similar to: [Bug 27720] New: Hard Hang on suspend - 8600M GS

Hi, I compiled drm & xf86-video-nouveau to test nouveau yesterday -- the X server couldn't start. Today, Telek pointed me to drm/linux-core/drm_pciids.h, where I added my card. This made nouveau detect my card, and the xerver started successfully. I didn't test further -- for example I didn't compile the mesa nouveau code to enable 3D. So what should I test ? Snark PS1:

H ello R-experts, I want to do ordination plots using vegan metaMDS. I have a where many cells have zero values. Data structure: X[1:10,1:14] Height.1 Height.2 Height.3 Height.4 Height.5 Height.6 Height.7 Height.8 Height.9 Height.10 Height.11 Height.12 Height.13 D30I1A 46 0 0 0 0 0 0 0 0 0 39 0 98 D30I1B

Dear All I am trying to do a partial canonical analysis of principal coordinates using Bray-Curtis distances. The capscale addin to R appears to be the only way of doing it, however, when I try and calculate a Bray-Curtis distance matrix either using Capscale or Vegedist (capscale I understand uses Vegedist anyway to calculate its distance matrix), R uses up all available memory on the computer,

I have tried without success to find a way including the square root symbol in lattice strips as part of my conditioning labels. I have tried supplementing by creating a list of vectors using the var.name function coupled with the expression function used in xlab/ylab. xyplot(adjusted_Rand_index~cluster|distance_measure, main="Level of agreement between partitions: Wards Method",

Hi, I need to run a PCoA (PCO) for a data set wich has both positive and negative values for variables. I  could not find any distancecoefficient other than euclidean distace running for the data set. Are there any other coefficient works with negtive values.Also I cannot get summary out put (the eigen values) for PCO as for PCA.   Thanks. Dilshan [[alternative HTML version deleted]]

Dear all, I'm getting an error in one of the stock examples in the 'mvpart' package. I tried: require(mvpart) data(spider) fit3 <- rpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method="dist") #directly from ?rpart summary(fit3) ...which returned the following: Error in apply(formatg(yval, digits - 3), 1,

How to calculate sorensen (bray-curtis) distance by dist function within the vegan package? Cheers Duccio

Does R have a function to calculate Bray-Curtis distance measures, which is probably one of the most frequently used and recommended dissimilarity measures in ecology? It isn't mentioned in dist().

I've been unable to find a R package that provides the means of performing Clarke & Ainsworth's BIO-ENV procedure or something comparable. Briefly, they describe a method for comparing two separate sample ordinations, one from species data and the second from environmental data. The analysis includes selection of the 'best' subset of environmental variables for explaining

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

Dear friends, what is this error message in gam???? I cannot understand what it means .... is it a bug? gam_bray_scot24_pc_0505<gam(bray~s(PC1,PC2,PC3,PC4,PC5, PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate) Error in if (length(data) != vl) { : missing value where TRUE/FALSE needed Calls: gam ... smooth.construct -> smooth.construct.tp.smooth.spec -> array In

Dear all, I am having a little trouble deciphering how to change the default x-axis labels in a lattice xyplot (or any type of lattice plot for that matter). I have tried using the "demo("labels") function but the code is truncated at precisely the wrong moment! All I am trying to do is to add superscript to two of the labels for which i tried using the expression function. It

Hello all, I recently used the Vegan library quite extensively (in the context of text similarity assessment) on an Ubuntu 6.06 LTS system with R version 2.2.1 (2005-12-20 r36812). The Vegan lib is version 1.6-10. I hit on a problem yesterday, though, when trying to install R and Vegan on two further computers - one Windows XP and one further Ubuntu 6.06 machine, taking either R version 2.4.0

I have tried without success to find a way including the square root symbol in lattice strips as part of my conditioning labels. I have tried supplementing by creating a list of vectors using the var.name function coupled with the expression function used in xlab/ylab. xyplot(adjusted_Rand_index~cluster|distance_measure, main="Level of agreement between partitions: Wards Method",

Package: logcheck Version: 1.2.69 The current ruleset "kernel" provided with this logcheck package don't match entries where the kernel timeline has leading spaces, like: [ 42.302707] For example, the following entry: Feb 4 17:05:24 hostname kernel: [ 144.591487] tun: Universal TUN/TAP device driver, 1.6 didn't matched the re: ^\w{3} [ :0-9]{11} [._[:alnum:]-]+

Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to

Hi there, I would like to find a more efficient way of permuting the rows and columns of a symmetrical matrix that represents ecological or actual distances between objects in space. The permutation is of the type used in a Mantel test. Specifically, the permutation has to accomplish something like this: Original matrix addresses: a11 a12 a13 a21 a22 a23 a31 a32 a33 Example

Dear All, I am using a Procrustes analysis to compare two NMDS ordinations for the same set of sites. One ordination is based on fish data, the other is based on invertebrate data. Ordinations were derived using metaMDS() from the {vegan} library as follows: fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100, wascores=TRUE, trace=TRUE, zero="add")

Dear R-help, We are conducting a distance-based redundancy analysis using capscale and then testing for statistical significance for six terms in the model for the constrained ordination using anova.cca in the vegan package. The significance test is sequential, i.e., testing for significance of a term only after accounting for all preceding terms. Could someone please provide us with either the

I'm getting lots of grief from reviewers about figures generated with the envfit function in the Vegan package. Has anyone else struggled to effectively explain this analysis? If so, can you share any helpful tips? The most recent comment I've gotten back: "What this shows is which NMDS axis separates the communities, not the relationship between the edaphic factor and the