Simon Knapp Sleepingwell

apsrm

Contributor License Agreement ("Agreement") v1.1.0

Thank you for your interest in the apsrm open source Project which is being administered by CSIRO Data61. This document describes the terms under which You may contribute software, bug fixes, configuration changes, documentation, or any other materials that you send to Us related to the Project (each a "Contribution") to the Project. This contributor license agreement ("Agreement") documents the rights granted by You to Us with respect to your Contributions.

Once agreed, these terms apply not only to your initial Contribution but also to all past Contributions and subsequent Contributions by You to the Project, unless we change the terms. When we change the terms, you will be asked to sign the new version of the agreement the next time you contribute.

We appreciate your participation in our Project, and your help in improving the Project, so we want you to understand what will be done with the Contributions. This license is for your protection

This is based on this very informative post.

Configuration settings

diff.submodule = log (so you get clearer container diffs when referenced submodule commits changed).
fetch.recurseSubmodules = on-demand (so you are confident new referenced commits for known submodules get fetched with container updates).
status.submoduleSummary = true (so git status gets useful again when a referenced submodule commit changed).

Adding or cloning

Initial add: git submodule add

	.PHONY: venv

	VENV_PATH=venv
	TIMESTAMP_FILE=$(VENV_PATH)/.f2pytest-creation-timestamp

	test: venv test.f90
	. $(VENV_PATH)/bin/activate && \
	python -m numpy.f2py -c test.f90 -m test

	venv: $(TIMESTAMP_FILE)

	# Script for extracting various data from https://doi.org/10.1371/journal.pcbi.1005697.s002

	#-------------------------------------------------------------------------------
	# Contact matricies for Australia
	#-------------------------------------------------------------------------------
	library(openxlsx)
	AusOtherLocationsContactMatrix <- as.matrix(read.xlsx(
	'contact_matrices_152_countries/MUestimates_other_locations_1.xlsx',
	sheet='Australia'))
	save(AusOtherLocationsContactMatrix,

	#include <vector>
	#include <utility>
	#include <iterator>
	#include <R.h>
	#include <Rdefines.h>

	template<typename Iter>
	SEXP makePolygon(Iter b, Iter e) {
	SEXP
	coords;

	<html>
	<!-- based example found at: http://blog.harakys.com/blog/2012/02/21/embed-markdown-into-your-html/ -->
	<header>
	<script src="http://code.jquery.com/jquery-1.10.1.min.js"></script>
	<script src="https://google-code-prettify.googlecode.com/svn/loader/run_prettify.js"></script>
	<script src="https://google-code-prettify.googlecode.com/svn/loader/prettify.js"></script>
	<script src="http://www.showdown.im/showdown/example/showdown.js"> </script>

	<script type="text/javascript">
	var generateHTML = function() {

	/*
	This program implements the BBP algorithm to generate a few hexadecimal
	digits beginning immediately after a given position id, or in other words
	beginning at position id + 1. On most systems using IEEE 64-bit floating-
	point arithmetic, this code works correctly so long as d is less than
	approximately 1.18 x 10^7. If 80-bit arithmetic can be employed, this limit
	is significantly higher. Whatever arithmetic is used, results for a given
	position id can be checked by repeating with id-1 or id+1, and verifying
	that the hex digits perfectly overlap with an offset of one, except possibly
	for a few trailing digits. The resulting fractions are typically accurate

	/*
	Copyright (C) 2006 Anthony M. Pasqualoni

	This program is free software; you can redistribute it and/or
	modify it under the terms of the GNU General Public License
	as published by the Free Software Foundation; either version 2
	of the License, or (at your option) any later version.

	This program is distributed in the hope that it will be useful,
	but WITHOUT ANY WARRANTY; without even the implied warranty of

	test.func <- function(n.samples) {
	nms <- c("Wichmann-Hill", "Marsaglia-Multicarry", "Super-Duper", "Mersenne-Twister", "Knuth-TAOCP-2002", "Knuth-TAOCP", "L'Ecuyer-CMRG")
	tmp <- lapply(nms, function(unif.rng.name) {
	RNGkind(unif.rng.name)
	nms <- c("Kinderman-Ramage", "Ahrens-Dieter", "Box-Muller", "Inversion")
	tmp <- sapply(nms, function(norm.rng.name) {
	RNGkind(, norm.rng.name)
	system.time(rnorm(n.samples))
	})[1:3,]
	# included here because I'm not sure if rziggurat uses the unif rng internally.

	# A wrapper around Rcartogram::cartogram for shape files.
	#
	# @param polys: Either a SpatialPolygonsDataFrame or the path to a shape file.
	# @param variable: Either a string giving the name of the variable to used in polys@data, or a vector
	# of the same length as polys@polygons.
	# @param nx: The number of columns in the raster used to represent the region.
	# @param ny: The number of rows in the raster used to represent the region.
	# @param buffer.by: The proportion width of the buffer to add to the region (see ?Rcartogram::addBoundary).
	#
	# @return The new boundaries as A SpatialPolygonsDataFrame with the attribute 'cartogram.scaling.var'.