `yname` is `TRUE`, the name of comparison between groups are shown.
`las`	numeric in 0,1,2,3; the style of axis labels. Default is 0. see also `par`.
`pch`	plotting 'character', i.e., symbol to use.
`pcol`	color code or name of the points.
`pcolbg`	background (fill) color for the open plot symbols given by 'pch = 21:25'.
`pcex`	character (or symbol) expansion of points.
`conf.level`	`default` and `glm` object only. the confidence interval. Default is 0.95. see also `ORci`.
`cilty`	line types of conficence intervals.
`cilwd`	line width of conficence intervals.
`cicol`	color code or name of conficence intervals.
`v`	the x-value(s) for vertical line.
`vlty`	line types of vertical line.
`vlwd`	line width of vertical line.
`vcol`	color code or name of vertical line.
`main`	a main title for the plot.

CIplot was made based on plot.TukeyHSD.

 #  File src/library/stats/R/TukeyHSD.R
 #  Part of the R package, https://www.R-project.org
 #
 #  Copyright (C) 2000-2001  Douglas M. Bates
 #  Copyright (C) 2002-2015  The R Core Team

plot, axis, points, par.

##### default (matrix or data.frame)
require(graphics)
x <- matrix(c(3, 1, 5,
              4, 2, 6), 2, 3, byrow = TRUE)
colnames(x) <- c("esti", "lwr", "upr")
rownames(x) <- c("A", "B")
CIplot(x, xlab = "difference", v = 2, las = 1)

##### 'htest' objects
require(graphics)

## t test
set.seed(1234)
a <- rnorm(10, 10, 2); b <- rnorm(10, 8, 2)
x <- t.test(a, b)
CIplot(x)

## binomial test
x <- binom.test(5, 20)
CIplot(x, xlim = c(0, 1))

## Fisher's exact test
x <- matrix(c(10, 7, 8, 9), 2, 2, byrow = TRUE)
res <- fisher.test(x)
CIplot(res, xlog = TRUE)


##### 'TukeyHSD' objects
require(graphics)

## Tukey test
aov1 <- aov(breaks ~ tension + wool, data = warpbreaks)
x <- TukeyHSD(aov1)

oldpar <- par(no.readonly = TRUE)
par(mfrow = c(1, 2))
CIplot(x, las = 1)
par(oldpar)

## example of line type and color
aov1 <- aov(breaks ~ tension, data = warpbreaks)
x <- TukeyHSD(aov1)
CIplot(x, las = 1,
       pcol = 2:4, pcolbg = 2:4, cicol = 2:4,
       vlty = 1, vcol = "gray")

##### 'glht' objects
require(graphics)

## Tukey test
require(multcomp)
aov1 <- aov(breaks ~ tension, data = warpbreaks)
x <- glht(aov1, linfct = mcp(tension = "Tukey"))
CIplot(x, las = 1)

## Dunnett test
x <- glht(aov1, linfct = mcp(tension = "Dunnett"))
CIplot(x, las = 1)


##### 'glm' object: logistic regression only!
## odds ratio
require(graphics)
require(MASS)
data(birthwt)
x <- glm(low ~  age + lwt + smoke + ptl + ht + ui, data = birthwt,
         family = binomial)
CIplot(x, las = 1)


##### 'posthocTGH' object
## Tukey or Games-Howell methos
require(graphics)
if (require(userfriendlyscience)) {
    x <- posthocTGH(warpbreaks$breaks, warpbreaks$tension)
    CIplot(x, las = 1)
}