[R] Euclidean distance function

[Rui Barradas]

Hello,

You don't need to write a function. Try the following.


nms <- paste0("species", 1:4)
mat <- matrix(rnorm(16), ncol=4, dimnames = list(nms, nms))
?dist
dist(mat)
dist(mat, diag = TRUE, upper = TRUE)

Hope this helps,

Rui Barradas

Em 24-08-2012 11:56, Arbuckle escreveu:
> Hi,
>
> I should preface this problem with a statement that although I am sure this
> is a really easy function to write, I have tried and failed to get my head
> around writing functions in R. I can use R where functions exist to do what
> I want done, but have found myself completely incapable of writing them
> myself.
>
> The problem is that I have a table with several rows of species and several
> columns of trait data for each species. Now what I want to do is, for each
> possible pair of species, extract the Euclidean distance between them based
> on specified trait data columns. While as far as I can see the dist()
> function could manage this to some extent for 2 dimensions (traits) for each
> species, I need a more generalised function that can handle n-dimensions.
> Ideally this function would allow me to choose which columns (traits) to use
> to calculate the Euclidean distance rather than having to reformat the
> dataset every time.
>
> In the hope of clarifying this with a simplified example, I want to take a
> dataset like this:
>
> Species     x          y          z          n
> spA          2.9     34.2     0.54    15.7
> spB          5.5     46.5     0.45    19.4
> spC          1.4     48.6     0.84    24.8
> spD          8.3     56.1     0.48    21.3
>
> Then extract the Euclidean distances using the general equation
> d=sqrt[(x2-x1)^2+(y2-y1)^2+...+(n2-n1)^2] for particular data columns. So in
> this example I might want the distances using the traits x, z and n, thereby
> specifying the equation to be d=sqrt[(x2-x1)^2+(z2-z1)^2+(n2-n1)^2], and
> return a distance matrix as follows (calculated distances represented by .
> for the purposes of this example):
>
> Species     spA     spB     spC
> spB              .
> spC              .           .
> spD              .           .           .
>
> I hope this makes sense. I only presume that this would be a quick and easy
> function to write on the basis that the underlying process is basically
> simple maths repeated for each pair of species. Again I have no experience
> in writing custom functions (no matter how simple) and just can't seem to
> get into my head how to go about it.
>
> I look forward to your response and hope someone gets bored enough to
> quickly write out the code to implement this function. Thank you in advance.
>
> Best wishes,
>
> Kev
>
>
>
> --
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>
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