Valentin Stefan valentinitnelav

🏠

Working from home

Research Associate @idiv-biodiversity and UFZ.

valentinitnelav / Check_taxa_names_Taxonstand&wikitaxa.R

Last active January 3, 2018 16:36

Check some taxa names with Taxonstand & wikitaxa

	# -----------------------------------------------------------------------------
	# Example to check some taxa names with Taxonstand & wikitaxa
	# -----------------------------------------------------------------------------
	my_sp <- fread("Output/taxa_to_check_VS.csv")
	my_sp
	# taxa
	# Thereianthus_spicatus
	# Eriocnema_fulva
	# Hebe_macrocarpa
	# Aspalathus_cymbriformis

valentinitnelav / chicks_plot.R

Created November 24, 2017 14:27

	library(ggplot2)
	library(ggsci) # for cool palettes

	# read data
	my_data <- read.csv("data/chickengrowthdiet.csv")
	str(my_data)
	# Diet should not be numeric but factor (or categorical)
	my_data$Diet <- factor(my_data$Diet)

	# -------------------------------------

valentinitnelav / CI_lm_ggplot.R

Created November 24, 2017 12:27

plot confidence intervals for linear model with ggplot using geom_smooth

	#####################################################
	# CI-s for linear model with ggplot
	#####################################################

	library(ggplot2)

	# -------------------------------------
	# Use simulated data from Mick Wu
	# -------------------------------------
	set.seed(1)

valentinitnelav / drunkwalks.R

Last active November 23, 2017 14:31

	setwd("share/")
	getwd()
	my_data <- read.table("data/drunkwalks_data.txt", header = TRUE)

	plot(my_data)

	aggreg <- table(my_data$SEX, my_data$DOMINANT_SIDE)
	rownames(aggreg) <- c("female", "male")
	colnames(aggreg) <- c("left-handed", "right-handed")

valentinitnelav / closest_geodesic_distance_parallel_foreach_example.R

Last active August 29, 2017 12:38

closest geodesic distance with doParallel and foreach - example

	# Example of using foreach parallel loop
	# This should work both on Linux and Windows without any modifications.

	# for an interesting intro, check:
	# http://bgc.yale.edu/sites/default/files/ParallelR.html

	library(foreach)
	library(doParallel)

	# Prepare cluster

valentinitnelav / Euclidean_buffer_distortions.R

Created August 2, 2017 22:20

Euclidean buffer - distortions

	require(rgeos)
	require(sp)
	require(plotKML)

	# Generate a random grid-points for a (almost) global bounding box
	b.box <- as(raster::extent(120, -120, -60, 60), "SpatialPolygons")
	proj4string(b.box) <- "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
	set.seed(2017)
	pts <- sp::spsample(b.box, n=100, type="regular")
	plot(pts@coords)

valentinitnelav / make_GeodesicBuffer.R

Last active April 12, 2018 02:47

Geodesic buffer for point data

	make_GeodesicBuffer <- function(XY.dg, dg.step=5, dst.m, crs){
	#######################################################################################################
	## Function to make a circle-buffer around given points (long-lat coordinates)
	## Is different from rgeos::gBuffer() by the fact that it allows the user to create
	## a geodesic buffer with a width expressed in metric units.
	## Otherwise the user needs to project and apply an Euclidian buffer with rgeos::gBuffer(),
	## which will introduce distortions that vary greatly with latitude and the radius of the circle buffer.
	## See also my question addressed here:
	## https://gis.stackexchange.com/questions/250389/euclidean-and-geodesic-buffering-in-r
	##

valentinitnelav / XML_read_tbl.R

Created April 8, 2017 19:02

Read <table> HTML tag with {XML} library

	# Read <table> HTML tag with {XML} library
	# ====================================================

	# Load library
	library(XML)

	# =======================
	# Read the web page [accessed 08-Apr-2017]
	# =======================
	link <- "http://www.theplantlist.org/1.1/statistics/"

valentinitnelav / rvest_read_tbl.R

Last active April 9, 2017 08:32

Read <table> HTML tag with {rvest} using CSS selectors

	# Read <table> HTML tag with {rvest} using CSS selectors
	# ====================================================

	# Load library
	library(rvest)

	# =======================
	# Read the web page [accessed 08-Apr-2017]
	# =======================
	link <- "http://www.theplantlist.org/1.1/statistics/"

valentinitnelav / rvest_Read_div.R

Last active April 8, 2017 16:34

Read <div> HTML tag with {rvest} using CSS selector

	# Read <div> HTML tag with {rvest} using CSS selector
	# ====================================================

	# Load library
	library(rvest)

	# -----------------------
	# Read the web page
	# -----------------------
	link <- "http://www.adirondacklakessurvey.org/alscrpt.inc.php?alscpond=020225B&pname=ALLEGANY%20BROOK%20POND"