similar to: Clustering question \ dist(datmat)

Hi, I was trying to get the optimal 'k' for the knn. To do this I was using the following function : knn.cvk <- function(datmat, cl, k = 2:9) { datmatT <- (datmat) cv.err <- cl.pred <- c() for (i in k) { newpre <- as.vector(knn.cv(datmatT, cl, k = i)) cl.pred <- cbind(cl.pred, newpre) cv.err <- c(cv.err, sum(cl != newpre)) }

hi all, i'm trying to plot a dendrogram with labeled leaves >rownames(f)<-v.names >v<-rowMeans(f, na.rm=T) >clust<-hclust(dist(v)) >dend<-as.dendrogram(clust,hang=0.05) >clust2<-cut(dend, h=0.5) >class(clust2$low[[1]]) >[1] "dendrogram" then >plot(clust2$low[[1]],horiz=TRUE,frame=F,type = "tr")) but my leaf labels do not fit

Please help, I have a strange problem. I've got a balanced panel data set. I use dummy variable regression and I've got results with lm function. summary(lm(y ~ post + t19961 + t19962 + t19963 + t19964 + t19971 + t19972 + t19973 + t19974 + t19981+factor( id))) The problem is that I would like to get my standard errors clustered but then gets the following error message: f<-(lm(y ~

hi, Excuse me asking three questions in a row for a day, but I had collected those questions as I'm still experimenting with R. This one is how do you compose plots with alot of data in one graph. First what I currently do is after i generated all the data I need to plot.. let say 5-6 arrays I do a plot() and then I created a function to scale the other data to approx fit the initial range so

Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 50000 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (50000 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and

Dear List, Apologies for this off-topic post but it is R-related in the sense that I am trying to understand what R is telling me with the data to hand. ROC curves have recently been used to determine a dissimilarity threshold for identifying whether two samples are from the same "type" or not. Given the bashing that ROC curves get whenever anyone asks about them on this list (and

I have constructed the function mml2 (below) based on the likelihood function described in the minimal latex I have pasted below for anyone who wants to look at it. This function finds parameter estimates for a basic Rasch (IRT) model. Using the function without the gradient, using either nlminb or optim returns the correct parameter estimates and, in the case of optim, the correct standard

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

Hi, I am currently working on some data and feel that NMDS would return an excellent result. With my current data set however I have been experiencing some problems and cannot carry out metaMDS. I have tried with a few smaller data sets which I created for practice sake and this has worked fine. I think it is the set up of my data set that is causing me trouble. I have 18 columns and 18 rows,

i'm working on some distance matrices and i was wondering if there is a way to export the matrices from R to excel. OG thanks [[alternative HTML version deleted]]

How can I get the log odds associated with the levels in strata() within a clogit() model? I'm running R-1.9.0 on a Linux platform. I am using clogit() to run a Rasch model in Item Response Theory in psychometrics. Symbolically, the model is: logit(p_{j,k}) = \log({\Pr(p_{j,k}) \over \Pr(1-p_{j,k})}) = \theta_j - \alpha_k, That is, the log odds of answering an test item correctly is

Hello, everybody, I hope somebody could help me with a dist() function. I have a data frame of size 2*4087 (col*row), where col corresponds to the treatment and rows are species, values are Hellinger distances, I should reconstruct a distance matrix with a dist() function. I know that "euclidean" method should be used. When I type: dist(dframe,"euclidean") it gives me a

Hi, I'm trying to estimate the parameters of a state space model of the following form measurement eq: z_t = a + b*y_t + eps_t transition eq y_t+h = (I -exp(-hL))theta + exp(-hL)y_t+ eta_{t+h}. The problem is that the distribution of the innovations of the transition equation depend on the previous value of the state variable. To be exact: y_t|y_{t-1} ~N(mu, Q_t) where Q is a diagonal

Please help, I have a strange problem. I've got a balanced panel data set. I use dummy variable regression and I've got results with lm function. summary(lm(y ~ post + t19961 + t19962 + t19963 + t19964 + t19971 + t19972 + t19973 + t19974 + t19981+factor( id))) The problem is that I would like to get my standard errors clustered but then gets the following error message: f<-(lm(y ~

Dear R users, I am using the function "constrOptim" to minimize the -1*log-likelihood where \beta_i>=0 i=1,...,p and \beta_0 is unconstrained. I construct u_i as 0 0 0 ... 0 0 1 0 ... 0 0 0 1 ... 0 . . . ... 0 . . . ... 0 .

I am relatively new to R, so this may be a much simpler question than it seems to me. I am trying to create a function that includes two summations, and can't figure out how. I am attaching the equation as a pdf file. This function will then be optimized over a chosen range of values, but right now I just need help with the function. Thank you. Zack Darnell Duke University -- Zack

HI all, I am currently setting up a HA devops configuration using puppet. I want to be able to run a single puppet master as the CA and the rest act as peering puppet masters. I have each puppet master running on passenger and I am proxying the SSL requests to the CA server following: http://docs.puppetlabs.com/guides/scaling_multiple_masters.html#option-2-redirect-certificate-traffic

Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]]

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Is there a way to prevent hwaddr/mac address spoofing between DomU''s? So in a way ''binding'' a mac-address on boot time with a virtual interface? (with something like ebtables/arptables/etc?) Stefan -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla -

Hi everyone,   I'm trying to do an Logistic Politomic Regression in R. Because I have my resposes variables and the aswer is 0 and 1 in 3 bacterial genes. Somebody know how to do this in R in a easy way?   Thank so much,   José Bustos Facultad de Ciencias Universidad Catolica Ssma. Concepcion Chile --- El lun, 31/8/09, r-help-request@r-project.org <r-help-request@r-project..org>