LCHansson

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## FORMATSNIPPETS.R ##
## ggplot format snippets ##
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benmarwick

# From http://cainarchaeology.weebly.com/r-package-for-seriation-via-ca.html

library(CAseriation)
data("perfect_seriation")
#loads the sample dataset 

check.ca.plot(perfect_seriation,1,2) 
#plot the Correspondence Analysis scatterplot of the first 2 dimensions in order #to inspect data structure (e.g., seeking for the horseshoe effect)

sort.table(perfect_seriation,1)

timelyportfolio

Tables Are Like Cockroaches
========================================================

As much as I would like to completely replace all tables with beautiful, intuitive, and interactive charts, tables like cockroaches cannot be eliminated. Based on this very [interesting discussion on the Perceptual Edge forum](http://sfew.websitetoolbox.com/post/Old-or-oldest-data-table-5702966) with source [Exploring the Origins of Tables for Information Visualization](http://api.viglink.com/api/click?format=go&key=ccc2217bc2b75c4bdf5f7e57267f0464&loc=http%3A%2F%2Fsfew.websitetoolbox.com%2Fpost%2FOld-or-oldest-data-table-5702966&v=1&libid=1365001395530&out=http%3A%2F%2Fcsis.pace.edu%2F~marchese%2FPapers%2FIV11%2FMarchese_IV%252711.pdf&ref=http%3A%2F%2Fwww.google.com%2Furl%3Fsa%3Dt%26rct%3Dj%26q%3D%26esrc%3Ds%26frm%3D1%26source%3Dweb%26cd%3D2%26ved%3D0CDoQFjAB%26url%3Dhttp%253A%252F%252Fsfew.websitetoolbox.com%252Fpost%252FOld-or-oldest-data-table-5702966%26ei%3DpERcUcvxPImY9QTKi4GwCg%26usg%3DAFQjCNFppNIFLhtMVC3W9Xklbffh8lAm

benmarwick

#### prepare workspace
rm(list = ls(all.names = TRUE))
gc()

#### get data into the R session 
# set R's working directory
setwd("C:/Users/Marwick/Downloads/JSTOR") # change this to where you downloaded the data!
# Get zip file of CSVs from JSTOR and unzip
# this may take a few minutes...
unzip("2013.4.20.FxFmBVYd.zip")

jiffyclub

package { "dkms":
    ensure => latest,
}

package { "chromium-browser":
    ensure => latest,
}

package { "emacs":
    ensure => latest,

benmarwick

# test of storing a DTM on disk...

# reproducible data
library(tm)
data(crude)
dtm <- DocumentTermMatrix(crude)

library(filehash)
dbCreate("testDB") 
db <- dbInit("testDB")

stephenturner

## See http://gettinggeneticsdone.blogspot.com/2013/06/customize-rprofile.html

## Load packages
library(BiocInstaller)

## Don't show those silly significanct stars
options(show.signif.stars=FALSE)

## Do you want to automatically convert strings to factor variables in a data.frame?
## WARNING!!! This makes your code less portable/reproducible.

christophergandrud

#' An R function for creating simple D3 javascript directed network graphs.
#'
#' d3SimpleNetwork creates simple D3 javascript network graphs.
#'
#' @param data a data frame object with three columns. The first two are the names of the linked units. The third records an edge value. (Currently the third column doesn't affect the graph.)
#' @param Source character string naming the network source variable in the data frame. If \code{Source = NULL} then the first column of the data frame is treated as the source.
#' @param Target character string naming the network target variable in the data frame. If \code{Target = NULL} then the second column of the data frame is treated as the target.
#' @param height numeric height for the network graph's frame area.
#' @param width numeric width for the network graph's frame area.
#' @param file a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If \code{file = NULL} then 

Thell

```{r setup, echo=FALSE, results='hide'}
chunkref <- local({
  function(chunklabel) {
    sprintf('[%s](#%s)', chunklabel, chunklabel )
  }  
})

secref <- local({
  function(seclabel) {
    sprintf('[%s](#%s)', seclabel, seclabel )

dgrapov

#check for and/or install dependencies
need<-c("RCurl","ggplot2","gridExtra","reshape2")
for(i in 1:length(need)){
  if(require(need[i], character.only = TRUE)==FALSE){ install.packages(need[i]);library(need[i], character.only = TRUE)} else { library(need[i],character.only = TRUE)}
}

if(require(pcaMethods)==FALSE){
  need<-c('Rcpp', 'rJava',
  'Matrix', 'cluster', 'foreign', 'lattice', 'mgcv', 'survival')
for(i in 1:length(need)){