Sleepingwell

# Copyright (C) 2013 Simon Knapp
#
# This program is free software; you can redistribute it and/or
# modify it under the any terms you wish.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

# To run this, type:

Sleepingwell

.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)

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

Sleepingwell

# 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,

Sleepingwell

#include <Python.h>

struct MyClass {
    int val;
    MyClass(void) : val(42) {}
};

#ifdef __cplusplus
extern "C" {
#endif // __cplusplus

Sleepingwell

# A simple script to load data from a shapefile into a spatialite db.
# Transfering the geometries is slow. It would probably be much faster to
# use WKB directly for the load, but I cannot get this to work.

# This is largely copied from
#   https://github.com/geoalchemy/geoalchemy/blob/master/examples/spatialite.py
import os, osgeo.ogr
from sqlite3 import dbapi2 as sqlite
from sqlalchemy.orm import sessionmaker
from sqlalchemy import event, create_engine, MetaData

Sleepingwell

install.packages('pracma')

mb <- rbind(
  c(1,1,0,0),
  c(0,0,1,1),
  c(1,0,1,0),
  c(0,1,0,1)
)

b <- c(24, 14, 26, 12, 12, 29, 11, 30, 12)

Sleepingwell

#include <stdio.h>
#include <string.h>
#include <assert.h>
#include "zlib.h"

#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
#  include <fcntl.h>
#  include <io.h>
#  define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
#else

Sleepingwell

#include "stdafx.h"
#include "emperical_dist.h"

void emperical_dist(double* vals, double* res, int* vlen, int* dlen) {
	int i, j, tmp, n = *vlen;
	double *valsAt, val; 
	for(i=0; i<*dlen; ++i, ++res){
		valsAt = vals;
		val = *res;
		tmp = 0;

Sleepingwell

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