aurora-mareviv’s gists

ofchurches / gist:da902a393ce8e529b33ca0a137cd5ff3

Last active April 28, 2020 00:40

tidy_tuesday_20200421

	library(tidyverse)
	library(tidytext)
	library(wordcloud)
	library(reshape2)

	# Plot 1: Sentiment wordcloud.

	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 / pmids.mareviv.csv

Last active November 16, 2016 20:21

We can make this file beautiful and searchable if this error is corrected: No commas found in this CSV file in line 0.

aurora-mareviv / pmid.tagcloud.R

Last active March 11, 2021 13:29

aurora-mareviv / myfirstsweave.Rnw

Created May 3, 2016 16:56

Sweave-startup

	% 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 / mthacases.R

Last active August 29, 2015 14:24

Sample size and power calculation for mtDNA association studies. Based in Samuels et al., AJHG 2006, PMC1424681

	################################
	### 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 / server.R

Last active August 29, 2015 14:14

Chi-square power / sample estimations with R!

	#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 / pmidata.2.R

Last active September 22, 2016 23:10

PMIDs database, semi-automatized

	#########################################################
	#### 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"])]

gavinsimpson / Deriv.R

Last active May 25, 2024 08:50

R functions to compute and plot the first derivative of a spline term in a GAM(M) fitted by `gam()` or `gamm()` in package mgcv

	################################################
	## Functions for derivatives of GAM(M) models ##
	################################################
	Deriv <- function(mod, n = 200, eps = 1e-7, newdata, term) {
	if(inherits(mod, "gamm"))
	mod <- mod$gam
	m.terms <- attr(terms(mod), "term.labels")
	if(missing(newdata)) {
	newD <- sapply(model.frame(mod)[, m.terms, drop = FALSE],
	function(x) seq(min(x), max(x), length = n))

mrdwab / cSplit.R

Last active March 14, 2023 05:03

The faster version of `concat.split` that makes use of `data.table` efficiency.

	cSplit <- function(indt, splitCols, sep = ",", direction = "wide",
	makeEqual = NULL, fixed = TRUE, drop = TRUE,
	stripWhite = FALSE) {
	message("`cSplit` is now part of the 'splitstackshape' package (V1.4.0)")
	## 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)))) {

aurora-mareviv / server.R

Last active July 7, 2017 19:55

Power estimations in Mitochondrial DNA association studies: a Samuels et al. impementation (with Graph)

	#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) {

	#########################################################
	#### 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.