Package 'CIplot'

Plot Confidential Interval

Description

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

Usage

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, ...)

Arguments

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.

Note

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

See Also

plot, axis, points, par.

Examples

##### 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)
}

---

Calculate odds ratios and their confidence intervals from glm object

Description

Calculate odds ratios and their confidence intervals from glm object

Usage

ORci(x, conf.level = 0.95)

Arguments

x	glm object (logistic regression only!).
conf.level	the confidence interval. Default is 0.95.

Value

an object ORci and matirix classes with four columns.

OR

odds ratio

lwr

lower conficence intarval

upr

upper conficence intarval

p.value

P value by logistic regression

Examples

require(graphics)
require(MASS)
data(birthwt)
x <- glm(low ~  age + lwt + smoke + ptl + ht + ui, data = birthwt,
         family = binomial)
OR1 <- ORci(x)
CIplot(OR1, las = 1)

---

Print Methods for Odds Ratios and their Confidence Intervals of ORci object

Description

Print odds ratios and their confidence intervals of ORci object.

Usage

## S3 method for class 'ORci'
print(x, ...)

Arguments

x	ORci object.see alse ORci.
...	other options for print such as digits.

See Also

glm, ORci.

Examples

require(MASS)
data(birthwt)
x <- glm(low ~  age + lwt + smoke + ptl + ht + ui, data = birthwt,
         family = binomial)
OR1 <- ORci(x)
print(OR1, digits = 3)

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