# Functions to Plot Confidence Interval

Plot confidence interval from the objects of statistical tests such as t.test(), var.test(), cor.test(), prop.test() and fisher.test() ('htest' class), Tukey test [TukeyHSD()], Dunnett test [glht() in 'multcomp' package], logistic regression [glm()], and Tukey or Games-Howell test [posthocTGH() in 'userfriendlyscience' package]. Users are able to set the styles of lines and points. This package contains the function to calculate odds ratios and their confidence intervals from the result of logistic regression.

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)``````

# Reference manual

install.packages("CIplot")

1.0 by Toshiaki Ara, 4 years ago

https://github.com/toshi-ara/CIplot

Report a bug at https://github.com/toshi-ara/CIplot/issues/

Browse source code at https://github.com/cran/CIplot

Authors: Toshiaki Ara

Documentation:   PDF Manual