R version 3.4.2 (2017-09-28) -- "Short Summer"
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>
> ### ceeboo 2007
>
> ## todo: special values NaN, NA, and Inf
>
> library("proxy")
Attaching package: 'proxy'
The following objects are masked from 'package:stats':
as.dist, dist
The following object is masked from 'package:base':
as.matrix
>
> set.seed(20070630)
>
> ##
>
> x <- matrix(runif(20),5,4)
> inherits(x, "matrix")
[1] TRUE
> rownames(x) <- LETTERS[1:5]
> y <- x
> y[2,] <- x[1,] <- 0
>
> x
[,1] [,2] [,3] [,4]
A 0.0000000 0.000000000 0.0000000 0.0000000
B 0.8390691 0.002929016 0.3449861 0.4751930
C 0.0377036 0.300615279 0.1399626 0.5143060
D 0.7621676 0.963274350 0.4358104 0.7934745
E 0.1211588 0.452265898 0.8005272 0.3062947
> y
[,1] [,2] [,3] [,4]
A 0.4595829 0.2462831 0.6662151 0.2658000
B 0.0000000 0.0000000 0.0000000 0.0000000
C 0.0377036 0.3006153 0.1399626 0.5143060
D 0.7621676 0.9632744 0.4358104 0.7934745
E 0.1211588 0.4522659 0.8005272 0.3062947
>
> ## user interfaces
>
> r <- .Call("R_minkowski_dist", x, NULL, FALSE, 1, PACKAGE = "proxy")
> all.equal(c(r), c(stats::dist(x, method = "minkowski", p = 1)))
[1] TRUE
> r
A B C D
B 1.6621772
C 0.9925875 1.3431883
D 2.9547267 1.4463526 1.9621392
E 1.6802466 1.7916865 1.1036817 2.0039138
> .Call("R_minkowski_dist", x, x, FALSE, 1, PACKAGE = "proxy")
A B C D E
A 0.0000000 1.662177 0.9925875 2.954727 1.680247
B 1.6621772 0.000000 1.3431883 1.446353 1.791686
C 0.9925875 1.343188 0.0000000 1.962139 1.103682
D 2.9547267 1.446353 1.9621392 0.000000 2.003914
E 1.6802466 1.791686 1.1036817 2.003914 0.000000
> .Call("R_minkowski_dist", x, y, FALSE, 1, PACKAGE = "proxy")
A B C D E
A 1.6378810 0.0000000 0.9925875 2.954727 1.680247
B 1.1534623 1.6621772 1.3431883 1.446353 1.791686
C 1.2509699 0.9925875 0.0000000 1.962139 1.103682
D 1.7776551 2.9547267 1.9621392 0.000000 2.003914
E 0.7192137 1.6802466 1.1036817 2.003914 0.000000
> .Call("R_minkowski_dist", x, y, TRUE, 1, PACKAGE = "proxy")
[1] 1.637881 1.662177 0.000000 0.000000 0.000000
>
> dfun <- paste("R",c("euclidean", "maximum", "manhattan", "canberra", "binary", "matching", "fuzzy", "mutual"),"dist", sep = "_")
>
> for (f in dfun) {
+ cat("\nTesting ",f,"\n\n",sep="")
+ r <- try(do.call(".Call", list(f, x, NULL, FALSE, PACKAGE = "proxy")))
+ if ( inherits(r, "try-error"))
+ next
+ s <- try(stats::dist(x, method = gsub("R_|_dist", "", f)))
+ if (!inherits(s, "try-error"))
+ print(all.equal(c(r), c(s)))
+ print(r)
+ print(do.call(".Call", list(f, x, x, FALSE, PACKAGE = "proxy")))
+ print(do.call(".Call", list(f, x, y, FALSE, PACKAGE = "proxy")))
+ print(do.call(".Call", list(f, x, y, TRUE, PACKAGE = "proxy")))
+ }
Testing R_euclidean_dist
[1] TRUE
A B C D
B 1.0241432
C 0.6130998 0.8799820
D 1.5258864 1.0186899 1.0627446
E 0.9766699 0.9763929 0.7138466 1.0209722
A B C D E
A 0.0000000 1.0241432 0.6130998 1.525886 0.9766699
B 1.0241432 0.0000000 0.8799820 1.018690 0.9763929
C 0.6130998 0.8799820 0.0000000 1.062745 0.7138466
D 1.5258864 1.0186899 1.0627446 0.000000 1.0209722
E 0.9766699 0.9763929 0.7138466 1.020972 0.0000000
A B C D E
