[R] help me understand how things work.
Hello I have some strange output from R and I try to understand how R works. Could you please help me with that? temp - rbind (c(10,1),c(99,98)) temp [,1] [,2] [1,] 101 [2,] 99 98 dist(temp) 1 2 131.6435 sqrt(dist(temp)) 1 2 11.47360 so far so good. until the nex line: when I try to do what i did before but adding the 1/(what I did before). I was expecting a number as a result of the division but unfortunately I took the following: 1/sqrt(dist(temp)) [1] 0.08715662 attr(,Size) [1] 2 attr(,Diag) [1] FALSE attr(,Upper) [1] FALSE attr(,method) [1] euclidean attr(,call) dist(x = temp) attr(,class) [1] dist Could you please help me understand what is this about? I would like to thank you in advance for your help Best REgards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help me understand how things work.
Hello Alex, Look at the help page for the dist function. You'll see it doesn't return a simple vector or matrix, rather a dist class object which is why you got a surprise when you tried to treat it like a simple value. The function is not really intended for spatial point distance calculations, but rather for multivariate analysis. Your example would work if you did it like this... d dist( temp )[1] dd - 1 / sqrt( d ) But if you want to have more than just two points in your matrix it will get ugly trying to work out the indices for the distances (although the dist help page gives you a formula). You'd be better for using a simple function... getdist - function(p1, p2) sqrt( (p1[1] - p2[1])^2 + (p1[2] - p2[2])^2 ) Or if you are going to do more complex point pattern analyses look at one of the many spatial packages for R such as spatstat. Hope this helps, Michael On 16 September 2010 20:02, Alaios ala...@yahoo.com wrote: Hello I have some strange output from R and I try to understand how R works. Could you please help me with that? temp - rbind (c(10,1),c(99,98)) temp [,1] [,2] [1,] 10 1 [2,] 99 98 dist(temp) 1 2 131.6435 sqrt(dist(temp)) 1 2 11.47360 so far so good. until the nex line: when I try to do what i did before but adding the 1/(what I did before). I was expecting a number as a result of the division but unfortunately I took the following: 1/sqrt(dist(temp)) [1] 0.08715662 attr(,Size) [1] 2 attr(,Diag) [1] FALSE attr(,Upper) [1] FALSE attr(,method) [1] euclidean attr(,call) dist(x = temp) attr(,class) [1] dist Could you please help me understand what is this about? I would like to thank you in advance for your help Best REgards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help me understand how things work.
Hi Alex, What is happening is that the ´dist´function calculates a distance matrix, and returns an object of the ´dist´ class. temp - rbind (c(10,1),c(99,98)) x=dist(temp) x 1 2 131.6435 class(x) [1] dist You can see a description of the ´dist´class at the end of the function´s help file. Do this: ?dist So when you do dist(temp) you do not just get a number. You get an object that has the distance between the points, plus additional information (i.e. the method used to calculate the distance, if the matrix contains only the lower triangle or also the upper triangle and the diagonal, etc.). If you do sqrt() or 1/ over this object it is still of the ´dist´ class: x=dist(temp) x=sqrt(x) class(x) [1] dist x=1/x class(x) [1] dist Notice that you still the right answer (0.08715662). For some reason R prints the attributes of the object when you do the inverse but not when you do the square root (I´m curious about why...If anyone has an answer please pitch in). If you only want to get a number, do this: x=as.numeric(dist(temp)) class(x) [1] numeric 1/sqrt(as.numeric(dist(temp))) [1] 0.08715662 All the best, Julián Julian Mariano Burgos Hafrannsóknastofnunin/Marine Research Institute Skúlagata 4, 121 Reykjavík, Iceland Sími/Telephone : +354-5752037 Bréfsími/Telefax: +354-5752001 Netfang/Email: jul...@hafro.is, jmbur...@uw.edu On Thu, Sep 16, 2010 at 10:02 AM, Alaios ala...@yahoo.com wrote: Hello I have some strange output from R and I try to understand how R works. Could you please help me with that? temp - rbind (c(10,1),c(99,98)) temp [,1] [,2] [1,] 101 [2,] 99 98 dist(temp) 1 2 131.6435 sqrt(dist(temp)) 1 2 11.47360 so far so good. until the nex line: when I try to do what i did before but adding the 1/(what I did before). I was expecting a number as a result of the division but unfortunately I took the following: 1/sqrt(dist(temp)) [1] 0.08715662 attr(,Size) [1] 2 attr(,Diag) [1] FALSE attr(,Upper) [1] FALSE attr(,method) [1] euclidean attr(,call) dist(x = temp) attr(,class) [1] dist Could you please help me understand what is this about? I would like to thank you in advance for your help Best REgards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help me understand how things work.
