slwu89’s gists

slwu89 / R_C_API2.c

Created June 26, 2018 00:59

how to call multiple functions with parameters and ... in C using R's C API

	/* evaluate 2 functions with ... (but must take same named args) */
	SEXP C_example(SEXP call, SEXP rho){

	SEXP args = CDR(call);

	/* make up some 'arguments' for our two functions we want to call */
	SEXP a1 = PROTECT(allocVector(REALSXP,1));
	SEXP b1 = PROTECT(allocVector(REALSXP,1));
	REAL(a1)[0] = 5.;
	REAL(b1)[0] = 10.;

slwu89 / getOmega.R

Last active October 25, 2018 17:42

test omega for mgdrive

	get_omega1 <- function(mu,lifespanReduction){
	lifespan <- (1/mu) * lifespanReduction
	get_omega_f <- function(omega,mu,lifespan){
	(1/(1-omega+(omega*mu)))-lifespan
	}
	return(uniroot(f=get_omega_f,interval=c(0,1),lifespan=lifespan,mu=mu,maxiter=1e4)$root)
	}

	# 10-25-2018
	get_omega <- function(mu,lifespan){

slwu89 / multinom.cpp

Last active June 20, 2018 23:07

testing various flavors of multinomial sampling algorithms

slwu89 / harmonicMean.cpp

Created May 30, 2018 17:05

quick test that templated harmonic mean works with int and float

	// CPP program to find harmonic mean of numbers.
	#include <bits/stdc++.h>
	using namespace std;

	template <typename T>
	float harmonicMean(T arr[], int n){
	// Declare sum variables and initialize
	// with zero.
	float sum = 0;
	for (int i = 0; i < n; i++)

slwu89 / lscape.R

Created May 16, 2018 20:58

make a point set, put a parameteric movement kernel on it and plot

	library(viridis)
	library(spatstat)
	library(truncdist)

	# source: https://github.com/slwu89/PlosCompBio_2013/blob/master/fig2/code/functionsModel.R
	points.clustered = function(n, meanParents = 10, clusteredness = .25, ...){
	meanDist = clusteredness / sqrt(meanParents)
	meanChildren = n / meanParents
	ps = rMatClust(meanParents, meanDist, meanChildren, ...)
	while(ps$n != n){

slwu89 / pf_fsm.tex

Created May 9, 2018 20:25

how to make finite state machine in tikz (latex)

	\documentclass[12pt]{article}
	\usepackage{pgf}
	\usepackage{tikz}
	\usetikzlibrary{arrows,automata}
	\usepackage[latin1]{inputenc}

	\begin{document}

	\begin{tikzpicture}[->,>=stealth',shorten >=1pt,auto,node distance=2.8cm,
	semithick]

slwu89 / classWithMapFunctions.cpp

Created April 30, 2018 17:58

example of using std::map to store string keys and values that are bound member functions with 1 parameters

	#ifndef human_hpp
	#define human_hpp

	#include <stdio.h>
	#include <iostream>
	#include <string>
	#include <random>
	#include <functional>
	#include <map>
	using namespace std::placeholders;

slwu89 / lumpedAgeModel.R

Created April 25, 2018 20:26

lumpedAgeModel.R

slwu89 / hypercubeWalk.R

Created April 24, 2018 00:21

walk on hypercube

	n_iter = 100
	n_nodes = 10
	trace = vector(mode="list",length = n_iter)
	trace[[1]] = sample(x = 1:n_nodes,size = n_nodes,replace = TRUE)
	for(i in 2:n_iter){
	trace[[i]] = trace[[i-1]]
	j = sample(x = 1:n_nodes,size = 1) # sample index
	trace[[i]][j] = sample(x = 1:n_nodes,size = 1) # flip n-bit
	}

slwu89 / simpleGillespie.R

Last active April 8, 2018 18:29

simple example of using a gillespie algorithm to simulate a ctmc with 2 events

Sean slwu89