Compilation Error using RcppArmadillo package in R with rowvec - rcpp

I am trying to compile the following code. Please see below what I have tried so far. Is there anything that I am missing. Any help would be appreciated.
#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]
using namespace Rcpp;
// [[Rcpp::export]]
List beta(const arma::rowvec beta,
const int n,
const int L1,
const int p,
const arma::mat YWeight1,
const arma::mat z){
double S0=0;
for(int i = 0;i < n; ++i){
arma::rowvec zr = z.rows(i,i);
S0 += exp(arma::as_scalar(beta*zr.t()));
}
List res;
res["1"] = S0;
return(res);
}
I can't copy the error but this is what I am getting.
no match for call to '(Rcpp::traits::input_parameter<const arma::Row<double>
and so on...

There is a rowvec converter. The issue here is:
filece5923f317b2.cpp:39:34: error: type 'Rcpp::traits::input_parameter::type' (aka 'ConstInputParameter >') does not provide a call operator
rcpp_result_gen = Rcpp::wrap(beta(beta, n, L1, p, YWeight1, z));
Few thoughts: 1. There is already a function called beta() and 2. there is a variable named beta that might be causing havoc with Rcpp attributes.
Solution:
Remove the using namespace Rcpp;
Rename the function away from beta() to beta_estimator().
Specify the length of Rcpp::List
Access by numeric index instead of string.
Corrected code:
#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::export]]
Rcpp::List beta_estimator( // renamed function
const arma::rowvec beta,
const int n,
const int L1,
const int p,
const arma::mat YWeight1,
const arma::mat z){
double S0 = 0;
for(int i = 0;i < n; ++i){
arma::rowvec zr = z.rows(i,i);
S0 += exp(arma::as_scalar(beta*zr.t()));
}
// Specify list length
Rcpp::List res(1);
res[0] = S0;
return(res);
}

Related

Pointer of arma::mat or arma::vet as arguments of Rcpp function for internal purpose only

I am developing an R package using RcppArmadillo. I was writing a few util functions, which manipulate arma::mat and arma::vec objects. So I was trying to use pointer of arma::mat (or arma::vec) as arguments of those functions. Just like the following C++ example (https://onlinegdb.com/mNczwaPaV), I just want to pass the address of object, then manipulate the object value:
#include <iostream>
using namespace std;
void plus_one(int *x){
*x = *x + 1;
}
int main(){
int x = 1;
plus_one(&x);
printf("%d", x);
return 0;
}
2
...Program finished with exit code 0
Press ENTER to exit console.
Here is a toy example I was trying. RStudio gave me the error message "called object type 'arma::vec *' (aka 'Col *') is not a function or function pointer."
#include <RcppArmadillo.h>
using namespace Rcpp;
//
// [[Rcpp::depends(RcppArmadillo)]]
void f2(arma::vec *v){
*v = (*v)%log(*v) + (1-(*v))*log(1-(*v));
}
void trim(arma::vec *v, double tol){
*v(find(*v<=0.0)).fill(tol);
*v(find(*v>=1.0)).fill(1-tol);
}
// [[Rcpp::export]]
arma::vec f1(arma::vec v){
trim(&v, 1e-8);
return(f2(&v));
}
/*** R
f1(seq(0,1,0.2))
*/
I don't think v.memptr() allows me to manipulate the vector by R-like vector operations. For example,
double* v_mem = v.memptr();
*v_mem+1;
does not give the entrywise addition result. (Here, I want is v+1 in R). Do you have any suggestions?
Thank you!

Bootstrapping using Rcpp

I am implementing a bootstrap procedure using Rcpp and seem to have hit a performance bottleneck (?). Basically, I am creating a boot matrix using RcppArmadillo, calling the fit_power_law function from igraph and estimating the power law coefficient. The code is as follows:
#include <RcppArmadillo.h>
#include <RcppArmadilloExtensions/sample.h>
using namespace Rcpp;
// [[Rcpp::depends(RcppArmadillo)]]
double alphaPLFit(const arma::vec& x) {
Environment igraph("package:igraph");
Function fit_power_law = igraph["fit_power_law"];
List p = fit_power_law(Named("x", x));
return p["alpha"];
}
arma::mat bootstraps(const arma::vec& x, int times) {
arma::mat bootMatrix;
for (int t = 0; t < times; ++t) {
arma::vec resample = RcppArmadillo::sample(x, x.n_elem, true);
bootMatrix.insert_cols(t, resample);
}
return bootMatrix;
}
// [[Rcpp::export]]
arma::vec bootAlphaPLFit(const arma::vec& x, int times) {
arma::mat bootMatrix = bootstraps(x, times);
arma::vec alphas(times);
for (int i = 0; i < times; ++i) {
double alpha = alphaPLFit(bootMatrix.col(i));
alphas[i] = alpha;
}
return alphas;
}
/***R
library(igraph)
sampleData <- degree(sample_pa(n = 1e5, m = 3, directed = FALSE))
system.time(bootAlphaPLFit(sampleData, 500))
*/
This takes about a minute to run on my computer. As a comparison, the boot function from the boot package takes about 30 seconds, with a custom statistic that calls igraph::fit_power_law and extracts alpha.
Is there any way to speed this up?

