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

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

Sleepingwell

/*
 * A 'functor descriptor' that can be used to generate a runtime polymorphic functor
 * for a set of input/ouput types. To be used to create python extensions in C++ for
 * wrapping with boost::python, such that the functors can be configured in Python
 * then applied to a number (greater than 1) of non-polymorphic input/output types
 * in C++ (the types used in practice will not be those in first_types and second
 * types, which are just for convenience).
 */

#include <new> // placement new

Sleepingwell

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

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

Sleepingwell

library(data.table)

nl <- 100
stp <- 50000
ss <- stp

ss <- seq(stp, length.out=20, by=stp)
times <- sapply(ss, function(ss) {
    mydata <- data.frame(
        to_location_id = as.factor(sample(nl, ss, T)),