问题
I'm looking for efficiency gains in calculating the (auto)covariance matrix from individual measurements over time t with t, t-1, etc..
In the data matrix, each row represents an individual and each column represents monthly measurements (the columns are in time order). Similar to the following data (although with some more co-variance).
# simulate data
set.seed(1)
periods <- 70L
ind <- 90000L
mat <- sapply(rep(ind, periods), rnorm)
Below is the (ugly) code I came up with to get the covariance matrix for measurements/ lagged measurements. It takes almost 4 seconds to run. I'm sure that by moving to data.table, thinking more and not relying on loops I could cut the time by a big amount. But since covariance matrices are ubiquitous I suspect there already exists a standard (and efficient) way to do this in R that I should know about first.
# Get variance covariance matrix for 0-5 lags
n_lags <- 5L # Number of lags
vcov <- matrix(0, nrow = n_lags + 1L, ncol = n_lags + 1)
for (i in 0L:n_lags) {
for (j in i:n_lags) {
vcov[j + 1L, i + 1L] <-
sum(mat[, (1L + (j - i)):(periods - i)] *
mat[, 1L:(periods - j)]) /
(ind * (periods - j) - 1)
}
}
round(vcov, 3)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.001 0.000 0.000 0.000 0.000 0.000
[2,] 0.000 1.001 0.000 0.000 0.000 0.000
[3,] 0.000 0.000 1.001 0.000 0.000 0.000
[4,] 0.000 0.000 0.000 1.001 0.000 0.000
[5,] -0.001 0.000 0.000 0.000 1.001 0.000
[6,] 0.000 -0.001 0.000 0.000 0.000 1.001
回答1:
@F. Privé's Rcpp implementation is a good starting place, but we can do better. You will notice in the main algorithm supplied by the OP that there are many replicated fairly expensive calculations. Observe:
OPalgo <- function(m, p, ind1, n) {
vcov <- matrix(0, nrow = n + 1L, ncol = n + 1)
for (i in 0L:n) {
for (j in i:n) {
## lower and upper range for the first & second multiplicand
print(paste(c((1L + (j - i)),":",(periods - i),"
",1L,":",(periods - j)), collapse = ""))
vcov[j + 1L, i + 1L] <-
sum(mat[, (1L + (j - i)):(periods - i)] *
mat[, 1L:(periods - j)]) /
(ind * (periods - j) - 1)
}
}
vcov
}
OPalgo(mat, periods, ind, n_lags)
[1] "1:70 1:70" ## contains "1:65 1:65"
[1] "2:70 1:69"
[1] "3:70 1:68"
[1] "4:70 1:67"
[1] "5:70 1:66"
[1] "6:70 1:65"
[1] "1:69 1:69" ## contains "1:65 1:65"
[1] "2:69 1:68"
[1] "3:69 1:67"
[1] "4:69 1:66"
[1] "5:69 1:65"
[1] "1:68 1:68" ## contains "1:65 1:65"
[1] "2:68 1:67"
[1] "3:68 1:66"
[1] "4:68 1:65"
[1] "1:67 1:67" ## contains "1:65 1:65"
[1] "2:67 1:66"
[1] "3:67 1:65"
[1] "1:66 1:66" ## contains "1:65 1:65"
[1] "2:66 1:65"
[1] "1:65 1:65"
As you can see, the product mat[,1:65] * mat[,1:65] is performed 6 times above. The only difference between the first occurrence and the last occurrence is that the first occurrence has an additional 5 columns. So instead of computing:
sum(mat[ , 1:70] * mat[ , 1:70])
sum(mat[ , 1:69] * mat[ , 1:69])
sum(mat[ , 1:68] * mat[ , 1:68])
sum(mat[ , 1:67] * mat[ , 1:67])
sum(mat[ , 1:66] * mat[ , 1:66])
sum(mat[ , 1:65] * mat[ , 1:65])
We can compute preCalc[1] <- sum(mat[ , 1:65] * mat[ , 1:65]) one time and use this in the other 5 calculations like so:
preCalc[1] + sum(mat[ , 66:70] * mat[ , 66:70])
preCalc[1] + sum(mat[ , 66:69] * mat[ , 66:69])
preCalc[1] + sum(mat[ , 66:68] * mat[ , 66:68])
preCalc[1] + sum(mat[ , 66:67] * mat[ , 66:67])
preCalc[1] + sum(mat[ , 66:66] * mat[ , 66:66])
In each of the above, we have reduce the number of multiplications by 90000 * 65 = 5,850,000 and the number of additions by 5,850,000 - 1 = 5,849,999 for a total of 11,699,999 arithmetic operations saved. The function below achieves this very thing.
