aurora-mareviv

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%% EPS TO PDF CONVERTER %%
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% Author: Mareviv
% Under GNU General Public License
% Paste this document entirely into a file with .TEX extension (.tex). Open it with TeXworks
% Tips for starting with LaTeX: http://talesofr.wordpress.com/2013/05/02/learning-latex-from-scratch/

\documentclass{article}

aurora-mareviv

###########################################
### Network graphs using package igraph ###
###########################################
# Author: Aurora-Mareviv
# Under GNU General Public License
# Script not intended for running using source()
# Simple script that draws a network

library(igraph)
load("my_directory/my_file.rda")

aurora-mareviv

#####################################################
### Network graphs from adjacency matrix - II part ##
#####################################################
# Author: Aurora-Mareviv
# Under GNU General Public License
# If we must construct an adjacency matrix:
# May be the cleanest way to plot links using igraph
# This Gist uses almost the same code as: https://gist.github.com/aurora-mareviv/5568957#file-gistfile1-r
# Paste and execute this simple code in a R console:

aurora-mareviv

#under GNU General Public License
#server.R
library(shiny)
library(ggplot2)

shinyServer(function(input, output) {
  
  
  ## My function:
  f <- function(min.cases, max.cases, p0, OR.cas.ctrl, Nh, sig.level) {

aurora-mareviv

#under GNU General Public License
#server.R
library(shiny)
library(ggplot2)
 
shinyServer(function(input, output) {
## My function:
f <- function(n.cases, p0, OR.cas.ctrl, Nh, sig.level) {
ncases <- n.cases
p0 <- p0

aurora-mareviv

##########################################
### COMMANDS TO START WITH R CONSOLE 1 ###
##########################################
# Under GNU-GPL license v.3

# First, install R: http://cran.r-project.org/
# Second, install and open R-Studio: http://www.rstudio.com/ide/download/desktop
# You can open this text file from inside R-studio, or with a basic text editor (like Notepad).

# Just copy and paste the following commands, and press ENTER to see the results.

aurora-mareviv

###########################################
### COMMANDS TO START WITH R ON ANDROID ###
###########################################
# Under GNU-GPL license

# R in Android installed via the apps "GNURoot" and "GNURoot Wheezy", and sources.list updated with the newest CRAN repositories.
# I strongly recommend to set the working directory of R to a folder that can be accessed from Android such as /sdcard

setwd("/sdcard/R")

aurora-mareviv

#########################################################
#### CAPTURE ARTICLE INFO, IMPACT FACTORS FROM PMIDs ####
#########################################################

# Script to retrieve and organise publications data from PubMed (http://www.ncbi.nlm.nih.gov/pubmed)
# Uses the function ReadPubMed from the package RefManageR. It reads the PubMed API similarly to the search engine in PubMed's page.

# First, automagically install needed libraries:
list.of.packages <- c("RCurl", "RefManageR", "devtools", "plyr", "XML", "data.table")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]

aurora-mareviv

cSplit <- function(indt, splitCols, sep = ",", direction = "wide", 
                   makeEqual = NULL, fixed = TRUE, drop = TRUE, 
                   stripWhite = FALSE) {
  ## requires data.table >= 1.8.11
  require(data.table)
  if (!is.data.table(indt)) setDT(indt)
  if (is.numeric(splitCols)) splitCols <- names(indt)[splitCols]
  if (any(!vapply(indt[, splitCols, with = FALSE],
                  is.character, logical(1L)))) {
    indt[, eval(splitCols) := lapply(.SD, as.character),

aurora-mareviv

ReadPubMed <- function (query, database = "PubMed", ...) 
{
    .params <- list(...)
    bad.ind <- which(!names(.params) %in% c("usehistory", "WebEnv", 
        "query_key", "retstart", "retmax", "field", "datetype", 
        "reldate", "mindate", "maxdate"))
    .parms <- .params
    if (length(bad.ind)) {
        warning("Invalid .params specified and will be ignored")
        .parms <- .parms[-bad.ind]