similar to: metaMDS Error, Nan similar or negative values

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,

Hello R-user community! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Presently I try to run the function metaMDS (vegan) using an existing dissimilarity-matrix. As I would like to start with this matrix I thought I could just give the matrix using the x= -argument Test<-metaMDS(x=Dist.Gower) Fehler in inherits(comm, "dist") :

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

Dear all, I have the following object: > print(x) An object of class "matrix.csr" Slot "ra": [1] 0.992056718 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 [7] 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 [13] 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 [19] 1.000000000 1.000000000 1.000000000

Hello everybody. I am trying to cluster circular data (data points which are angles), thus i can not use the "dist" function in "mclust" to generate my distance matrix, I am using the function " Dij = 0.5*( 1 - cos(theta_i - theta_j)). The thing is "hclust" will not accept this distance matrix, i tried to put it in a data frame, but again i get an error message

Hi, I wonder why factor scores produced by factanal are correlated, and I'd appreciate any hints from people that may help me to get a deeper understanding why that's the case. By the way: I'm a psychologist used to SPSS, so that question my sound a little silly to your ears. Here's my minimal example: *********************************************** v1 <-

Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account. I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such

Friends I am new to R (and statistics) so am struggling a bit. Briefly... I am interested in getting the P-Value from cor(X) where X is a matrix. I have found cor.test. Verbosely... I have 4 vectors and can generate the corellation matrix... > cor(cbind(X1, X2, X3, X4)) X1 X2 X3 X4 X1 1.00000000 -0.06190365 -0.156972795 0.182547517 X2

Dear professor, I am currently using Design package and the cph formula for assessing multivariable analysis. I am tryng to get the C-index for my survival model based on Dxy coefficient. I am confused since there is a negative value. Do I need to used the absolute Dxy ? index.orig training test optimism index.corrected n Dxy -0.341357727 -0.344002740

Dear Rs I have two vectors A and B where A is V1 d 1 0.000100000 1.123278 2 0.002186431 1.120448 3 0.004351214 1.106661 4 0.006515998 1.107713 5 0.008680781 1.107667 6 0.013010348 1.106353 7 0.019504698 1.104077 8 0.034658181 1.103202 9 0.051976447 1.103200 10 0.073624280 1.094825 11 0.093085682 1.085123 12 0.095250465 1.087325 13 0.132051782 1.086158 14 0.168853098

Hi all R-users, If I have a matrix with numeric elements as follows, the values are rounded when I try to refer to a specifici element using [], the value is rounded. The same thing happens if the matrix is read from a file, the values are stored to the correct precision but then when I try to refer to a specific element (such as using [], it is rounded. How do I avoid this rounding?

Dear R help My problem is very similar to the analysis detailed here. If we use the mayo dataset provided with the survivalROC package the estimate for Somer's Dxy is very negative -0.56. The Nagelkerke R2 is positive though 0.32. I know there is a difference between explained variation and predictive ability but I am surprised there is usch a difference given that even a non predictive model

Hello, I am having trouble specifying a suitable nlme model. My data structure is described by gd <- groupedData(ppath ~ lcut | exp, outer = ~ bait, inner = ~ weight, data = d) i.e. the response (ppath) of several subjects (sub) was measured at levels of a continuous variable (lcut). Subjects were given either of one level of a factor (bait), and all subjects were measured at two levels

Dear R-hep, I'm trying to get the first derivative of a smooth from a gam model like: model<-gam(y~s(x,bs="cr", k=5)+z) and need the derivative: ds(x)/dx. Since coef(model) give me all the parameters, including the parameters of the basis, I just need the 1st derivative of the basis s(x).1, s(x).2, s(x).3, s(x).4. If the basis were generated with the function

Dear all, Hi, I have the problems about converting the matrix to adjacency matrix.Here's my example, a b c d e fa 1.0000000 0.4048823682 0.1228531 0.49046991 0.4945158868 0.307443317b 0.4048824 1.0000000000 0.4367475 0.96949219 0.0007378596 0.560747765c 0.1228531 0.4367474719 1.0000000 0.40037341 0.3157538204

Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to

Dear useRs, I'm having trouble with what is likely a very simple issue with a simple graph. I have data in the format pasted below - total from which this is a subset is > 3 million rows. I'm plotting "Window" on the x axis, and either of the other two columns on the y axis. In both the second and third columns, the values are in a range from 0 to 1. I want to be able to plot

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

Hello, When I am writing in sqldf or RSQLite I lose the decimals in my matrix. The only way I can get decimals is by multiplying by 1.00000, etc. I have tried manipulating the options, but it is only effective once I multiply by 1.0000. I appreciate any suggestions! Thanks! Example: z <- sqldf ("select ST, SUM(AGEP*PWGTP)*1.000000000/SUM(PWGTP)*1.00000000000000 as wgtage from ss09

Eigen seems to be giving different results in 0.64 : eigen(matrix( c(0.00000000, 0.0000000, 0.00000000, 1.000000000, 0.01262442, -0.1141633, 0.04989433, 0.006112607, 0.04781087, 0.4177869, -0.15569656, 0.074242237, 0.20167331, 0.2531109, -0.04973573, 0.034046467) ,4,4))$values R: [1] 0.35519256 -0.29294606 -0.26637369 -0.03168619 S: [1] 0.4689288205 -0.4246063863 -0.2810596564