fasterAlgo <- function(m, p, ind1, n) {
vcov <- matrix(0, nrow = n + 1L, ncol = n + 1)
preCals <- vapply(1:(n + 1L), function(x) sum(m[ , x:(p - n + x - 2L)] *
m[ , 1L:(p - n - 1L)]), 42.42)
for (i in 0L:n) {
for (j in i:n) {
myNum <- preCals[1L + j - i] + sum(m[, (p - n + j - i):(p - i)] * m[, (p - n):(p - j)])
vcov[j + 1L, i + 1L] <- myNum / (ind * (p - j) - 1)
}
}
vcov
}
## outputs same results
all.equal(OPalgo(mat, periods, ind, n_lags), fasterAlgo(mat, periods, ind, n_lags))
[1] TRUE
Benchmarks:
## I commented out the print statements of the OPalgo before benchmarking
library(microbenchmark)
microbenchmark(OP = OPalgo(mat, periods, ind, n_lags),
fasterBase = fasterAlgo(mat, periods, ind, n_lags),
RcppOrig = compute_vcov(mat, n_lags), times = 5)
Unit: milliseconds
expr min lq mean median uq max neval cld
OP 2775.6110 2780.7207 2843.6012 2784.976 2899.7621 2976.9356 5 c
fasterBase 863.3897 863.9681 865.5576 865.593 866.7962 868.0409 5 b
RcppOrig 160.1040 161.8922 162.0153 162.235 162.4756 163.3697 5 a
As you can see, with this modification we see at least a 3 fold improvement but the Rcpp is still much faster. Let's implement the above concept in Rcpp.
// [[Rcpp::export]]
NumericMatrix compute_vcov2(const NumericMatrix& mat, int n_lags) {
NumericMatrix vcov(n_lags + 1, n_lags + 1);
std::vector<double> preCalcs;
preCalcs.reserve(n_lags + 1);
double myCov;
int i, j, k1, k2, l;
int n = mat.nrow();
int m = mat.ncol();
for (i = 0; i <= n_lags; i++) {
myCov = 0;
for (k1 = i, k2 = 0; k2 < (m - n_lags - 1); k1++, k2++) {
for (l = 0; l < n; l++) {
myCov += mat(l, k1) * mat(l, k2);
}
}
preCalcs.push_back(myCov);
}
for (i = 0; i <= n_lags; i++) {
for (j = i; j <= n_lags; j++) {
myCov = preCalcs[j - i];
for (k1 = m - n_lags + j - i - 1, k2 = m - n_lags - 1; k2 < (m - j); k1++, k2++) {
for (l = 0; l < n; l++) {
myCov += mat(l, k1) * mat(l, k2);
}
}
myCov /= n * (m - j) - 1;
vcov(i, j) = vcov(j, i) = myCov;
}
}
return vcov;
}
## gives same results
all.equal(compute_vcov2(mat, n_lags), compute_vcov(mat, n_lags))
[1] TRUE
New benchmarks:
microbenchmark(OP = OPalgo(mat, periods, ind, n_lags),
fasterBase = fasterAlgo(mat, periods, ind, n_lags),
RcppOrig = compute_vcov(mat, n_lags),
RcppModified = compute_vcov2(mat, n_lags), times = 5)
Unit: milliseconds
expr min lq mean median uq max neval cld
OP 2785.4789 2786.67683 2811.02528 2789.37719 2809.61270 2883.98073 5 d
fasterBase 866.5601 868.25555 888.64418 869.31796 870.92308 968.16417 5 c
RcppOrig 160.3467 161.37992 162.74899 161.73009 164.38653 165.90174 5 b
RcppModified 51.1641 51.67149 52.87447 52.56067 53.06273 55.91334 5 a
Now the enhanced Rcpp solution is around 3x faster the original Rcpp solution and around 50x faster than the original algorithm provided by the OP.
