aurora-mareviv

library(tidyverse)
library(tidytext)
library(wordcloud)
library(reshape2)
library(tidygraph)
library(ggraph)

gdpr_text <- readr::read_tsv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2020/2020-04-21/gdpr_text.tsv')

#base on https://www.tidytextmining.com/sentiment.html

aurora-mareviv

pmId
23552565
26655164
26077880
26164471
25135986
24978892
24467976
24180712

aurora-mareviv

#########################################################
#### CAPTURE ABSTRACTS FROM PMIDs & MAKE A WORDCLOUD ####
#########################################################

# GNU-GPL license
# Author: Mareviv (https://talesofr.wordpress.com)

# Script to retrieve and mine abstracts 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.
# This script creates two directories in your working directory: 'corpus1' for the abstracts file, and 'wordcloud' to store the plot.

aurora-mareviv

# server.R

shinyServer(function(input, output) {
  
  f <- function(seed, ncases, branches){
    set.seed(seed)
    branch <- branches
    if(branch==2){ # table creation
      rond1 <- round(ncases/2, 0)
      rond2 <- ncases-rond1

aurora-mareviv

% This is a Sweave template from TalesofR.wordpress.com.
% When a line is preceeded by a "%" sign, it will be ignored by the program.
% You can write what you want in this way. It usually serves for making invisible comments.
% If you want to make a comment inside the chunk of R code, the symbol to start the line must be "#", instead of "%"
% Let's start with the template:

\documentclass{article}
\begin{document}

% chunks of R code are initiated by "<>=", and ended by "@"

aurora-mareviv

################################
### 1. FORMULA SAMUELS CALC ####
####### NCMIN-HAPLOGROUPS ######
################################

# Under GPL license
# AUTHOR: A. Baluja

# Original formulae in Samuels et al., AJHG 2006, PMC1424681. Written in R by A. Baluja.

aurora-mareviv

#under GNU General Public License
#server.R

library(shiny)
library(pwr)

shinyServer(function(input, output) {

  ## My pwr function:
  f <- function(eff.size, n.observs, degfree, signif) {

aurora-mareviv

######################################
### DOWNLOAD JOURNAL ABBREVIATIONS ###
######################################
 
# URL: ftp://ftp.ncbi.nih.gov/pubmed/J_Medline.txt
 
cit <- read.csv("ftp://ftp.ncbi.nih.gov/pubmed/J_Medline.txt", quote = "", sep = "\t", row.names = NULL, stringsAsFactors = FALSE)
 
# Tidy the original data and create data.frame
names(cit)[1] <- "X"

aurora-mareviv

####################################
### DOWNLOAD IMPACT FACTORS 2014 ###
####################################
 
# url: http://www.citefactor.org/journal-impact-factor-list-2014.html
# download lots of tables, then join them
# tabs <- getURL(url)
# tabs <- readHTMLTable(tabs, stringsAsFactors = F)

library(RCurl)

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]