boennecd

Provides a faster version of the kinship2::makefamid function if sourced using Rcpp::sourceCpp. It also provides a new implementation and quite different implementation based largely on C++ called makefamid_new. You can try the functions by calling

download.file("https://gist.githubusercontent.com/boennecd/d42fc0ced67033c222ddc8c95945af00/raw/makefamid-fast.cpp", 
              src_file <- paste0(tempfile(), ".cpp"))
Rcpp::sourceCpp(src_file)

	#####
	# simple version which stores the indices in a full matrix and then copy
	# them back later
	f1 <- function(n){
	stopifnot(is.integer(n), n > 1L)
	nq <- n * (n + 1L) / 2L

	o <- matrix(0L, n, n)
	o[lower.tri(o, diag = TRUE)] <- 1:nq
	o[upper.tri(o)] <- t(o)[upper.tri(o)]

	/* Weibull_mix.cpp */
	#include <Rcpp.h>
	using Rcpp::NumericVector;

	/* Computes the survival probability of a Weibull mixture. No checks are
	* made on the length of the input vectors. */
	// [[Rcpp::export]]
	NumericVector Surv_Weibull_mix(
	NumericVector const t, NumericVector const ps, NumericVector const gs,
	NumericVector const ls){

	# probit-issue-simulate.R
	library(Rcpp)
	# 'Weibull_mix.cpp' is at
	# https://gist.github.com/boennecd/770cd7db6f0fa1b6829311ef005436b7
	Rcpp::sourceCpp("Weibull_mix.cpp")

	# Simulate potentially right censored outcomes from a generalized survival
	# model with a given link function and a mixed weibull distribution as the
	# baseline.
	#

	---
	title: Faster Multivariate Normal densities with RcppArmadillo and OpenMP
	author: Nino Hardt, Dicko Ahmadou
	license: GPL (>= 2)
	tags: armadillo openmp featured
	summary: Fast implementation of Multivariate Normal density using RcppArmadillo and OpenMP.
	---

	The Multivariate Normal density function is used frequently
	for a number of problems. Especially for MCMC problems, fast

	// [[Rcpp::depends(RcppArmadillo)]]
	#include <RcppArmadillo.h>

	/* d vech(chol(X)) / d vech(X). See mathoverflow.net/a/232129/134083
	*
	* Args:
	* X: symmetric positive definite matrix.
	* upper: logical for whether vech denotes the upper triangular part.
	*/
	// [[Rcpp::export]]

	## Essentially identical to
	## https://github.com/r-hub/rhub-linux-builders/blob/7af50594ab7a3076adb6e52cce5a912d513a9faa/fedora/Dockerfile
	##
	## in the start
	FROM fedora:30

	## Set a default user. Available via runtime flag
	RUN useradd docker

	RUN dnf install -y \

	#include <Rcpp.h>
	#include <memory.h>

	std::unique_ptr<size_t[]> get_commutation_unequal_vec
	(unsigned const n, unsigned const m, bool const transpose){
	unsigned const nm = n * m,
	nnm_p1 = n * nm + 1L,
	nm_pm = nm + m;
	std::unique_ptr<size_t[]> out(new size_t[nm]);
	size_t * const o_begin = out.get();

	/// tmb_includes.h
	#ifndef TMB_INCLUDES_H
	#define TMB_INCLUDES_H

	/* TMB */
	#include <TMB.hpp>

	namespace CppAD {
	inline double Value(double const x){
	return x;

	# assign function to simulate a number of independent pedigrees along with
	# the observed survival times for the last generation simulated from a
	# mixed generalized survival model.
	#
	# Args:
	# max_depth: maximum depth of the families (number of generations less
	# one).
	# max_members: roughly maximum number of members in each pedigree in each
	# family.
	# sds: standard deviation of the genetic effect.