Update
We can do even better. We can reverse the ranges of the indices i/j so as to continuously update preCalcs. This allows up to only compute the product of one new column every iteration. This really comes into play as n_lags increases. Observe:
// [[Rcpp::export]]
NumericMatrix compute_vcov3(const NumericMatrix& mat, int n_lags) {
NumericMatrix vcov(n_lags + 1, n_lags + 1);
std::vector<double> preCalcs;
preCalcs.reserve(n_lags + 1);
int i, j, k1, k2, l;
int n = mat.nrow();
int m = mat.ncol();
for (i = 0; i <= n_lags; i++) {
preCalcs.push_back(0);
for (k1 = i, k2 = 0; k2 < (m - n_lags); k1++, k2++) {
for (l = 0; l < n; l++) {
preCalcs[i] += mat(l, k1) * mat(l, k2);
}
}
}
for (i = n_lags; i >= 0; i--) { ## reverse range
for (j = n_lags; j >= i; j--) { ## reverse range
vcov(i, j) = vcov(j, i) = preCalcs[j - i] / (n * (m - j) - 1);
if (i > 0 && i > 0) {
for (k1 = m - i, k2 = m - j; k2 <= (m - j); k1++, k2++) {
for (l = 0; l < n; l++) {
## updating preCalcs vector
preCalcs[j - i] += mat(l, k1) * mat(l, k2);
}
}
}
}
}
return vcov;
}
all.equal(compute_vcov(mat, n_lags), compute_vcov3(mat, n_lags))
[1] TRUE
Rcpp benchmarks only:
n_lags <- 50L
microbenchmark(RcppOrig = compute_vcov(mat, n_lags),
RcppModified = compute_vcov2(mat, n_lags),
RcppExtreme = compute_vcov3(mat, n_lags), times = 5)
Unit: milliseconds
expr min lq mean median uq max neval cld
RcppOrig 7035.7920 7069.7761 7083.4961 7070.3395 7119.028 7122.5446 5 c
RcppModified 3608.8986 3645.8585 3653.0029 3654.7209 3663.716 3691.8202 5 b
RcppExtreme 324.8252 330.7381 332.9657 333.5919 335.168 340.5054 5 a
The newest implementation is now over 20x faster than the original Rcpp version and well over 300x faster than the original algorithm when n-lags is large.
回答2:
Just translating your code in Rcpp:
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericMatrix compute_vcov(const NumericMatrix& mat, int n_lags) {
NumericMatrix vcov(n_lags + 1, n_lags + 1);
double myCov;
int i, j, k1, k2, l;
int n = mat.nrow();
int m = mat.ncol();
for (i = 0; i <= n_lags; i++) {
for (j = i; j <= n_lags; j++) {
myCov = 0;
for (k1 = j - i, k2 = 0; k2 < (m - j); k1++, k2++) {
for (l = 0; l < n; l++) {
myCov += mat(l, k1) * mat(l, k2);
}
}
myCov /= n * (m - j) - 1;
vcov(i, j) = vcov(j, i) = myCov;
}
}
return vcov;
}
This is at least 10 times as fast as the R algorithm. Yet, I feel like it could be optimized further.
来源：https://stackoverflow.com/questions/45045318/efficient-calculation-of-var-covar-matrix-in-r