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]]
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 <alaios at 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 at 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. >
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) > x1 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:>?distSo 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: julian@hafro.is, jmburgos@uw.edu On Thu, Sep 16, 2010 at 10:02 AM, Alaios <alaios@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. >-- [[alternative HTML version deleted]]
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 <mvalle@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,] 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.
--
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]]
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 <mvalle at cscs.ch>
> *To:* Alaios <alaios at 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,] 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 at r-project.org <mailto:R-help at 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