Using c++11's std::async inside an abstract base class

Why doesn't making threads like this work inside of an abstract base class? I'm trying to abstract away all of the multithreading details for users who derive from this base class. I don't understand why it says "no type named 'type'" when I clearly write that callbackSquare returns type int.
#include <iostream>
#include <future>
#include <vector>
class ABC{
public:
std::vector<std::future<int> > m_results;
ABC(){};
~ABC(){};
virtual int callbackSquare(int& a) = 0;
void doStuffWithCallBack();
};
void ABC::doStuffWithCallBack(){
for(int i = 0; i < 10; ++i)
m_results.push_back(std::async(&ABC::callbackSquare, this, i));
for(int j = 0; j < 10; ++j)
std::cout << m_results[j].get() << "\n";
}
class Derived : public ABC {
Derived() : ABC() {};
~Derived(){};
int callbackSquare(int& a) {return a * a;};
};
int main(int argc, char **argv)
{
std::cout << "testing\n";
return 0;
}
The strange errors I'm getting are:
/usr/include/c++/5/future:1709:67: required from 'std::future<typename std::result_of<_Functor(_ArgTypes ...)>::type> std::async(std::launch, _Fn&&, _Args&& ...) [with _Fn = int (ABC::*)(int&); _Args = {ABC*, int&}; typename std::result_of<_Functor(_ArgTypes ...)>::type = int]'
/usr/include/c++/5/future:1725:19: required from 'std::future<typename std::result_of<_Functor(_ArgTypes ...)>::type> std::async(_Fn&&, _Args&& ...) [with _Fn = int (ABC::*)(int&); _Args = {ABC*, int&}; typename std::result_of<_Functor(_ArgTypes ...)>::type = int]'
/home/taylor/Documents/ssmworkspace/callbacktest/main.cpp:16:69: required from here
/usr/include/c++/5/functional:1505:61: error: no type named 'type' in 'class std::result_of<std::_Mem_fn<int (ABC::*)(int&)>(ABC*, int)>'
typedef typename result_of<_Callable(_Args...)>::type result_type;
^
/usr/include/c++/5/functional:1526:9: error: no type named 'type' in 'class std::result_of<std::_Mem_fn<int (ABC::*)(int&)>(ABC*, int)>'
_M_invoke(_Index_tuple<_Indices...>)
Your problem can be reproduced with any function that accepts a reference:
#include <future>
int f(int& a)
{
return a * a;
}
int main()
{
int i = 42;
auto r = std::async(f, i);
}
Accepting a reference in your code is risky since the variable will be modified by the loop iteration, creating a data race because the called function also accesses the variable.
Change the function to accept the input parameter by value, or call std::async by passing std::ref(i) or std::cref(i) (in case the function accepts a const reference) if you acknowledge the risk.

Multithreading in C++ using reference classes - ThreadStart constructor issues?