A 0.8867716 0.0000000 0.6130998 1.525886 0.9766699
B 0.5918315 1.0241432 0.8799820 1.018690 0.9763929
C 0.7208543 0.6130998 0.0000000 1.062745 0.7138466
D 0.9680706 1.5258864 1.0627446 0.000000 1.0209722
E 0.4202848 0.9766699 0.7138466 1.020972 0.0000000
[1] 0.8867716 1.0241432 0.0000000 0.0000000 0.0000000
Testing R_maximum_dist
[1] TRUE
A B C D
B 0.8390691
C 0.5143060 0.8013655
D 0.9632744 0.9603453 0.7244640
E 0.8005272 0.7179103 0.6605646 0.6410087
A B C D E
A 0.0000000 0.8390691 0.5143060 0.9632744 0.8005272
B 0.8390691 0.0000000 0.8013655 0.9603453 0.7179103
C 0.5143060 0.8013655 0.0000000 0.7244640 0.6605646
D 0.9632744 0.9603453 0.7244640 0.0000000 0.6410087
E 0.8005272 0.7179103 0.6605646 0.6410087 0.0000000
A B C D E
A 0.6662151 0.0000000 0.5143060 0.9632744 0.8005272
B 0.3794862 0.8390691 0.8013655 0.9603453 0.7179103
C 0.5262524 0.5143060 0.0000000 0.7244640 0.6605646
D 0.7169912 0.9632744 0.7244640 0.0000000 0.6410087
E 0.3384240 0.8005272 0.6605646 0.6410087 0.0000000
[1] 0.6662151 0.8390691 0.0000000 0.0000000 0.0000000
Testing R_manhattan_dist
[1] TRUE
A B C D
B 1.6621772
C 0.9925875 1.3431883
D 2.9547267 1.4463526 1.9621392
E 1.6802466 1.7916865 1.1036817 2.0039138
A B C D E
A 0.0000000 1.662177 0.9925875 2.954727 1.680247
B 1.6621772 0.000000 1.3431883 1.446353 1.791686
C 0.9925875 1.343188 0.0000000 1.962139 1.103682
D 2.9547267 1.446353 1.9621392 0.000000 2.003914
E 1.6802466 1.791686 1.1036817 2.003914 0.000000
A B C D E
A 1.6378810 0.0000000 0.9925875 2.954727 1.680247
B 1.1534623 1.6621772 1.3431883 1.446353 1.791686
C 1.2509699 0.9925875 0.0000000 1.962139 1.103682
D 1.7776551 2.9547267 1.9621392 0.000000 2.003914
E 0.7192137 1.6802466 1.1036817 2.003914 0.000000
[1] 1.637881 1.662177 0.000000 0.000000 0.000000
Testing R_canberra_dist
[1] TRUE
A B C D
B 4.000000
C 4.000000 2.356997
D 4.000000 1.409165 2.157322
E 4.000000 2.348575 1.682606 1.824656
A B C D E
A NA 4.000000 4.000000 4.000000 4.000000
B 4 0.000000 2.356997 1.409165 2.348575
C 4 2.356997 0.000000 2.157322 1.682606
D 4 1.409165 2.157322 0.000000 1.824656
E 4 2.348575 1.682606 1.824656 0.000000
A B C D E
A 4.000000 NA 4.000000 4.000000 4.000000
B 1.868964 4 2.356997 1.409165 2.348575
C 1.919038 4 0.000000 2.157322 1.682606
D 1.547657 4 2.157322 0.000000 1.824656
E 1.039972 4 1.682606 1.824656 0.000000
[1] 4 4 0 0 0
Testing R_binary_dist
[1] TRUE
A B C D
B 1
C 1 0
D 1 0 0
E 1 0 0 0
A B C D E
A 0 1 1 1 1
B 1 0 0 0 0
C 1 0 0 0 0
D 1 0 0 0 0
E 1 0 0 0 0
A B C D E
A 1 0 1 1 1
B 0 1 0 0 0
C 0 1 0 0 0
D 0 1 0 0 0
E 0 1 0 0 0
[1] 1 1 0 0 0
Testing R_matching_dist
Error in .Call("R_matching_dist", structure(c(0, 0.839069103589281, 0.037703595822677, :
"R_matching_dist" not available for .Call() for package "proxy"
Testing R_fuzzy_dist
Error in stats::dist(x, method = gsub("R_|_dist", "", f)) :
invalid distance method
A B C D
B 1.0000000
C 1.0000000 0.6719380
D 1.0000000 0.4770877 0.6640679
E 1.0000000 0.6979540 0.5844973 0.6036897
A B C D E
A 0 1.0000000 1.0000000 1.0000000 1.0000000
B 1 0.0000000 0.6719380 0.4770877 0.6979540
C 1 0.6719380 0.0000000 0.6640679 0.5844973
