The .First function runs whenever R starts up.  It is typically used to configure R in the way that the user prefers.

'aaa.readme.rda' contains John Miyamoto's utility functions for organizing functions and objects. This file was last updated on 2014-02-18.

all.pairs takes a vector x as input and returns all pairs of elements of x.  Optionally it can return all pairs of non-identical elements.  

ARGUMENTS:

x is a vector

nonidentical.only = TRUE (default) means that only non-identical pairs are returned.  Otherwise identical pairs are allowed in the output.

area.under computes the coordinates of a polygon corresponding to the area under a curve. 

x is either a vector or a 2-column matrix.  If x is a 2-column matrix, y must be NA; x[,1] and x[,2] are, respectively the x and y values of the curve.  If x is a vector, y must be a vector of the same length.

The x matrix or cbind(x,y) determines one edge of the polygon;  the other edge is determined by x and bottom or by x[,1] and  bottom.  If output.coordinates is TRUE (default), then the function  outputs the coordinates of the polygon; otherwise it does not.   If make.polygon is TRUE, the function plots the polygon; otherwise it does not (default).

'barplot' is in the 'graphics' package.  It creates a bar plot
with vertical or horizontal bars.  See the documentation of 'barplot' for
general information, and see 'doc(error.bars)' for instructions re how
to add error bars to a barplot.  Some of the key arguments for 'barplot' are:
'height' either a vector or matrix of values describing the bars which
make up the plot. If height is a vector, the plot consists of a sequence
of rectangular bars with heights given by the values in the vector.
If 'height' is a matrix and beside is FALSE then each bar of the
plot corresponds to a column of height, with the values in the column
giving the heights of stacked sub-bars making up the bar. If height is
a matrix and beside is TRUE, then the values in each column are
juxtaposed rather than stacked.
'width' = optional vector of bar widths.
'space' = the amount of space (as a fraction of the average bar width)
left before each bar. May be given as a single number or one number per
bar. If height is a matrix and beside is TRUE, space may be specified
by two numbers, where the first is the space between bars in the same
group, and the second the space between the groups. If not given explicitly,
it defaults to c(0,1) if height is a matrix and beside is TRUE, and
to 0.2 otherwise.
'names.arg' = a vector of names to be plotted below each bar or group
of bars. If this argument is omitted, then the names are taken from
the names attribute of height if this is a vector, or the column
names if it is a matrix.
'beside' = a logical value. If FALSE, the columns of height are
portrayed as stacked bars, and if TRUE the columns are portrayed as
juxtaposed bars.
'horiz' = a logical value. If FALSE, the bars are drawn vertically
with the first bar to the left. If TRUE, the bars are drawn
horizontally with the first at the bottom.