bargraph.CI: Bar Graph of Calculated Means and CI

In mutualism/sciplot: Scientific Graphing Functions for Factorial Designs

Bar Graph of Calculated Means and CI

Description

Barplot of the mean and standard error (or other summary statistics) of a response variable for one-way or higher experimental designs.

Usage

bargraph.CI(x.factor, response, group=NULL, split=FALSE,
    xlab=NULL, ylab=NULL, col=NULL, angle=NULL, density=NULL,
    lc=TRUE, uc=TRUE, legend=FALSE, ncol=1,
    leg.lab=NULL, x.leg=NULL, y.leg=NULL, cex.leg=1,
    bty="n", bg="white", space=if(split) c(-1,1),
    err.width=if(length(levels(as.factor(x.factor)))>10) 0 else .1,
    err.col="black", err.lty=1,
    fun = function(x) mean(x, na.rm=TRUE),
    ci.fun= function(x) c(fun(x)-se(x), fun(x)+se(x)),
    ylim=NULL, xpd=FALSE, data=NULL, subset=NULL, ...)

Arguments

x.factor	a factor (required) whose levels will form the x axis.
response	a numeric variable giving the response.
group	grouping factor (optional) whose levels will form groups of bars for each level of x.factor.
split	logical. Should groups of bars be displayed back to back. See details below.
xlab	default x-axis label. If not specified will parse name from x.factor. To leave blank set to NA
ylab	default y-axis label. If not specified will parse name from response. To leave blank set to NA
col	default color(s) for bars.
angle	default angle of shading lines.
density	default density of shading lines.
lc, uc	logical. Should upper or lower CI be drawn?
legend	logical. Should a legend be included?
ncol	number of columns to use for legend.
leg.lab	legend labels for trace factors.
x.leg, y.leg	optional values to over ride the default legend placement.
cex.leg	character expansion value for legend labels.
bty	line type of bounding box for legend. Defaults to 'none'.
space	set spacing for bars.
err.width	set width of whiskers for error bars.
err.col	color for error bars. Defaults to "black".
err.lty	line type for error bars.
bg	background color of legend.
fun	the function to compute the summary statistic. Should return a single real value. Defaults to mean with NA values removed.
ci.fun	the functions to compute the CI. Should return a vector of length 2 defining the lower and upper limits of the CI's. Defaults to the mean +/- 1 standard error, with NA values removed.
ylim	range of y axis.
xpd	defualts to xpd=FALSE (in contrast to barplot) to cut off the range of data plotted.
data	an optional data frame.
subset	an optional expression indicating the subset of the rows of 'data' that should be used in the plot.
...	further graphical parameters. See barplot() for additional options.

Details

Plots a response as a function of treatment (factor) combinations for one-way and higher designs. This is a "wrapper" function for barplot that adds confidence intervals - barplot should be consulted for details. Note that the option "beside=TRUE" from barplot is hardcoded and that the default for value xpd is FALSE. If the option split is specified, the response associated with the second grouping factor will be made negative and displayed back-to-back with the first.

See Also

barplot, se

Examples

data(ToothGrowth)

# One way design
bargraph.CI(x.factor = dose, response = len, data = ToothGrowth) 

# Two-way design with options
bargraph.CI(dose, len, group = supp, data = ToothGrowth,
            xlab = "Dose", ylab = "Growth", cex.lab = 1.5, x.leg = 1,
            col = "black", angle = 45, cex.names = 1.25,
            density = c(0,20), legend = TRUE)

mutualism/sciplot documentation built on July 8, 2023, 2:40 a.m.