I appreciate any help, and would like to thank you in advance. I'm working on a project for one of my classes. Essentially performing merge sort using multithreading and reference classes. In main I'm just trying to create an initial thread that will begin the recursive mergesort. Each time the array is split a new thread is spawned to handle that subroutine. I don't need all of it done, i just don't under stand why my Thread constructor and ThreadStart delegate are not working. Thanks again!!
#include <iostream>
#include <vector>
#include <string>
#include <time.h>
#include <cstdlib>
using namespace System;
using namespace System::Threading;
public ref class MergeSort
{
private: int cnt;
public: MergeSort()
{
cnt = 0;
}
public: void mergeSort(char a[], int from, int to)
{
Thread^ current = Thread::CurrentThread;
if(from == to)
return;
int mid = (from + to)/2;
//Sort the first and the second half
//addThread(a, from, mid);
//addThread(a, mid+1, to);
//threads[0]->Join();
//threads[1]->Join();
merge(a, from, mid, to);
}
public: void merge(char a[], int from, int mid, int to)
{
Thread^ current = Thread::CurrentThread;
while (current ->ThreadState == ThreadState::Running)
{
int n = to-from + 1; // Size of range to be merged
std::vector<char> b(n);
int i1 = from; //Next element to consider in the first half
int i2 = mid + 1; //Next element to consider in the second half
int j = 0; //Next open position in b
//As long as neight i1 or i2 is past the end, move the smaller element into b
while(i1 <= mid && i2 <= to)
{
if(a[i1] < a[i2])
{
b[j] = a[i1];
i1++;
}
else
{
b[j] = a[i2];
i2++;
}
j++;
}
//Copy any remaining entries of the first half
while(i1 <= mid)
{
b[j] = a[i1];
i1++;
j++;
}
while(i2 <= to)
{
b[j] = a[i2];
i2++;
j++;
}
//Copy back from temporary vector
for(j = 0; j < n; j++)
a[from+j] = b[j];
}
}
};
void main()
{
char A[10];
for(int i = 0; i < 10; i++)
{
A[i] = ((char) ((rand() % (122-65)) + 65));
}
array<Thread^>^ tr = gcnew array<Thread^>(10);
MergeSort^ ms1 = gcnew MergeSort();
ThreadStart^ TS = gcnew ThreadStart(ms1, &MergeSort::mergeSort(A, 0, 10));
tr[0] = gcnew Thread(TS);
tr[0] -> Start();
system("pause");
}
The issue you are facing here is how to construct a ThreadStart delegate. You are trying to do too many things in the ThreadStart constructor. You cannot pass in arguments at this point because all it is looking for is a start location for the thread.
The delegate should be:
ThreadStart^ TS = gcnew ThreadStart(ms1, &MergeSort::mergeSort);
Since however you are passing in some state, I would recommend doing a bit more research on how that is done using C++\CLI. This MSDN topic should give you a start.
Edit:
Never mind, the problem was that I had to change the parameter of the method I tried to pass from Int32 to Object^.
I´m having a similar issue, though i think my problem are not the arguments. I´m passing those through during thread->Start().
I think my problem is rather that I´m trying to start the thread using a method of a ref class.
invalid delegate initializer -- function does not match the delegate type
Is the error I´m getting. Any Ideas?
void AddForcesAll() {
for (int index = 0; index < n; index++) {
Thread^ thread = gcnew Thread (gcnew ParameterizedThreadStart(this, &Bodies::AddForces));
thread->Start(index);
}
The Syntax worked fine for me for non referenced classes.

How do I set up a function to convert vector of strings to vector of integers in VC++?

The question is in the title. Need help figuring out why my code compiles but doesn't work as intended. Thanks!
//This example demonstrates how to do vector<string> to vectro<int> conversion using a function.
#include <iostream>
#include <string>
#include <vector>
#include <sstream>
using namespace std;
vector<int>* convertStringVectorToIntVector (vector<string> *vectorOfStrings)
{
vector<int> *vectorOfIntegers = new vector<int>;
int x;
for (int i=0; i<vectorOfStrings->size(); i++)
{
stringstream str(vectorOfStrings->at(i));
str >> x;
vectorOfIntegers->push_back(x);
}
return vectorOfIntegers;
}
int main(int argc, char* argv[]) {
//Initialize test vector to use for conversion
vector<string> *vectorOfStringTypes = new vector<string>();
vectorOfStringTypes->push_back("1");
vectorOfStringTypes->push_back("10");
vectorOfStringTypes->push_back("100");
delete vectorOfStringTypes;
//Initialize target vector to store conversion result
vector<int> *vectorOfIntTypes;
vectorOfIntTypes = convertStringVectorToIntVector(vectorOfStringTypes);
//Test if conversion is successful and the new vector is open for manipulation
int sum = 0;
for (int i=0; i<vectorOfIntTypes->size(); i++)
{
sum+=vectorOfIntTypes->at(i);
cout<<sum<<endl;
}
delete vectorOfIntTypes;
cin.get();
return 0;
}
The code above has only one problem: You are deleting your vectorOfStringTypes before you pass it to your conversion function.
Move the line delete vectorOfStringTypes; to after you have called your convert function and the program works as intended.

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