Brewster Malevich brews

Natural scientist employed as a senior research developer.

brews / fire_stacker.R

Last active October 6, 2015 20:03

Combine multiple FHX files for Ellis.

	#! /usr/bin/env Rscript
	# 2015-02-25 S. B. Malevich

	# Combine all FHX files in the current working directory and try to output it
	# as a single FHX file (`OUTFILE`). You need to have "firehistory.R" in the
	# same directory, too.

	ARGS <- commandArgs(TRUE)

	source("firehistory.R")

brews / .vimrc

Last active December 3, 2016 18:40

My vimrc file

	call plug#begin('~/.vim/plugged')
	Plug 'sickill/vim-monokai'
	Plug 'dikiaap/minimalist'
	Plug 'w0ng/vim-hybrid'
	Plug 'vim-airline/vim-airline'
	Plug 'vim-airline/vim-airline-themes'
	"Plug 'scrooloose/nerdtree'
	Plug 'scrooloose/syntastic'
	Plug 'scrooloose/nerdcommenter'
	Plug 'ctrlpvim/ctrlp.vim'

brews / animate_bignetcdf.py

Last active November 14, 2015 17:06

Big netCDF animation example for Goddard

	#! /usr/bin/env python3
	# 2015-11-13
	# S. B. Malevich <malevich@email.arizona.edu>

	# Animate netCDF files. Can use in shell like:
	#
	# ./animate_bignetcdf.py SSH 5days_SSH_Brewster.nc ./plots/
	#
	# This is ./animate_bignetcdf.py [variable_name] [netCDF_file] [output_dir]

brews / download_ITRDB.sh

Created April 28, 2016 20:44

	#! /usr/bin/env bash
	# 2016-04-28
	# Download everything from a specific directory in the ITRDB.

	TARGET_URL="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/measurements/northamerica/usa/*"
	WAIT_SECONDS=1

	wget -r -nH --cut-dirs=7 -w $WAIT_SECONDS --tries=10 $TARGET_URL -o log.txt

brews / fire_season_plot.R

Last active May 25, 2016 15:50

firescar season plot example

	plot_season <- function(x, binwidth=10) {
	# Plot seasonality of fire scars through time.
	#
	# Args:
	# x : An fhx object.
	# binwidth : Integer. The bin-size (number of years in each bar) for the
	# output plot. Default is 10.
	#
	# Returns:
	# A ggplot2 object.

brews / parse_itrdb_example.R

Last active October 6, 2016 15:30

Example for someone on how to parse everything from the ITRDB.

	require(dplR)


	# setwd ("/you/had/your/path/here")


	# Global variables. We'll use these below. I put them here so we can easily
	# change them, if need be.
	PATH_ITRDB <- 'itrdb.csv'
	GREP_PATTERN <- '/usa/.?\\.rwl' # matches strings that end in "/usa/.rwl"

brews / spag_spline.R

Created December 7, 2016 20:37

	# 2011-04-04
	# v0.2
	# Copyright 2011 C. Guiterman & S. B. Malevich <malevich@email.arizona.edu>
	# Based on dplR spag.plot function - by A. Bunn.
	# Function to add a spline to dplR's spagetti plot.

	require(dplR)
	#source('ffcsaps.R')

	spag.spline <- function(rwl, zfac=1, spline.nyrs=32, f=0.5, spline.col=2,

brews / matern.py

Created July 14, 2017 17:56

Python Matérn correlation function for given distances and parameters. Comparable to `geoR`'s `matern()`

	import scipy
	import numpy as np

	def matern(u, phi, kappa):
	"""Computes Matérn correlation function for given distances and parameters

	Roughly based on the matern function from Ribeiro and Diggle's 'geoR'
	package for R.

	Parameters:

brews / scrape_IMPD_example.R

Last active July 14, 2017 22:25

How to pull hyperlinks and FHX files from an html directory, read with read_fhx() in an somewhat error-resistant way

	# 2017-07-14
	# S. Brewster Malevich <malevich@email.arizona.edu>

	# How to pull hyperlinks from an html directory, read with read_fhx() in a
	# somewhat error-resistant way.

	# There are a couple ways to do this. Python or `wget` would be far
	# better options, but let's do this with R.

	# Another thing, this pesters the poor NCDC server every time you run this.

brews / make_comparison.sh

Created February 1, 2018 16:16

compare CCSM3 TraCE21ka TS with regridded TOS

	#! /usr/bin/env bash

	# 2018-01-12
	# Make a netCDF file that's diff between TS and TOS (TS - TOS).

	cp data/regrid/tos_sfc_Odec_CCSM3_TraCE21ka_TSREGRID.nc data/combined_tmp.nc
	ncks -A data/ts_sfc_Adec_CCSM3_TraCE21ka.nc data/combined_tmp.nc
	ncap2 -s 'tdif=(ts-tos)' data/combined_tmp.nc data/combined.nc

	# Cleanup