similar to: Removing any text beginning with...

Hello, I’m trying to perform a REML analysis using the lmer() function (lme4 package). Well, it seems to work well, except that I’m not getting any p-value (see example below). Can someone tell me what I did wrong? Thanks for your help, Amélie > library(gdata) > dive <- read.xls("C:/Documents and Settings/Amelie/My Documents/Postdoc/CE 2005-2006/divebydive.xls",

| Confirmed for R-devel (current) on Ubuntu 17.10. But ... isn't the regexp | you use wrong, ie isn't R-devel giving the correct answer? No, I don't think R-devel is correct (or at least consistent with the documentation). My interpretation of gsub("(\\w)", "\\U\\1", entry, perl = TRUE) is "Take every word character and replace it with itself, converted to

Hello, Could someone explain to me why I get so different histograms, in terms of bar spacing, depending on the number of counts entered ? (see example below) > test <- c(0,1,1,1,1,0,0,0,0,0,2,3,2,2,2,3,3,4,5,6,7,5,4,3,4,2,2) > hist(test) I obtain this kind of histogram (what I actually want), i.e. large bars with no space between them x xx xxx xxxx xxxxx xxxxxx

Hi - I'm having a problem trying to use the function GLMM() from lme4. Here is what happens: > library(lme4) Loading required package: Matrix Loading required package: lattice > f1 <- GLMM(success~yearF, data=quality, random=~1|bandnumb, family=binomial, method=PQL) Error: couldn't find function "GLMM" I remember having used lme4 before, without any problem.

Hello, The 179th and 180th elements of my list of lists look like this: [[179]] [[179]]$desc [1] ">ipi|IPI00646510|IPI00646510.2 ISOFORM P60-HCK OF TYROSINE-PROTEIN KINASE HCK." [[179]]$seq [1] "MGGRSSCEDPGCPRDEERAPRMGCMKSKFLQVGGNTFSKTETSASPHCPVYVPDPTSTIKPGPNSHNSNTP GIREAGSEDIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEE

Hello, I’m trying to fit the following model: Dependent variable: MAXDEPTH (the maximum depth reached by a penguin during a given dive) Fixed effects: SUCCESSMN (an index of the “individual quality” of a bird), STUDYDAY (the day of the study, from -5 to 20, with 0=Dec 20), and the interaction SUCCESSMN*STUDYDAY Random effect: BIRD (the bird id, as each bird is performing several dives)

I think the problem in R-devel happens when there are non-ASCII characters in any of the strings passed to gsub. txt <- vapply(list(as.raw(c(0x41, 0x6d, 0xc3, 0xa9, 0x6c, 0x69, 0x65)), as.raw(c(0x41, 0x6d, 0x65, 0x6c, 0x69, 0x61))), rawToChar, "") txt #[1] "Am?lie" "Amelia" Encoding(txt) #[1] "unknown" "unknown" gsub(perl=TRUE,

I was told to re-raise this issue with R-dev: In the documentation of R-dev and R-3.4.3, under ?gsub > replacement > ... For perl = TRUE only, it can also contain "\U" or "\L" to convert the rest of the replacement to upper or lower case and "\E" to end case conversion. However, the following code runs differently: tempf <- tempfile()

I am new to R (ex SAS user) , and I cannot merge two data frames without getting duplicated rows in the results. How to avoid this happening without using the unique() function? 1. First data frame is called "tmv" with 6 variables and 239 rows: > tmv[1:10,] temps nom prenom sexe dist style 1 01:59:36 Cyr Steve H 45 free 2 02:09:55 Gosselin

Dear all, I would like to add mixed effects in a multinomial model and I am trying to use MCMCglmm for that. The main problem I face: my data set consits of a trapping data set, where the observation at eah trap (1 or 0 for each species) have been aggregated per traplines. Therefore we have a proportion of presence/absence for each species per trapline. ex: ID_line mesh habitat Apsy Mygl

Dear all, I am trying to model variation of distribution of species assemblages according to environmental variables. For that I use a log linear multinomial regression. In order to select variables that mostly discriminate the assemblages, I tried to apply a hierarchical partitioning protocol to my data set. For that I have adapted the all.regs() for multinomial model. The problem is that I

Hello, I am using the function mda of the mda library in order to discriminate 4 groups with 8 explanatory variables. I only have 66 observations. I tested all possible combinations of those variable and run for each the Mixture Discriminant Analysis. For some iterations, I got an error message: "error in kmeans(xx, start): initial centers are not distinct". I understood that the

Hi folks, I'm a Linux user from Germany (more details about me at ameliezapf.com) and use Wine to run Origin 6.1 (the scientific graphics program). That seems to all go fine, and indeed it did when I used the Wine included in SuSE 9.0 (Wine20030813). Now I've upgraded to SuSE 9.2 (Wine 20040813) and suddenly, the paper sizes do not get handed through to Origin anymore. No matter if I

Hello Amelie, I don't have an answer to your question, but I just wanted to point out this page I noticed recently ( http://hlplab.wordpress.com/2009/05/07/multinomial-random-effects-models-in-r/), which might be helpful. I'm also interested in figuring out how to do a multinomial glmm, so if you find out anything I'd be happy to hear more about it! Based on what I've found so

Hi, I am running a mixed-effect model with a nested-random effect. I am interested in gut parasites in moose. I has three different type of treatment that I applied to moose which are from different "families". My response variable is gut parasites and the factors are moose families which is nested within treatment. My data is balanced. To answer this question, I used the lme function

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

Hi Is it possible to open a connection to an FTP site such that I can read the directory listing? Eg: URL <- url("ftp://ftp.ensembl.org", open="r") Error in url("ftp://ftp.ensembl.org", open="r") : unable to open connection URL <- url("ftp://ftp.ensembl.org") open(URL) Error in open.connection(URL) : unable to open connection I think

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr

Hi Guys, working on a "merge" for 2 data frames. Using the command: x <- merge(annotatedData, UCSCgenes, by.x="names", by.y="Ensembl.Gene.ID", all.x=TRUE) names and Ensembl.Gene.ID are columns with similar elements from the x and y data frames. annotatedData has 8909 entries, so has x(as expected). x has columns for UCSCgenes, but there is no data in them, all

Dear all, I have a data which is in text file and i would like to import the data to R. From the manual, i?ve found the read.table command function is the most appropriate but when i wrote the command an error had occur. It say ?Error in read.table"C:/Users/user/Documents/cfa-1.txt", header = T, sep = "\t",skip=10) :more columns than column names?. Please help me with this as