Daichi Narushima dceoy

## install_vboxadd.sh
#!/usr/bin/env bash

if [[ -f "/etc/lsb-release" ]]; then
  apt-get --version
  sudo apt-get -y update
  sudo apt-get -y install gcc make
elif [[ -f "/etc/redhat-release" ]]; then
  if `dnf --version`; then
    sudo dnf -y update
    sudo dnf -y install gcc make

## PPTP_client.sh
sudo yum -y install ppp pptp pptp-setup
sudo pptpsetup --create "vpn" --server "vpn.example.jp" --username "vpnuser" --password "vpnpass" --encrypt

# configuration
# -> /etc/ppp/peers/vpn
# -> /etc/ppp/chap-secrets

# connection
sudo pppd call vpn updetach

## cran_pkg_load.R
#!/usr/bin/env Rscript

load_pkgs <- function(pkgs, repos = 'http://cran.rstudio.com/') {
  update.packages(checkBuilt = TRUE, ask = FALSE, repos = repos)
  sapply(pkgs,
         function(p) {
           if (! p %in% installed.packages()[,1]) install.packages(p, dependencies = TRUE, repos = repos)
           require(p, character.only = TRUE)
         })
}

## row_fisher_df.R
#!/usr/bin/env Rscript

# fisher test on each row
row_fisher <- function(row, alt = 'two.sided', cnf = 0.95) {
  f <- fisher.test(matrix(row, nrow = 2), alternative = alt, conf.level = cnf)
  return(c(row,
           p_val = f$p.value,
           or = f$estimate[[1]],
           or_ll = f$conf.int[1],
           or_ul = f$conf.int[2]))

## accordion.html
<!DOCTYPE html>
<html lang="en">
<head>
  <meta charset="UTF-8">
  <title>Accordion</title>
  <meta name="author" content="d4i"/>
  <style>
    .accordion {
      list-style: none;
    }

## d3_word_clouds.html
<!DOCTYPE HTML>
<html lang="en">
  <head>
    <meta charset="UTF-8">
    <title>D3 Word Clouds</title>
    <meta name="author" content="d4i"/>
  </head>
  <body>
    <script src="https://rawgit.com/mbostock/d3/master/d3.min.js"></script>
    <script src="https://rawgit.com/jasondavies/d3-cloud/master/d3.layout.cloud.js"></script>

## forest_plot.R
#!/usr/bin/env Rscript

sapply(c('data.table', 'ggplot2'), function(p) require(p, character.only = TRUE))

or_ci <- fread('odds_ratio.csv')

forest <- ggplot(or_ci, aes(x = group, y = odds_ratio, ymin = ci_lower, ymax = ci_upper, colour = class)) +
            geom_hline(aes(yintercept = 1), colour = '#4400FF', linetype = 2) +
            geom_pointrange(size = 0.7, shape = 15) +
            scale_y_log10(limits = c(0.01, 100), breaks = c(0.1, 1, 10)) +

## heatmap.R
#!/usr/bin/env Rscript

sapply(c('data.table', 'ggplot2'), function(p) require(p, character.only = TRUE))

mtx <- fread('matrix.csv')

heatmap <- ggplot(mtx, aes(x = col, y = row, fill = val)) +
             geom_tile() +
             scale_fill_gradient(trans = 'log', breaks = c(10, 100, 1000), low = 'grey', high = 'blue') +
             labs(x = 'col', y = 'row')

## glm_confint.R
#!/usr/bin/env Rscript

# Diabetes survey on Pima Indians
#
# variables:
#   'glucose'   Plasma glucose concentration at 2 hours in an oral glucose tolerance test
#   'diabetes'  Diabetes pedigree function
#   'test'      test whether the patient shows signs of diabetes (coded 0 if negative, 1 if positive)
data(pima, package = 'faraway')

## mcmc_logit.R
#!/usr/bin/env Rscript

sapply(c('dplyr', 'data.table', 'MASS', 'MCMCpack'), function(p) require(p, character.only = TRUE))

# Biopsy Data on Breast Cancer Patients
#
# variables:
#   'V1'     clump thickness.
#   'V4'     marginal adhesion.
#   'class'  "benign" or "malignant".
	#!/usr/bin/env bash

	if [[ -f "/etc/lsb-release" ]]; then
	apt-get --version
	sudo apt-get -y update
	sudo apt-get -y install gcc make
	elif [[ -f "/etc/redhat-release" ]]; then
	if `dnf --version`; then
	sudo dnf -y update
	sudo dnf -y install gcc make
	sudo yum -y install ppp pptp pptp-setup
	sudo pptpsetup --create "vpn" --server "vpn.example.jp" --username "vpnuser" --password "vpnpass" --encrypt

	# configuration
	# -> /etc/ppp/peers/vpn
	# -> /etc/ppp/chap-secrets

	# connection
	sudo pppd call vpn updetach
	#!/usr/bin/env Rscript

	load_pkgs <- function(pkgs, repos = 'http://cran.rstudio.com/') {
	update.packages(checkBuilt = TRUE, ask = FALSE, repos = repos)
	sapply(pkgs,
	function(p) {
	if (! p %in% installed.packages()[,1]) install.packages(p, dependencies = TRUE, repos = repos)
	require(p, character.only = TRUE)
	})
	}
	#!/usr/bin/env Rscript

	# fisher test on each row
	row_fisher <- function(row, alt = 'two.sided', cnf = 0.95) {
	f <- fisher.test(matrix(row, nrow = 2), alternative = alt, conf.level = cnf)
	return(c(row,
	p_val = f$p.value,
	or = f$estimate[[1]],
	or_ll = f$conf.int[1],
	or_ul = f$conf.int[2]))
	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>Accordion</title>
	<meta name="author" content="d4i"/>
	<style>
	.accordion {
	list-style: none;
	}
	#!/usr/bin/env Rscript

	sapply(c('data.table', 'ggplot2'), function(p) require(p, character.only = TRUE))

	or_ci <- fread('odds_ratio.csv')

	forest <- ggplot(or_ci, aes(x = group, y = odds_ratio, ymin = ci_lower, ymax = ci_upper, colour = class)) +
	geom_hline(aes(yintercept = 1), colour = '#4400FF', linetype = 2) +
	geom_pointrange(size = 0.7, shape = 15) +
	scale_y_log10(limits = c(0.01, 100), breaks = c(0.1, 1, 10)) +
	#!/usr/bin/env Rscript

	sapply(c('data.table', 'ggplot2'), function(p) require(p, character.only = TRUE))

	mtx <- fread('matrix.csv')

	heatmap <- ggplot(mtx, aes(x = col, y = row, fill = val)) +
	geom_tile() +
	scale_fill_gradient(trans = 'log', breaks = c(10, 100, 1000), low = 'grey', high = 'blue') +
	labs(x = 'col', y = 'row')
	#!/usr/bin/env Rscript

	# Diabetes survey on Pima Indians
	#
	# variables:
	# 'glucose' Plasma glucose concentration at 2 hours in an oral glucose tolerance test
	# 'diabetes' Diabetes pedigree function
	# 'test' test whether the patient shows signs of diabetes (coded 0 if negative, 1 if positive)
	data(pima, package = 'faraway')
	#!/usr/bin/env Rscript

	sapply(c('dplyr', 'data.table', 'MASS', 'MCMCpack'), function(p) require(p, character.only = TRUE))

	# Biopsy Data on Breast Cancer Patients
	#
	# variables:
	# 'V1' clump thickness.
	# 'V4' marginal adhesion.
	# 'class' "benign" or "malignant".