similar to: Re: clustering polypeptide sequences

Hi all, I have a data frame with sequences of x and y from a map. I would like to know it both ways: 1. How to make a matrix from that; 2. how to make a data frame of all points in a map. Probably it is a silly question, but please tell me where to read about it or tell me how to do it. Miha Staut

Hi all, I tried to produce some kriged surfaces with geoR (latest version). The size of the grid should be around 900 x 650 cells (what I find is not a very big grid), and the number of points is around 2500. The command krige.conv stopped after arround 5 min saying it can not allocate a vector with around 1.5 billion units. Sounds reasonable. Is there a workaround? How would I partition the

Dear All I would like to use filled.contour to plot something with arrows on it. I did it in this way: filled.contour(1:nx,1:nz,u,col=gray(rev((0:20/20)))) for (j in zseq ) for (i in xseq) arrows(i, j, i+u[i,j],j+w[i,j],length=angleng,angle=angarrow,code=2, lwd=1,col="black") The peoblem is that the arrows use the whole device area, including the key on the right hand side of the

Gents: (alas, I think no ladies need to be included in the salutation) The apply() Help file says "... If the calls to FUN return vectors of different lengths, apply returns a list of length dim(X)[MARGIN]. " Shouldn't that be: "If the calls to FUN return vectors of different lengths, apply returns a list of length prod(dim(X)[MARGIN]). " Also, might you wish to add:

Dear R support network I have a problem that is driving me crazy. I have a dataframe with about 74000 landscapes which I call "land". A landscape is a 2km -by- 2km square. Land has three columns: land$lat, land$long, and land$description. The last one holds a NON-unique (integer) description of each landscape. There are maybe 100 distinct descriptions. Identifying landscapes that

Dear R users, Does anyone have a function for putting a legend on an image plot? I couldn't locate an R equivalent of image.legend....has anyone written such a thing? kind regards andy --------------------------------------------------------------------- J. Andy Royle, U.S. Fish and Wildlife Service - Office of Migratory Bird Management; 11510 American Holly Drive , Laurel, MD

vector with a sequence starting from 1 to sum of all the values of the raster data and length(the same length as the sum). In another data frame (G) I have got a vector with the environment variables (G$xseq and G$yseq). How can I combine the x and y coordinates with tha raster data to form a data.frame? length(G$xseq)=3099 length(G$yseq)=5032 rastername=rst length(rst)=(3099*5032) Next

Hi R-help, ? I have fit a cox ph model to my data, but have beenreceiving an error when trying to fit a model to the nomogram. Here is the codeand corresponding error: ? ? >nomogramCF = nomogram(cph_age6_40avp4, +????????????????????lp.at= seq(-10,10,by =0.5),lp = TRUE, +?????????????????????? +??????????????????????funlabel="5year survival",

Full_Name: Roger Bivand Version: 0.99.0 OS: RH Linux 6.1 Submission from: (NULL) (158.37.60.152) I am working on an interface between R and the GRASS geographical information system, written in R, with no dynamically loaded code. I have written full examples, and tested then under R 0.90.1, both by entering example() for each function and R CMD check, both of which worked without problem. Under

Hi to all, I'm trying to run Battery3 with Wine, but I'm experiencing some problems. 1. When I launch Battery (command line) I see these messages: --- fixme:win:RegisterDeviceNotificationW (hwnd=0x50062, filter=0x32fcb0,flags=0x00000004) returns a fake device notification handle! JackActivationCount::Signal value = 0 ref = 5 JackActivationCount::Signal value = 0 ref = 5

Dear R-helpers, I'm having a problem in using plot.design in Design Library. Tho following example code produce the error: > n <- 1000 # define sample size > set.seed(17) # so can reproduce the results > age <- rnorm(n, 50, 10) > blood.pressure <- rnorm(n, 120, 15) > cholesterol <- rnorm(n, 200, 25) > sex <-

Hello, I am using Dr. Harrell's design package to make a nomogram. I was able to make a beautiful one without stratifying, however, I will need to stratify to meet PH assumptions. This is where I go wrong, but I'm not sure where. Non-Stratified Nomogram:

Hello, I have a question about how to plot a series of data. The folloqing is my data matrix of n > n 25p 5p 2.5p 0.5p 16B-E06.g 45379 4383 5123 45 16B-E06.g 45138 4028 6249 52 16B-E06.g 48457 4267 5470 54 16B-E06.g 47740 4676 6769 48 37B-B02.g 42860 6152 19276 72 35B-A02.g 48325 12863 38274 143 35B-A02.g 48410 12806 39013 175 35B-A02.g 48417 9057 40923

Hi Function sequence() repeatedly concatenates its output, and this is slow. It is possible to improve on the performance of sequence by defining myseq <- function(x){unlist(sapply(x,function(i){1:i}))} The following session compares the performance of myseq(), and sequence(), at least on my G5: > identical(sequence(1:50),myseq(1:50)) [1] TRUE > system.time(ignore <-

Hi Function sequence() repeatedly concatenates its output, and this is slow. It is possible to improve on the performance of sequence by defining myseq <- function(x){unlist(sapply(x,function(i){1:i}))} The following session compares the performance of myseq(), and sequence(), at least on my G5: > identical(sequence(1:50),myseq(1:50)) [1] TRUE > system.time(ignore <-

Dear all, I try to use read.table to get the data from a tab delimited file, and some of the data is shown below: 3185 heterogeneous nuclear ribonucleoprotein F 3187 heterogeneous nuclear ribonucleoprotein H1 (H) 3188 heterogeneous nuclear ribonucleoprotein H2 (H') 3189 heterogeneous nuclear ribonucleoprotein H3 (2H9) 3190 heterogeneous nuclear ribonucleoprotein K ///

Hello R-help group, I have a question about merging lists. I have two lists: Genes list (hSgenes) name chr strand start end transStart transEnd symbol description feature ENSG00000223972 1 1 11874 14412 11874 14412 DEAD/H box polypeptide 11 like 1DEAD/H box polypeptide 11 like 3DEAD/H box polypeptide 11 like 9 ;;

Hi, I have encountered this problem quite a few times and thought I would ask. Let's say that I have two endpoints, a and b, which are integers. If a <= b, I would like to get a:b, but if a > b, then numeric(0), for example: myseq(3,5) => 3:5 myseq(3,3) => 3 myseq(3,2) => numeric(0) The operator : just gives decreasing sequences in the latter case, and I could not coax seq

Last Friday, I noticed that it is difficult to work with regression models in which there are factors. It is easier to do the old fashioned thing of coding up "dummy" variables with 0-1 values. The predict function's newdata argument is not suited to insertion of hypothetical values for the factor, whereas it has no trouble with numeric variables. For example, if one uses a

Dear All, I am using the plotrix library to plot some matrices. I have a problem: some of my data are outliers, hence using a linear color scale does not work very well (you would see too many cells having a similar, indistinguishable color). See the code snipped at the end of the email. Plotting the logarithm of the data gets the job done, but my problem is that I would like to write in every