S.notes			yandell				29 sep 1994

This file will be updated occassionally with tidbits about S.
Best that you read it here rather than copy it to your directory.

SAS is only available on the "atlas" computer.

S LIBRARY ACCESS

S is available on "atlas" and "bayes".
Splus is only available on "atlas".

The S function "library()" can attach a library of functions and/or data
to enhance the S system.  For instance,

	> library(data)

attaches the datasets used in the "Statistical Models in S" book (the
functions are already attached).

The command

	> library(pda)

attaches my "Practical Data Analysis" library of routines.  The command

	> library(help="pda")

will show you a brief synopsis of pda commands available.  Some commands
have help pages.  For instance, try

	> help(lsd.plot)

The command 

	> search()

shows what directories you currently search for functions and data.
Normally you need not check this.  However, it can tell you which
frame contains pda.

CHANGING PLOT AXES

You can turn off an axis with the "xaxt" or "yaxt" option (see "par()").
Then you can manually but text and/or axes with "mtext()" or "axis()".

> plot(1:10,1:10,xaxt="n")
> ?par
...	[lots of lines of explanation of plot options!]

xaxt="c"    axis type.  Type "n" (null) can be used to  cause  an
       axis  to  be  set up by a high-level routine, but then not
       plotted.  Values "s", "t", and "l" mean that the  axis  is
       standard, time, or logarithmic, respectively.  However, it
       is difficult to change xaxt to  anything  other  than  "n"
       since xaxp parameters must be kept consistent with xaxt.

...

> mtext(c("a","b","c"),1,1,at=c(2,5,7))
> ?mtext

Text in the Margins of a Plot

USAGE:
       mtext(text, side=3, line=0, outer=FALSE, at=)
ARGUMENTS:
text:     character vector to be plotted.
side:     side (1,2,3,4 for bottom, left, top, or right).
line:     line (measured out from the plot in units of  standard-
       sized character heights).  The default values of graphical
       parameter mar allow characters can be placed at values  of
       line  less than or equal to 4 on the bottom, 3 on left and
       top, and 1 on the right.
outer:    logical flag, should plotting be done in outer margin?
at:    optional vector of  positions  at  which  text  is  to  be
       plotted.   If  side  is  1  or  3,  at  will  represent x-
       coordinates.  If side is 2 or  4,  at  will  represent  y-
       coordinates.   at can be used for constructing specialized
       axis labels, etc.

> axis(1,at=c(1,3,9))
> ?axis

Add an Axis to the Current Plot

USAGE:
       axis(side, at=, labels=TRUE, ticks=TRUE,
            distn=, line=0, pos=, outer=FALSE)
ARGUMENTS:
side:     side of plot for axis (1,2,3,4 for bottom,  left,  top,
       right).
at:    optional vector of positions at which the ticks  and  tick
       labels  will be plotted.  If side is 1 or 3, at represents
       x-coordinates.  If side  is  2  or  4,  at  represents  y-
       coordinates.   If  at  is  omitted,  the  current axis (as
       specified by the xaxp or yaxp parameters, see par) will be
       plotted.
labels:   optional.  If labels is logical, it  specifies  whether
       or not to plot tick labels.  Otherwise, labels must be the
       same length as at, and label[i] is plotted  at  coordinate
       at[i].
ticks:    if TRUE, tick marks and axis line will be plotted.
...

PLOTTING TEXT INSTEAD OF POINTS

The commands "mplot()" and "mpoints()" are short routines I wrote.
They are part of pda.  They use the "text()" command.

> mplot(1:10,1:10,pch=letters[1:10])
> ?mplot
No documentation available for mplot
> mplot
function(a, b, pch, xlim = range(a), ylim = range(b), xlab = deparse(substitute(
        a)), ylab = deparse(substitute(b)), main = "", ...)
{
        plot(a, b, type = "n", xlim = xlim, ylim = ylim, xlab = xlab, ylab = 
                ylab, main = main, ...)
        mpoints(a, b, mch = pch, ...)
}

> text(1:10,10:1,labels=LETTERS[1:10])
> ?text

Plot Text

USAGE:
       text(x, y, labels=seq(along.with=x), cex=, col=)
ARGUMENTS:
x,y:   coordinates of points.  The coordinates can  be  given  by
       two  vector arguments or by a single argument x which is a
       time-series, a complex vector, a matrix with 2 columns, or
       a  list  containing  components  named  x  and y.  Missing
       values (NAs) are allowed.  Labels are not plotted  at  any
       point with a missing x or y coordinate.
labels:    normally,  labels[i]  is   plotted   at   each   point
       (x[i],y[i]).   However,  if  labels is a logical vector of
       the same length as x and y, the value i is plotted at each
       (x[i],y[i])  for  which labels[i] is TRUE.  Missing values
       (NAs) are allowed.
...