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Koen Hufkens khufkens

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khufkens / pdf2tiff.sh
Created Apr 14, 2017
Converts PDF figures to tiff files for publication
View pdf2tiff.sh
#!/bin/bash
# batch convert pdf to tiff files
# takes one argument, resolution in dpi
# use: pdf2tiff.sh 150
# will convert all pdfs in the current
# directory to tiff files at 150dpi
files=`ls *.pdf`
for i in $files;do
@khufkens
khufkens / plant2phenocam.sh
Created Apr 14, 2017
Renames Wingscape Plantcam files to the PhenoCam file format
View plant2phenocam.sh
#!/bin/bash
# convert wingscape PlantCam files
# and moves the files into the desired file structure
# for easy processing with the PhenoCam GUI or toolkit
#
# NOTE: requires a running version of linux/Mac or cygwin
# with exif installed.
#
# USE: plant2phenocam.sh MYSITE
@khufkens
khufkens / NCDC_BDTcl.sh
Created Apr 14, 2017
NCDC Batch Download Tool (command line) - downloads station data from the National Climatic Data Center
View NCDC_BDTcl.sh
#!/bin/bash
# Bash script to download all NCDC weather records for
# a list of stations (Station number (AWS/WMO/DATSAV3 number))
# (it's easy to adjust the script to take any selection
# of years, just replace the ncftpls query for the years
# with a years file of your own liking or a range in the
# for loop e.g. years 2001 - 2010 = {2001..2010..1} )
#
# raw data is downloaded, extracted from gz files
@khufkens
khufkens / swath2grid.sh
Created Apr 14, 2017
Converts MOD04 'swath' data to gridded data, using internal ground control point data.
View swath2grid.sh
#!/bin/bash
#
# swath to grid conversion for
# MOD04 reflectance data
#
# get the reprojection information
gdal_translate -of VRT HDF4_EOS:EOS_SWATH:"$1":mod04:Mean_Reflectance_Land land.vrt
gdal_translate -of VRT HDF4_EOS:EOS_SWATH:"$1":mod04:Mean_Reflectance_Ocean ocean.vrt
@khufkens
khufkens / extract_MODIS_phenology_layer.r
Created Apr 14, 2017
Extract MODIS phenology dates (as DOY) from the MCD12Q2 HDF files and export as tiff.
View extract_MODIS_phenology_layer.r
# calculate adjusted phenology dates
# for greenness onset and maximum
extract_MODIS_phenology_layer <- function(value="increase",tiles_file="mytiles.txt"){
# load required libraries
require(raster)
require(MODIS) # to import the SDS layers
# list all hdf files, and extract unique years
@khufkens
khufkens / robinson_map.r
Last active May 17, 2017
An example of the robinson maps often used to represent global modelling data
View robinson_map.r
library(raster)
library(maps)
library(maptools)
library(sf)
library(scales)
# set coordinate systems
robinson = CRS(" +proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs")
latlon = CRS("+init=epsg:4326")
@khufkens
khufkens / tropicos_species_distribution.r
Created Oct 18, 2017
Scrape Tropicos for species distribution information
View tropicos_species_distribution.r
#' @param species: genus species or genus
#' @param quiet: TRUE / FALSE provides verbose output
#' @keywords Tropicos, species distribution
#' @examples
#'
#' # with defaults, outputting a data frame with species distribution
#' # for Clematis
#' df <- tropicos.species.distribution()
#' # returns NA if no data are present
#' [requires the rvest package for post-processing]
@khufkens
khufkens / MCD12Q1_median_class.js
Created Nov 12, 2017
Median MODIS Land Cover (MCD12Q1) Map
View MCD12Q1_median_class.js
// years to process (from start year t0 to end year t1)
var t0 = "2001";
var t1 = "2014";
var LC = ee.ImageCollection('MCD12Q1')
.select('Land_Cover_Type_1')
.filterDate(t0.concat("-01-01"),t1.concat("-12-31"))
.median();
// Create a geometry representing an export region.
@khufkens
khufkens / daymet_server_tests.r
Created Apr 27, 2018
Daymet single pixel server tests
View daymet_server_tests.r
# load required libraries
if(!require(devtools)){install.package("devtools")}
if(!require(daymetr)){devtools::install_github("khufkens/daymetr")}
library("daymetr")
# no delay calls
no_delay = unlist(lapply(1:100, function(...){
# download data
error = try(download_daymet(silent = TRUE))
@khufkens
khufkens / el_nino_precip_analysis.r
Created May 10, 2018
CHIRP drought / precipitation differences between the Amazon and Congo Basin during the 2015 El Nino
View el_nino_precip_analysis.r
# map El Nino drought in the Amazon and Africa
library(raster)
library(tidyverse)
library(maps)
library(RColorBrewer)
# set colour theme
colours = brewer.pal(11,"RdBu")
# download CHIRP data
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