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# solarized light color scheme for my TexShop setup

defaults write TeXShop background_R 0.99
defaults write TeXShop background_G 0.96
defaults write TeXShop background_B 0.89

defaults write TeXShop commandred 0.0
defaults write TeXShop commandgreen 0.0
defaults write TeXShop commandblue 1.0

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# check if you need to install these packages
pkg <- c("RODBC", "ggplot2")
inst <- pkg %in% installed.packages()
# inst
if (length(pkg[!inst]) > 0) {
  install.packages(pkg[!inst])
} 
# load all required packages into session
lapply(pkg, library, character.only = TRUE)

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# http://trinkerrstuff.wordpress.com/2014/05/12/handling-s3methods-death-in-roxygen-4-0-0/

pth <- "C:/Users/trinker/qdap/R"

fls <- file.path(pth, dir(pth))

FUN <- function(x) {
    cont <- readLines(x)
    cont[grepl("#' @S3", cont)] <- "#' @export"
    cont[length(cont) + 1] <- ""

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## Add an alpha value to a colour
add.alpha <- function(col, alpha=1){
  if(missing(col))
    stop("Please provide a vector of colours.")
  apply(sapply(col, col2rgb)/255, 2, 
                     function(x) 
                       rgb(x[1], x[2], x[3], alpha=alpha))  
}

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# http://randyzwitch.com/automated-re-install-of-packages-for-r-3-0/
# if using RStudio, make sure to unload all packages that are pre-loaded except for utils: 
# we have to use the install.packages() function in utils for the re-installation

# Get currently installed packages
package_df <- as.data.frame(installed.packages("/Library/Frameworks/R.framework/Versions/2.15/Resources/library"))
package_list <- as.character(package_df$Package)

package_list  # get a package list installed on R 2.15.X
length(package_list)

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# load required libraries
library(shiny)
library(plyr)
library(ggplot2)
library(googleVis)
library(reshape2)


####creation of example data on local directory for uploading####

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Follow the steps at http://cufflinks.cbcb.umd.edu/tutorial.html

1. Download Cufflinks version 2.0.2 (BETA), Source code
2. tar -zxvf cufflinks-2.0.2.tar.gz (before final installation, make sure related tools are installed! See below)

Installing Boost C++ libraries
1. Download Boost at http://www.boost.org/users/download/
2. The bjam boost engine is also required. If MacPort is installed, then use the command sudo port install boost. It will take care of everything.
3. If #2 won't work, try (preferred way!)
  tar -xzf boost_1_50_0.tar.gz

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library(randomForest)

# download Titanic Survivors data
data <- read.table("http://math.ucdenver.edu/RTutorial/titanic.txt", h=T, sep="\t")
# make survived into a yes/no
data$Survived <- as.factor(ifelse(data$Survived==1, "yes", "no"))                 

# split into a training and test set
idx <- runif(nrow(data)) <= .75
data.train <- data[idx,]

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library(stringr)

names(iris)
#[1] "Sepal.Length" "Sepal.Width"  "Petal.Length" "Petal.Width"  "Species"
names(iris) <- str_replace_all(names(iris), "[.]", "_")
names(iris)
#[1] "Sepal_Length" "Sepal_Width"  "Petal_Length" "Petal_Width"  "Species"

s <- c("Go to Heaven for the climate, Hell for the company.")
str_extract_all(s, "[H][a-z]+ ")

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library(sqldf)

sqldf("SELECT
        day
        , avg(temp) as avg_temp
      FROM beaver2
      GROUP BY
        day;")

#   day avg_temp