search for: pcnm

Hello- I am using the vegan package PCMN() because I need to use option of row weights (I am using CCA following the selection of the significant/positive PCNM variables). In the library PCNM (PCNM function), the Moran's I is calculated for you as part of the function. I see that I need to calculate Moran's I separately in order to retain the eigenfunctions with positive spatial correlation but could use help in doing so...I have looked up Moran...

Background: OS: Linux Ubuntu Dapper R : Version 2.3.1 (2006-06-01) Emacs 21.4.1 ESS Colleagues This is neither a bug report, nor a complaint, so I think this is the appropriate list. I am getting an odd font problem with a pdf generated using pdf(file = "../figures/PCNM.models.larvae.fluor.zoo.stability.2001.and.2002.pdf", title="", family="serif", pointsize=10, width=6.75, height=8.625) The figure produced from my code is here: <http://www.members.iinet.net.au/~s.mcclatchie/aslo/PCNM.models.larvae.fluor.zoo.stability.2001.and.20...

...the following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to track down the cause of the error. Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed In addition: There were 50 or more warnings (use warnings() to see the first 50) traceback() 9: ordistep(my...

...mycorrhizal community, so that in each plot I got about 15 pieces of root containing some ectomycorrhizal fungus on it (response variables). My purpose is to explain the spatial variation of the ectomycorrhizal diversity thanks to the soil variables I will have measured. To do so, I want to use a PCNM (or MEM). My problem is that : All the 24 plots are considered as points since I only give the central coordinates of each plot, so that the euclidean distance between them is overestimated. Two adjacent, contiguous, plots are considered to be 25 m apart, while the distance should be 0, since the...

...is I have been trying the command - ABUNDTMRT <- mvpart(abundance ~ environ + spatial, data.frame,margin=0.08,cp=0,xv="1se",xval=nrow(abundance),xvmult=100,which=4) where abundance is as above, environ is the environmental factors (from above) and spatial is the eigenfunctions from a PCNM analysis. data.frame is the environ and spatial factors as a data.frame. This gives the error - "Error in `[[<-.data.frame`(`*tmp*`, preds, value = c(72L, 72L, 80L, 72L, : replacement has 504 rows, data has 168" As I am new to this, I am not sure if I am entering an incorrect for...

...he following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to track down the cause of the error. Nevil Amos Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed In addition: There were 50 or more warnings (use warnings() to see the first 50) > traceback(...

I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et al 2004 as suggested by Legendre and . FORTIN (2010). I