Koen Hufkens khufkens

Founder of BlueGreen Labs | PhD | Addressing climate change through data driven methods

khufkens / downsample_extract_hwsd.R

Last active July 7, 2021 17:38

Downsample (or extract) HWSD data

	# Downsample HWSD data to the scale of 0.5 degree
	# WFDEI / CRU data

	library(raster)
	library(hwsdr)
	library(tidyverse)

	# get mu_global at 0.5 degrees from the
	# ORNL DAAC (which is easier than reading in
	# that monstrous BIL file)

khufkens / equi2polar.sh

Created July 1, 2021 11:49

Convert equirectangular files to polar projections (upward looking)

	#!/bin/bash
	# convert equirectangular 2 fisheye

	files=`ls *.jpg`

	for i in $files;
	do
	noext=`echo $i \| cut -d'.' -f1`

	echo $noext

khufkens / format_phenor_data.R

Created May 28, 2021 11:36

Download and format phenocam sites in phenor

	# required libraries
	library(phenor)

	# where to store the data
	out_dir <- "data-raw/"

	# sites to process, stored in a csv file
	# with columns site, veg_type, roi (check for extra spaces
	# which can mess with name formatting)
	sites <- read.table("data/sites.csv", sep = ",", header = TRUE)

khufkens / crop_and_animate.sh

Created April 3, 2021 10:11

Animate virtual forest images

	#!/bin/bash

	# crop section of images
	mogrify -crop 2770x2304+3560+296 *.jpg

	# compile into animated gif
	convert -delay 100 -loop 0 -depth 8 -resize '640x' -quality 75% *.jpg anim.gif

khufkens / MODIS_arctic_sites_download.R

Last active August 21, 2020 20:06

MODIS arctic sites data request

khufkens / orient_images.sh

Created November 19, 2019 20:52

Line to run on all images before CV processing

	# aligns virtual orientation with physical orientation
	mogrify -auto-orient *.png

khufkens / montage.sh

Last active June 19, 2020 20:24

Montage of example numbers for zooniverse project

montage *.png -bordercolor White -border 5x5 -colorspace Gray -gravity center -tile 7x -geometry +10+0 ~/montage.jpg

khufkens / ghent_air_quality_vmm.R

Created June 12, 2019 12:49

Ghent air quality study VMM rehash

	# Ghent air pollution analysis
	# parametric t-tests
	# non-parametric Mann-Whitney U test

	# download and collate the data
	pdf_data <- paste0(pdftools::pdf_text("https://klimaat.stad.gent/sites/default/files/nota_circulatieplangent_3.pdf")[2],
	collapse = " ")

	# some regular expression moving about
	subset <- gsub(',', ".", pdf_data)

khufkens / cold_front_geopotential_transect.R

Last active April 19, 2019 14:27

Cold front transect along geopotential heights

	# Before you start install all the referenced packages below
	# including the development release of ecmwfr you will also
	# need the rnaturalearthdata in addition to the normal package
	# To run the code copy and paste segments as this is still
	# rough around the edges and requires user interaction to
	# set your CDS API key.

	# load libraries
	if(!require(devtools)){install.packages("devtools")}
	devtools::install_github("khufkens/ecmwfr")

khufkens / essential_climate_variables_animation.R

Last active April 3, 2020 12:43

Downloads and animates CDS essential climate variables

	# Before you start install all the referenced packages below
	# including the development release of ecmwfr you will also
	# need the rnaturalearthdata in addition to the normal package
	# To run the code copy and paste segments as this is still
	# rough around the edges and requires user interaction to
	# set your CDS API key.

	# load libraries
	if(!require(devtools)){install.packages("devtools")}
	devtools::install_github("khufkens/ecmwfr")