I fixed by adding this: k - sqrt(dist(temp)) k returns sort of a list. So I need to select the first item which is the result. a - k[1] Can someone explain me why k[1] is needed for that? Best Regards Alex From: Mario Valle mva...@cscs.ch Sent: Thu, September 16, 2010 1:28:31 PM Subject: Re: [R] help me understand how things work. ?dist BTW, to me this does not happens. x - matrix(rnorm(100), nrow=5) d - dist(x) 1/sqrt(d) 1/sqrt(dist(x)) Hope it helps mario On 16-Sep-10 12:02, Alaios wrote: Hello I have some strange output from R and I try to understand how R works. Could you please help me with that? temp- rbind (c(10,1),c(99,98)) temp [,1] [,2] [1,] 101 [2,] 99 98 dist(temp) 1 2 131.6435 sqrt(dist(temp)) 1 2 11.47360 so far so good. until the nex line: when I try to do what i did before but adding the 1/(what I did before). I was expecting a number as a result of the division but unfortunately I took the following: 1/sqrt(dist(temp)) [1] 0.08715662 attr(,Size) [1] 2 attr(,Diag) [1] FALSE attr(,Upper) [1] FALSE attr(,method) [1] euclidean attr(,call) dist(x = temp) attr(,class) [1] dist Could you please help me understand what is this about? I would like to thank you in advance for your help Best REgards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help me understand how things work.
print(k) and you see a lower triangular distance matrix. k[1] selects distances between 1 and 2 k[2] selects distances between 1 and 3 and so on. you have a distance matrix, not a single distance value, so you have to select which distance you need. Ciao! mario On 16-Sep-10 14:38, Alaios wrote: I fixed by adding this: k - sqrt(dist(temp)) k returns sort of a list. So I need to select the first item which is the result. a - k[1] Can someone explain me why k[1] is needed for that? Best Regards Alex *From:* Mario Valle mva...@cscs.ch *To:* Alaios ala...@yahoo.com *Sent:* Thu, September 16, 2010 1:28:31 PM *Subject:* Re: [R] help me understand how things work. ?dist BTW, to me this does not happens. x - matrix(rnorm(100), nrow=5) d - dist(x) 1/sqrt(d) 1/sqrt(dist(x)) Hope it helps mario On 16-Sep-10 12:02, Alaios wrote: Hello I have some strange output from R and I try to understand how R works. Could you please help me with that? temp- rbind (c(10,1),c(99,98)) temp [,1] [,2] [1,] 101 [2,] 99 98 dist(temp) 1 2 131.6435 sqrt(dist(temp)) 1 2 11.47360 so far so good. until the nex line: when I try to do what i did before but adding the 1/(what I did before). I was expecting a number as a result of the division but unfortunately I took the following: 1/sqrt(dist(temp)) [1] 0.08715662 attr(,Size) [1] 2 attr(,Diag) [1] FALSE attr(,Upper) [1] FALSE attr(,method) [1] euclidean attr(,call) dist(x = temp) attr(,class) [1] dist Could you please help me understand what is this about? I would like to thank you in advance for your help Best REgards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle http://www.cscs.ch/%7Emvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
