Jaime Ashander ashander

Fisheries landings example

First you'll need to install a few packages if you don't already have them

install.packages(c("plyr", "ggplot2", "rfisheries"))

# Next load up the package
library(rfisheries)

kill iterm2 from Activity Monitor
open a terminal
login to tmux and back up using tmux resurrect or similar

pkill iTerm
ps |grep tmux
kill -9 # for each [pid] correesponding to a `tmux -CC` process, 
 # you could use pkill instead if you got the pattern right?

	data(PlantGrowth)
	pg<-subset(PlantGrowth,group!='ctrl')
	pg$group=factor(pg$group)

	pg1= pg[pg$group=='trt1',]
	pg2= pg[pg$group=='trt2',]

	hist(pg$weight)
	lines(density(pg1$weight), col='blue')
	lines(density(pg2$weight), col='red')

	latex input: mmd-tufte-handout-header
	Title: Tufte latex from Rmd example
	Base Header Level: 2
	latex mode: memoir
	author: Jaime Ashander
	copyright: 2011 Jaime Ashander
	This work is licensed under a Creative Commons License.
	http://creativecommons.org/licenses/by-nc-sa/3.0/
	latex input: mmd-natbib-plain
	latex input: mmd-tufte-handout-begin-doc

	checking build system type... i386-apple-darwin10.8.0
	checking host system type... i386-apple-darwin10.8.0
	checking for gcc... gcc-4.2
	checking whether the C compiler works... yes
	checking for C compiler default output file name... a.out
	checking for suffix of executables...
	checking whether we are cross compiling... no
	checking for suffix of object files... o
	checking whether we are using the GNU C compiler... yes
	checking whether gcc-4.2 accepts -g... yes

	# get data from html tables in ESA archive
	# http://www.esapubs.org/archive/mono/M081/023/suppl-1.htm
	library(XML)
	root <- 'http://www.esapubs.org/archive/mono/M081/023'
	tips <- c('limn.html', 'latitudes.html', 'fish.html', 'acronyms.html')

	dat <- lapply(tips, function(t)
	readHTMLTable(paste(root, t, sep='/')))

	## urls were updated for gdam2 -- should go to gadm.org to update for each run of this
	## http://gadm.org/country
	## choose a country and R spdf from dropdown

	## eg for
	##for AFG sends POST req http://gadm.org/download?OK=OK&_submit_check=1&cnt=AFG_Afghanistan&thm=R%23R%20data
	##returns page with list of download links (likely based on your location and data availability)
	## part of the page looks like
	##
	## download

	## @knitr my-external-chunk
	set.seed(111)
	rnorm(100)