D 1 0.4770877 0.6640679 0.0000000 0.6036897
E 1 0.6979540 0.5844973 0.6036897 0.0000000
A B C D E
A 1.0000000 0 1.0000000 1.0000000 1.0000000
B 0.5180002 1 0.6719380 0.4770877 0.6979540
C 0.6445909 1 0.0000000 0.6640679 0.5844973
D 0.5581104 1 0.6640679 0.0000000 0.6036897
E 0.3562808 1 0.5844973 0.6036897 0.0000000
[1] 1 1 0 0 0
Testing R_mutual_dist
Error in .Call("R_mutual_dist", structure(c(0, 0.839069103589281, 0.037703595822677, :
"R_mutual_dist" not available for .Call() for package "proxy"
>
> ## no longer optimized
>
> .Call("R_ejaccard", x, NULL, FALSE, PACKAGE = "proxy")
A B C D
B 0.0000000
C 0.0000000 0.2957500
D 0.0000000 0.5298998 0.4107824
E 0.0000000 0.3549987 0.4459170 0.5179277
> .Call("R_ejaccard", x, x, FALSE, PACKAGE = "proxy")
A B C D E
A 1 0.0000000 0.0000000 0.0000000 0.0000000
B 0 1.0000000 0.2957500 0.5298998 0.3549987
C 0 0.2957500 1.0000000 0.4107824 0.4459170
D 0 0.5298998 0.4107824 1.0000000 0.5179277
E 0 0.3549987 0.4459170 0.5179277 1.0000000
> .Call("R_ejaccard", x, y, FALSE, PACKAGE = "proxy")
A B C D E
A 0.0000000 1 0.0000000 0.0000000 0.0000000
B 0.6794648 0 0.2957500 0.5298998 0.3549987
C 0.3820854 0 1.0000000 0.4107824 0.4459170
D 0.5374164 0 0.4107824 1.0000000 0.5179277
E 0.8157020 0 0.4459170 0.5179277 1.0000000
> .Call("R_ejaccard", x, y, TRUE, PACKAGE = "proxy")
[1] 0 0 1 1 1
>
> .Call("R_cosine", x, NULL, FALSE, PACKAGE = "proxy")
A B C D
B 0.0000000
C 0.0000000 0.5179092
D 0.0000000 0.7485219 0.8416675
E 0.0000000 0.5245741 0.6848730 0.7514756
> .Call("R_cosine", x, x, FALSE, PACKAGE = "proxy")
A B C D E
A 1 0.0000000 0.0000000 0.0000000 0.0000000
B 0 1.0000000 0.5179092 0.7485219 0.5245741
C 0 0.5179092 1.0000000 0.8416675 0.6848730
D 0 0.7485219 0.8416675 1.0000000 0.7514756
E 0 0.5245741 0.6848730 0.7514756 1.0000000
> .Call("R_cosine", x, y, FALSE, PACKAGE = "proxy")
A B C D E
A 0.0000000 1 0.0000000 0.0000000 0.0000000
B 0.8175510 0 0.5179092 0.7485219 0.5245741
C 0.5909955 0 1.0000000 0.8416675 0.6848730
D 0.8046383 0 0.8416675 1.0000000 0.7514756
E 0.9026897 0 0.6848730 0.7514756 1.0000000
> .Call("R_cosine", x, y, TRUE, PACKAGE = "proxy")
[1] 0 0 1 1 1
>
> x <- matrix(x > 0.5, 5,4)
> y <- matrix(y > 0.5, 5,4)
>
> .Call("R_bjaccard", x, NULL, FALSE, PACKAGE = "proxy")
1 2 3 4
2 0.0000000
3 0.0000000 0.0000000
4 0.0000000 0.3333333 0.3333333
5 0.0000000 0.0000000 0.0000000 0.0000000
> .Call("R_bjaccard", x, x, FALSE, PACKAGE = "proxy")
[,1] [,2] [,3] [,4] [,5]
[1,] 1 0.0000000 0.0000000 0.0000000 0
[2,] 0 1.0000000 0.0000000 0.3333333 0
[3,] 0 0.0000000 1.0000000 0.3333333 0
[4,] 0 0.3333333 0.3333333 1.0000000 0
[5,] 0 0.0000000 0.0000000 0.0000000 1
> .Call("R_bjaccard", x, y, FALSE, PACKAGE = "proxy")
[,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0.0000000 0.0000000 0
[2,] 0 0 0.0000000 0.3333333 0
[3,] 0 0 1.0000000 0.3333333 0
[4,] 0 0 0.3333333 1.0000000 0
[5,] 1 0 0.0000000 0.0000000 1
> .Call("R_bjaccard", x, y, TRUE, PACKAGE = "proxy")
[1] 0 0 1 1 1
>
> ###
>
> proc.time()
user system elapsed
0.288 0.040 0.325
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