your suggestions in MRMs
Kristi, You're completely missing the point, I think. Instead of providing X,Y coordinates in the sample dataset graze within the ecodist package, I provided one location, X if you'd like, called sitelocation. If you look at the example in ?MRM, data(graze) LOAR10.mrm <- MRM(dist(LOAR10) ~ dist(sitelocation) + dist(forestpct), data=graze, nperm=100) This is a toy example,with only one species, geographic distance, and another potential explanatory variable. dist(LOAR10) - species distance; you'd use whatever set of species you're studying dist(sitelocation) - geographic distance, you'd use your x and y coordinates as in dist(xy.matrix) dist(forestpct) - you'd use whatever variable or variables are appropriate for your study I concealed the location of these sites BEFORE I made the data public, which is why there's one location variable instead of x,y coordinates. Each row of graze is a single site, with some information associated. You don't need to conceal your location for your own analysis. You just need to use the appropriate data within the dist() command to calculate the distances, and with the appropriate distance metrics if Euclidean isn't appropriate for your data. Reading the papers cited in ?MRM might help you understand the logic a bit better. Sarah
On Wed, Apr 8, 2015 at 3:01 PM, Kristi Glover <kristi.glover at hotmail.com> wrote:
Hi Sarah,
Thanks for the reply. I again looked at the example, but I did not find the
way to calculate the location variable. All example in the document
("ecodist") has the Euclidean distance. did not find the example to conceal
the absolute location. There are some example:
page 21 and 22 : iris.md <- distance(iris[,1:4], "mahal"): it is calculated
distance matrix using four variables (I understood this one)
page 26: space.d <- distance(space, "eucl"), here space is XY coordinate, so
on
I am just wondering how I can conceal my absolute location (XY) and make my
data compatible to your data set so that I can use your functions. I am
sorry for bothering you, Sarah.
example of my data set: column names (site, XY coordinates, temp, years)
site1, 25.01;34.78 (XY cordicnate), 35degree celcius; year2001
site1, 25.01;34.78 (XY cordicnate), 33degree celcius; year2002
site2, 25.05; 35.56 (XY coordinate); 37degree celcius; year2001
site2, 25.05; 35.56 (XY coordinate); 32degree celcius; year2002
Thanks
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Date: Wed, 8 Apr 2015 14:23:27 -0400 Subject: Re: [R] your suggestions in MRMs From: sarah.goslee at gmail.com To: kristi.glover at hotmail.com CC: r-help at r-project.org Kristi, The row names are utterly arbitrary. Each row is a separate site, and sitelocation is a location variable (both intended to conceal the absolute location, which is confidential since it's on private property). It is NOT the Euclidean distance, nor is a row representing a pair of sites. If you look at the full example, dist() is used to calculate the Euclidean distance as part of the MRM code. Sarah On Wed, Apr 8, 2015 at 1:49 PM, Kristi Glover <kristi.glover at hotmail.com> wrote:
Hi R Users,
I was trying to perfom multiple regression on resemblance matrices
(MRMs). This technique in avaiable in "ecodist" package and looked at the
example data to know how I need to organize my data set. I think the data is
distance matrix but I was wondering the rows name. For example, there are
(these are the subset of the data of "graze")
sitelocation forestpct
1.1.2001 12.187743 63.88
1.2.2001 12.186077 71.33
2.1.2001 12.406362 72.45
2.2.2001 12.416265 77.13
3.1.1998 8.409213 18.35
if we look at the first row, 1.1.2001: sitelocation (column) is 12.187..
which is the euclidean distance between two points (XY cordinates). But I
was confused at the row name where 1.1.2001 which is to me is site1 and
site1 of 2001. Isn't it supposed to be "0" if both are the same site. I
think I misunderstood it. Any one can help me about what it is?
I put the example for your reference
install.packages("ecodist")
library(ecodist)
data(graze)
graze[1:5,1:2]
Thanks for your help
KG
-- Sarah Goslee http://www.functionaldiversity.org