similar to: [R-sig-Geo] Comparing spatial point patterns - Syrjala test

Dear Lists, At several stations distributed regularly in space[1], we sampled repeatedly (4 times) the abundance of organisms and measured environmental parameters. I now want to compare the spatial distribution of various species (and test wether they differ or not), or to compare the distribution of a particular organism with the distribution of some environmental variable.

-----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of r-help-request at r-project.org Sent: Monday, February 11, 2008 12:00 PM To: r-help at r-project.org Subject: R-help Digest, Vol 60, Issue 11 Send R-help mailing list submissions to r-help at r-project.org To subscribe or unsubscribe via the World Wide Web, visit

Hello everyone, I am looking at the joint spatial distribution of 2 kinds of organisms (estimated on a grid of points) and want to test for significant association or dissociation. My first question is: do you know a nice technique to do that, considering that I have a limited number of points (36) but that they are repeated (4 times)? I did GLMs to test for correlations between the

Hello everybody, This is probably a classic but I cannot find an answer to this on the mailing list (i.e. with a google search restricted to the mailing list archive). Setting: par(new=T) plot(x,y) works but plot(x,y,new=T) doesn't while it is said in plot's help that ... arguments are passed to par. What am I missing? JiHO --- http://jo.irisson.free.fr/

Hello everyone, I am (happily) using ggplot2 for all my plotting now and I wondered is there is an easy way to specify xlim and ylim somewhere when using the ggplot syntax, as opposed to the qplot syntax. Eg. qplot(data=mtcars,y=wt, x=qsec,xlim=c(0,30)) <-> ggplot(mtcars, aes(y=wt, x=qsec)) + geom_point() + ??? Indeed the ggplot syntax is in general more flexible and powerful and

Hello all, I am sure I am missing something obvious but I cannot find the function I am looking for. I have a data frame with three columns: X, Y and Z, with X and Y being grid coordinates and Z the value associated with these coordinates. I want to transform this data frame in a matrix of Z values, on the grid defined by X and Y (and, as a plus, fill the X.Y combinations which do no

Hello everyone, I have two data.frames that look like calib: place zoom scale left 0.65 8 left 0.80 5.6 left 1.20 3 right 0.65 8.4 right 0.80 6 right 1.20 2.9 X: ... place zoom .... ... left 0.80 .... ... left 1.20 .... ... right 0.65 .... ... NA NA .... ... right 0.8 .... ... left 1.20 .... and I want to get the corresponding values of 'scale' in a new column

Hello all, I discovered that the pdf device uses fonts to represent "points" symbols (as in plot(...,type="p",...) ). Namely it uses ZapfDingbats with symbol U+25cf. This can lead to problems when the font is not available, or available in another version (such as points being replaced by other symbols, or worst: slightly displaced). Furthermore, it also causes

Hi everyone, Hi ggplot users in particular, ggplot makes it very easy to plot things given their names when you use it interactively (and therefore can provide the names of the columns). qplot(x,foo,data=A) where A has columns (x,y,foo,bar) for example but I would like to use this from inside a function to which the name of the column is given. I cannot find an elegant way to make this

Hi everyone, Hi Hadley, I am a heavy user of coord_equal() in ggplot2 since most of my data is spatial, on x,y coordinates. Everything works. However by enforcing an aspect ratio of 1 for the plotting region, coord_equal() usually wastes a lot of space if the region of interest is not a perfect square. For example: x=runif(10) a=data.frame(x=x*3,y=x) ggplot(data=a, aes(x=x,y=y)) +

Hello everyone, A recent (in 2.5 I suspect) change in R is giving me trouble. I want to apply a function (tolower) to all the columns of a data.frame and get a data.frame in return. Currently, on a data.frame, both apply (for arrays) and lapply (for lists) work, but each returns its native class (resp. matrix and list): apply(mydat,2,tolower) # gives a matrix lapply(mydat,tolower) # gives

Hello eveybody, I am studying the vertical distribution of plankton and want to study its variations relatively to several factors (time of day, species, water column structure etc.). So my data is special in that, at each sampling site (each observation), I don't have *one* number, I have *several* numbers (abundance of organisms in each depth bin, I sample 5 depth bins) which

Hello, As suggested in "De'ath, 2002. Multivariate regression trees: A new technique for modelling species-environment relationships. Ecology, 83 (4):1105-1117" (for those interested), I am trying to compare the performance of a multivariate regression tree to a cluster analysis. A simple partitioning with k clusters (as done by `pam`) seemed straightforward and appropriate

Hello everyone, I am sorry if this has already been asked but I can't find it. I want to superpose two lattice plots, namely a levelplot and a contourplot of two different variables with the same x-y scale. I found information about panel.superpose but it does not seem to correspond to what I want (I have two different variables, not groups of the same variable) How can I do this?

Hello R users, I have numerical data sampled on two grids, each one shifted by 0.5 from the other. For example: grid1 = expand.grid(x=0:3, y=0.5:2.5) grid2 = expand.grid(x=0.5:2.5, y=0:3) gridFinal = expand.grid(x=0.5:2.5, y=0.5:2.5) plot(gridFinal, xlim=c(0,3), ylim=c(0,3), col="black", pch=19) points(grid1, xlim=c(0,3), ylim=c(0,3), col="red", pch=19) points(grid2,

Dear List, I am trying to get R's terminal output to a file and to the terminal at the same time, so that I can walk through some tests and keep a log concurrently. The function 'sink' with the option split=TRUE seems to do just that. It works fine for most output but for objects of class htest, the terminal output is incomplete (the lines are there but empty). Here is an

Hello, I am facing a problem with lapply which I ''''think''' may be a bug. This is the most basic function in which I can reproduce it: myfun <- function() { foo = data.frame(1:10,10:1) foos = list(foo) fooCollumn=2 cFoo = lapply(foos,subset,select=fooCollumn) return(cFoo) } I am building a list of dataframes, in each of which I want to keep only column

Hello everyone (and Hadley in particular), I often need to plot data from multiple datasets on the same graph. A common example is when mapping some values: I want to plot the underlying map and then add the points. I currently do it with base graphics, by recording the maximum region in which my map+point will fit, plotting both with these xlim and ylim parameters, adding par (new=T)

Hello everyone, I've been advised to use merge to extract information from two data.frames with a number of common columns, but I cannot get a grasp on how it sorts the result. With sort=FALSE, I would expect it to give the result back sorted exactly as the input was but it seems it is not always the case, especially when there are repeats in the input. For example: > a =

Hello everyone, I often create some local "libraries" of functions (.R files with only functions in them) that I latter call. In scripts that call a function from such library, I would like to be able to test whether the function is already known in the namespace and, only if it is not, source the library file. I.e. what `require` does for packages, I want to do with my local