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png(filename = "Figures/web.R.png", width = 28, height = 21, units = "cm", res = 100)
#plotweb(mat, text.rot = 55, col.high = NULL, col.low = NULL, low.lablength = 7, labsize = 2)
dev.off()

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BEGIN	{
			FS = "\t"
		}
		## should be possible to catch logs & other extras by finding unsplit lines
		{ 

		n = split($2, lines, /[A-Z]'?[A-Z][A-Za-z'\[\] ]*:/, speaker)

		if (n == 1) {
			printf "%s\t%s\t%s\t%s\n", $1, 1, "extra", $2

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source("fn.incidence.R")
insect<-read.csv("insect.community.csv",sep=";")
brom<-read.csv("bromeliads.csv")
insect.pres <- insect
insect.pres[,3:27] <- as.numeric(insect.pres[,3:27]>0)
taxo.insect <- read.csv("Cardoso.insects.csv",sep=";")
insect.common <- commonize()

a.b <- sapply(1:dim(insect.common)[1],log.reg,simplify=FALSE)
a.b <- do.call(cbind,a.b)

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BEGIN			{FS = ","
			 genus = "0"}
$1 ~ /[A-Z][a-z]/	{genus = $1}
{
$2 = genus
printf "%s	%s\n", $1, $2
}

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## create the logical matrices for subsetting
## x matrix to subset
## n number of rows or columns in each subset (by subset I mean a small square from the larger matrix)
select_matrix <- function(x, n){
  mod <- ncol(x) %% n
  if(mod != 0) stop("not a divisor")
  
  if(ncol(x) != nrow(x)) stop("not a square")
  

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print_num <- function(num){
  print(num)
}

print_num_x <- function(num = x){
  print(num)
}

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require("yaml")
require("lubridate")

#' Make a correct SWC blog post
#' 
#' Automatically formats the necessary YAML header for a
#' Software Carpentry Teacher training blog post. Writes
#' this header to a file with the correct name. The file is
#' created in your current working directory.
#' 

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#' convert positional information to two columns
#' 
#' Sometimes text is organized by position. This function
#' turns positional group labels (e.g headers ) into the levels of a grouping variable
#' @param x character vector containing group labels followed by group members
#' @param pattern regular expression that identifies the group labels
fill_down <- function(x, pattern){
  ## find matches of the pattern 
  x <- as.character(x)
  value_matches <- grepl(pattern = pattern, x = x)

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Installing package into ‘/home/andrew/R/x86_64-pc-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package ‘RTidyHTML’ ...
cc -Iinclude -fPIC   -c -o access.o access.c
cc -Iinclude -fPIC   -c -o alloc.o alloc.c
cc -Iinclude -fPIC   -c -o attrask.o attrask.c
cc -Iinclude -fPIC   -c -o attrdict.o attrdict.c
cc -Iinclude -fPIC   -c -o attrget.o attrget.c
cc -Iinclude -fPIC   -c -o attrs.o attrs.c
cc -Iinclude -fPIC   -c -o buffio.o buffio.c

aammd

make -Bnd | make2graph -s | circo -Tpng -o out_circ.png