similar to: Heat Map for species - code from Numerical Ecology with R

R version 3.2.2. library(vegan) I was to look at community tables from my dendrograms and am trying out the vegemite command. This is the error I get: Error in vegemite(apst, apst.clusters) : Cowardly refusing to use longer than 1 char symbols: Use scale I thought the problem was that I was using the log transformed data, but I tried it on the raw (which is single digit numbers), and still

Hello everyone, I am currently using the mvpart package and would like to change the color scheme it uses, and was hoping someone could help me out. All of the papers I have found have used a grayscale but I can't seem to figure out how they did that! Currently, mvpart plots barplots in a repeating sequence of 3 shades of blue. So if you have 6 response variables the same shade of blue is used

Hi all, >From a list of strings, I desire to filter out the followings: 1. Digits at the beginning of the strings 2. Character "SPE" following the digits (if it exists) 3. Any characters followed by hyphen The following produces the desired result, but would like to know whether this can be done more efficiently. Any suggestions would be much appreciated. dat <- c("2148

Dear list, I want to calculate SPE (squared prediction error) in x-space, can someone help? Here are my codes: fit.pls<- plsr(Y~X,data=DAT,ncomp=3,scale=T,method='oscorespls',validation="CV",x= T) actual<-fit.pls$model$X pred<-fit.pls$scores %*% t(fit.pls$loadings) SPE.x<-rowSums((actual-pred)^2) Am I missing something here? Thanks in advance. Stella Sim

Dear all, I have run the confint() function according to below and I get the following error message: > confint(stepAIC.glm.spe.var.konn2.abund, level=0.95) Waiting for profiling to be done... Error: missing value where logical needed In addition: Warning message: NaNs produced in: sqrt((fm$deviance - OriginalDeviance)/DispersionParameter) or > confint(stepAIC.glm.spe.var.konn2.abund,

Dear R-gurus, Just supose I have a dara.frame that looks like myDF<-read.table(stdin(),head=T,sep=",") codID,namesp,k1,k2,k3,k4 1,spA,2,5,6,3 2,spB,4,5,4,6 3,spC,2,1,5,6 4,spC,5,4,3,2 5,spD,1,2,3,4 6,spE,2,4,3,1 I need to update the columns k1-k4 with the namesp, but considering the math between Kx and codID. My desired output must looks like: codID,namesp,k1,k2,k3,k4

Hello, I've got an ISDN PRI circuit terminating in a Cisco AS5350, which in turn is talking to an Asterisk server via SIP for call origination and termination. Seems simple enough, and it works for the most part, but: 1) Caller ID name data comes in on the PRI, but doesn't appear to get handed off to the Asterisk server via SIP, at least not in any format that Asterisk

Dear all, Is there any function for calculating confidence limits for coefficients in an lm() object? I know of the confint() function in the MASS library working very well on my binomial GLMs and I have tried it (using glm () , family=gaussian) but it gives NAs according to below. Does the confint() function not accept gaussian GLMs? Could there be convergence problems in the GLM? Note the

Hello, I am using vegan to do an NMDS plot and I would like to suppress the labels for the loading vectors. Is this possible? Alternatively, how can I avoid overlap? Many thanks for the help. Example code: #perform NMDS using metaMDS() function spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS", autotransform=F, trymax=1000) #calculate the loading (i.e.,

Hi, I am a new R user and am trying to construct a palaeoenvironmental transfer function (weighted averaging method) using the package rioja. I've managed to insert the two matrices (the species abundance and the environmental data) and have assigned them to the y and x values respectively. When I try and enter the 'WA' function though, I get an 'Error in FUN' message (see

Hello, I am making some use of ROC curve analysis. I find much help on the mailing list, and I have used the Area Under the Curve (AUC) functions from the ROC function in the bioconductor project... http://www.bioconductor.org/repository/release1.5/package/Source/ ROC_1.0.13.tar.gz However, I read here... http://www.medcalc.be/manual/mpage06-13b.php "The 95% confidence interval for

Full_Name: Xiaobao Wang Version: R 1.7.1 OS: Windows XP Submission from: (NULL) (24.45.25.102) accidentally done the following: rpt.dir <- paste("c:/report/testR","bestsub",spe="/") dir.create(rpt.dir) (spe should be sep). Now the directory "c:/report/testR bestsub " cannot be removed. I tried to remove it from Windows Explorer and got the message

Dear list, I am new to lattice plots. I want to make a barchart with 10 and more levels. I need to use a grey scale for printing purposes. The problem is that with 10 or more levels in factors it is very difficult to distinguish each level in the plot and legend, since the greys are very similar (some levels have value of zero and don't appear). Here is an example of my problem: df <-

Hello, I'm having trouble figuring out how to see resulting groups (clusters) from my hclust() output. I have a very large matrix of 4371 plots and 29 species, so simply looking at the graph is impossible. There must be a way to 'print' the results to a table that shows which plots were in what group, correct? I've attached the matrix I'm working with (the whole thing

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Hi Jean-Marc, We needed to use a release version of the SDK because this part of production code for our Sony implementations. I'm not sure how stable that branch is. Is the encoding and decoding already stable? In other words, what is not stable about that branch? Thanks, --------------------------- Saad Nader Middleware Engineer Powered By Gamespy, IGN -----Original Message----- From:

Aside from the fact that you're checking for i64 specifically instead of generally checking for illegal types, how much of this is really PPC specific? Would this be a reasonable enhancement to the SDAG logic in general? -Hal On 1/4/19 8:03 AM, Nemanja Ivanovic wrote: The changes seem fine to me. I don't think this is excessively intrusive and it accomplishes what is needed by targets

Hi, I am clustering objects using the agnes() function and the UPGMA clustering method (function = "average"). Everything works well, but apparently something is wrong with the dendrogram. For example: x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3) y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115) xy<-cbind(x,y) library(cluster) UPGMA.orig<-agnes(x)

Hi Nemanja, I'm attaching a patch that builds on D54583 and implements what we discussed on IRC earlier today. Particularly: * Make LowerCallTo() a virtual function, so it can be wrapped by a subclass. * Implement LowerCallTo() in PPCTargetLowering to wrap TargetLowering::LowerCallTo() and legalize the return node when targeting SPE. * Augment PPCTargetLowering::LowerCall_32SVR4() to

I'm trying to fix a bug in the PowerPC SPE backend that prevents a bunch of FreeBSD ports from building, including gtk20. The attached file, generated from the following C source, triggers the "Def == PreviousDef" assertion in isNopCopy(): typedef float a; typedef struct { a b, c; } complex; d(complex *e, complex *h) { double f = h->c, g = h->b; i(g); e->c = g *