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read.tps = function(data) {
  # Reads the .tps file format produced by TPSDIG 
  # (http://life.bio.sunysb.edu/morph/ into a single data frame
  # USAGE: R> read.tps("filename.tps")
  a = readLines(data) # so we can do some searching and indexing
  LM = grep("LM", a) # find the line numbers for LM
  ID.ind = grep("ID", a) # find the line numbers for ID
  # and the ID values, SCALE values, and image names
  ID = gsub("(ID=)(.*)", "\\2", grep("ID", a, value=T)) 
  SCALE = gsub("(SCALE=)(.*)", "\\2", grep("SCALE", a, value=T)) 

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SankeyR <- function(inputs, losses, unit, labels, format="plot"){
########################
# SankeyR version 1.01 (updated August 10, 2010)
# is a function for creating Sankey Diagrams in R.
# See http://www.sankey-diagrams.com for excellent examples of Sankey Diagrams.
# 
# OPTIONS:
# 'inputs' is a vector of input values
# 'losses' is a vector of loss values
# 'unit' is a string of the unit

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plotmatrix2 <- function (data, mapping = aes())
{
    grid <- expand.grid(x = 1:ncol(data), y = 1:ncol(data))
    grid <- subset(grid, x != y)
    all <- do.call("rbind", lapply(1:nrow(grid), function(i) {
        xcol <- grid[i, "x"]
        ycol <- grid[i, "y"]
        data.frame(xvar = names(data)[ycol], yvar = names(data)[xcol], 
            x = data[, xcol], y = data[, ycol], data)
    }))

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#' Creates a dialog box using tcl/tk to get input from the user.
#' 
#' This function will create a tcl/tk dialog box to get user input. It has been
#' written to be extensible so the R programmer can easily create a dialog with
#' any number of varaibles with custom labels and data conversion of the user
#' entered data. The function will return a list where the element names are
#' \code{vars} and the value is the user input. By default, all entry will be
#' converted using the \code{as.character} function. However, this can easily be
#' altered using the \code{fun} parameter. For example, if integers are required,
#' use \code{fun=c(as.integer, ...)}. It is also possible to write custom

low-decarie

tell application "Microsoft PowerPoint"
   activate
   
   set theView to view of document window 1
   
   repeat with slideNumber from 1 to count of slides of active presentation
       
       go to slide theView number slideNumber
       
       tell slide slideNumber of active presentation

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######################################
## Function calls a PGLMM for logistic regression
## Created by Matthew Helmus
######################################

PGLMM.fit<-function(dat=NULL,Y=NULL,X=NULL,VV=NULL,sp.init=0.5,maxit=25,exitcountermax=50) # [B,B0,s,S95int,LL,flag]=PGLMM_nosparse_funct(Y,X,VV,s)
{
    if (!require(corpcor))
    {
      stop("The 'corpcor' package is required")

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######################################
## Function that organizes the data so that PGLMM can be fit
## Created by Matthew Helmus
##
## attempt at fixing the function for use with larger data sets
## diag is replaced with Matrix:::Diagonal
######################################

require(Matrix)

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stat_smooth_func <- function(mapping = NULL, data = NULL,
                        geom = "smooth", position = "identity",
                        ...,
                        method = "auto",
                        formula = y ~ x,
                        se = TRUE,
                        n = 80,
                        span = 0.75,
                        fullrange = FALSE,
                        level = 0.95,