\HeaderA{Special}{Special Functions of Mathematics}{Special}
\aliasA{beta}{Special}{beta}
\aliasA{choose}{Special}{choose}
\aliasA{digamma}{Special}{digamma}
\aliasA{factorial}{Special}{factorial}
\aliasA{gamma}{Special}{gamma}
\aliasA{lbeta}{Special}{lbeta}
\aliasA{lchoose}{Special}{lchoose}
\aliasA{lfactorial}{Special}{lfactorial}
\aliasA{lgamma}{Special}{lgamma}
\aliasA{polygamma}{Special}{polygamma}
\aliasA{psigamma}{Special}{psigamma}
\aliasA{trigamma}{Special}{trigamma}
\keyword{math}{Special}
\begin{Description}\relax
Special mathematical functions related to the beta and gamma
functions.
\end{Description}
\begin{Usage}
\begin{verbatim}
beta(a, b)
lbeta(a, b)

gamma(x)
lgamma(x)
psigamma(x, deriv = 0)
digamma(x)
trigamma(x)

choose(n, k)
lchoose(n, k)
factorial(x)
lfactorial(x)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{a, b, x, n}] numeric vectors.
\item[\code{k, deriv}] integer vectors.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The functions \code{beta} and \code{lbeta} return the beta function
and the natural logarithm of the beta function,
\deqn{B(a,b) = \frac{\Gamma(a)\Gamma(b)}{\Gamma(a+b)}.}{B(a,b) = (Gamma(a)Gamma(b))/(Gamma(a+b)).}
The formal definition is
\deqn{B(a, b) = \int_0^1 t^{a-1} (1-t)^{b-1} dt}{integral_0^1 t^(a-1) (1-t)^(b-1) dt}
(Abramowitz and Stegun section 6.2.1, page 258).

The functions \code{gamma} and \code{lgamma} return the gamma function
\eqn{\Gamma(x)}{} and the natural logarithm of the absolute value of the
gamma function.  The gamma function is defined by
(Abramowitz and Stegun section 6.1.1, page 255)
\deqn{\Gamma(x) = \int_0^\infty t^{a-1} e^{-t} dt}{integral_0^Inf t^(a-1) exp(-t) dt}
\code{factorial(x)} is \eqn{x!}{} and identical to
\code{gamma(x+1)} and \code{lfactorial} is \code{lgamma(x+1)}.

The functions \code{digamma} and \code{trigamma} return the first and second
derivatives of the logarithm of the gamma function.
\code{psigamma(x, deriv)} (\code{deriv >= 0}) computes the
\code{deriv}-th derivative of \eqn{\psi(x)}{}.
\deqn{\code{digamma(x)} = \psi(x) = \frac{d}{dx}\ln\Gamma(x) =
\frac{\Gamma'(x)}{\Gamma(x)}}{\code{digamma(x)} = psi(x) = d/dx {ln Gamma(x)} = Gamma'(x) / Gamma(x)}
This is often called the \sQuote{polygamma} function, e.g. in
Abramowitz and Stegun (section 6.4.1, page 260); and its higher
derivatives (\code{deriv = 2:4}) have occasionally been called
\sQuote{tetragamma}, \sQuote{pentagamma}, and \sQuote{hexagamma}.

The functions \code{choose} and \code{lchoose} return binomial
coefficients and their logarithms.  Note that \code{choose(n,k)} is
defined for all real numbers \eqn{n}{} and integer \eqn{k}{}.  For \eqn{k
\ge 1}{k >= 1} as \eqn{n(n-1)\cdots(n-k+1) / k!}{n(n-1)...(n-k+1) / k!},
as \eqn{1}{} for \eqn{k = 0}{} and as \eqn{0}{} for negative \eqn{k}{}.
\\ \code{choose(*,k)} uses direct arithmetic (instead of
\code{[l]gamma} calls) for small \code{k}, for speed and accuracy
reasons.  Note the function \code{\LinkA{combn}{combn}} (package
\pkg{utils}) for enumeration of all possible combinations.

The \code{gamma}, \code{lgamma}, \code{digamma} and \code{trigamma}
functions are generic: methods can be defined for them individually or
via the \code{\LinkA{Math}{Math}} group generic.
\end{Details}
\begin{References}\relax
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
\emph{The New S Language}.
Wadsworth \& Brooks/Cole. (For \code{gamma} and \code{lgamma}.)

Abramowitz, M. and Stegun, I. A. (1972)
\emph{Handbook of Mathematical Functions.} New York: Dover.
Chapter 6: Gamma and Related Functions.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{Arithmetic}{Arithmetic}} for simple, \code{\LinkA{sqrt}{sqrt}} for
miscellaneous mathematical functions and \code{\LinkA{Bessel}{Bessel}} for the
real Bessel functions.  Note that \code{\LinkA{gammaCody}{gammaCody}(x)} is
considerably faster than \code{gamma(x)} but slightly less accurate
and (potentially) less reliable.

For the incomplete gamma function see \code{\LinkA{pgamma}{pgamma}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
require(graphics)

choose(5, 2)
for (n in 0:10) print(choose(n, k = 0:n))

factorial(100)
lfactorial(10000)

## gamma has 1st order poles at 0, -1, -2, ...
## this will generate loss of precision warnings, so turn off
op <- options("warn")
options(warn = -1)
x <- sort(c(seq(-3,4, length=201), outer(0:-3, (-1:1)*1e-6, "+")))
plot(x, gamma(x), ylim=c(-20,20), col="red", type="l", lwd=2,
     main=expression(Gamma(x)))
abline(h=0, v=-3:0, lty=3, col="midnightblue")
options(op)

x <- seq(.1, 4, length = 201); dx <- diff(x)[1]
par(mfrow = c(2, 3))
for (ch in c("", "l","di","tri","tetra","penta")) {
  is.deriv <- nchar(ch) >= 2
  nm <- paste(ch, "gamma", sep = "")
  if (is.deriv) {
    dy <- diff(y) / dx # finite difference
    der <- which(ch == c("di","tri","tetra","penta")) - 1
    nm2 <- paste("psigamma(*, deriv = ", der,")",sep='')
    nm  <- if(der >= 2) nm2 else paste(nm, nm2, sep = " ==\n")
    y <- psigamma(x, deriv=der)
  } else {
    y <- get(nm)(x)
  }
  plot(x, y, type = "l", main = nm, col = "red")
  abline(h = 0, col = "lightgray")
  if (is.deriv) lines(x[-1], dy, col = "blue", lty = 2)
}
par(mfrow = c(1, 1))

## "Extended" Pascal triangle:
fN <- function(n) formatC(n, width=2)
for (n in -4:10) cat(fN(n),":", fN(choose(n, k= -2:max(3,n+2))), "\n")

## R code version of choose()  [simplistic; warning for k < 0]:
mychoose <- function(r,k)
    ifelse(k <= 0, (k==0),
           sapply(k, function(k) prod(r:(r-k+1))) / factorial(k))
k <- -1:6
cbind(k=k, choose(1/2, k), mychoose(1/2, k))

## Binomial theorem for n=1/2 ;
## sqrt(1+x) = (1+x)^(1/2) = sum_{k=0}^Inf  choose(1/2, k) * x^k :
k <- 0:10 # 10 is sufficient for ~ 9 digit precision:
sqrt(1.25)
sum(choose(1/2, k)* .25^k)


\end{ExampleCode}
\end{Examples}

