search for: asmethod

...not sure such a declaration should do any harm in theory, but in practice it seems to trigger subtle bugs in the methods package. + seth --- a/src/library/methods/R/as.R +++ b/src/library/methods/R/as.R @@ -37,9 +37,6 @@ as <- test <- ext at test asMethod <- .makeAsMethod(ext at coerce, ext at simple, Class, Clas canCache <- (!is(test, "function")) || identical(body(test), - if(canCache) { # make into method definition - asMethod <- .asCoerceMethod(asMethod, sig, FALSE) -...

..."),each=160)) fam<-factor(rep(c(1:8,9:16,1:8,9:16),each=20)) dat<-data.frame(reps,sex,geno,fam) and I built the following model: lmer(reps~sex+geno+(1|fam),data=dat,family=binomial) and tried also lmer(reps~sex/geno+(1|fam),data=dat,family=binomial) but I keep getting this error: asMethod(object) : matrix is not symmetric [1,2] Does someone have an idea where the error might come from? Thank you very much in advance! Olivier Sex-chromosome turnovers induced by deleterious mutation load [[alternative HTML version deleted]]

...vector" by class "matrix". Class "array" by class "matrix". Creating a default Matrix object works fine: > m1 <- new("Matrix") But, when I try to set its value I get the following error: > m3 <- new("Matrix", 1) Error in asMethod(object, Class, value) : unused argument(s) ( ...) or > m2 <- new("Matrix", matrix(1)) Error in asMethod(object, Class, value) : unused argument(s) ( ...) I also tried to declare a class MyInteger that extends the class integer, but the same errors: > setClass("MyIn...

Hi: I was trying to use apply on a sparse matrix from package Matrix, and I get the error: Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106 Is there a way to apply a function to all the rows without bumping into this problem? Here is a simplified example: > dim(sm) [1] 72913 43052 > class(sm) [1] "dgCMatrix" attr(,"p...

Hi, Calling gdistance::shortestPath gives me the error Error in asMethod(object) : not a symmetric matrix; consider forceSymmetric() or symmpart() The output of dput(.traceback()) is pairlist("stop(\"not a symmetric matrix; consider forceSymmetric() or symmpart()\")", "asMethod(object)", "as(Laplacian,\"symmetricMatri...

Hi, I'm having trouble writing .pnm images which I think is due to a problem with my colour space. The pixmap object seems to be looking for 72 of 8 colours (one per cell?) which doesn't seem healthy... > library(pixmap) > x <- pixmapIndexed(rep(1:8, 9), nrow=6, col=rainbow(8)) > x Pixmap image Type : pixmapIndexed Size : 6x12 Resolution : 1x1

...ppears the following problem. Attaching package: 'lme4' The following object(s) are masked from 'package:stats':     AIC Error in names(argNew)[1] <- names(formals(new))[[1]] :   replacement has length zero Calls: initial ... lmerFactorList -> lapply -> FUN -> as -> asMethod -> fac2sparse Execution halted However, when I use this package in R-2.11.0, it can work to run the simulation as I do in R-2.11.1. How could we fix this problem? Thank you so much. Sincerely, Joe [[alternative HTML version deleted]]

I have a pretty large sparse matrix of integers: > dim(tasa) [1] 91650 37651 I need to add one to it in order to take logs, but I'm getting the following error: > tasa = log(tasa + 1) CHOLMOD error: problem too large Error in asMethod(object) : Cholmod error `problem too large' I have 2 Gb of RAM, and the current workspace is barely 300mb. Is there any workaround to this? Anyone has any experience with this error? Thanks, -Jose -- Jose Quesada, PhD. http://www.andrew.cmu.edu/~jquesada

...ng at the presence/absence of water shrews against habitat and other factors e.g so I used this: m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1) But i keep getting this error up Error in mer_finalize(ans) : Downdated X'X is not positive definite, 16.> summary(m1)Error in asMethod(object) : matrix is not symmetric [1,2] What does this mean and now can I fix it? Sophie [[alternative HTML version deleted]]

I have a pretty large sparse matrix of integers: > dim(tasa) [1] 91650 37651 I need to add one to it in order to take logs, but I'm getting the following error: > tasa = log(tasa + 1) CHOLMOD error: problem too large Error in asMethod(object) : Cholmod error `problem too large' I have 2 Gb of RAM, and the current workspace is barely 300mb. Is there any workaround to this? Anyone has any experience with this error? Thanks, -Jose -- Jose Quesada, PhD. http://www.andrew.cmu.edu/~jquesada

...21, 3, 7, ... . . . and then apply eclat from arules package to find frequent patterns. 1) I ran the following code: file<-read.csv("D:/R/Practice/Data_Input_NUM.csv") file <- file[!duplicated(file),] eclat(split(file$TRN_TYP,file$CIN)) but it gave me the following error: Error in asMethod(object) : can not coerce list with transactions with duplicated items 2) I ran this code: file<-read.csv("D:/R/Practice/Data_Input_NUM.csv") file_new<-file[,c(3,6)] # because my file Data_Input_NUM has many other columns as well, so I selecting only CIN and TRN_TYP file_new <- f...

...get this error that I can't understand: > refit(dolo4.model4,cbind(uu,50-uu)) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "refit", for signature "mer", "matrix" if I try: > refit(dolo4.model4,uu) Error in asMethod(object) : matrix is not symmetric [1,2] I get this error message that I can no more understand but which suggests that refit expects two columns. the initial model was: > dolo4.model4 at call glmer(formula = cbind(sortis, restes) ~ mean.co2 + (1 | sujet), data = dollo4.df, family = bino...

...offset(log(PR)) (Intercept) YR -4.2830507147 0.0005085944 Random effects: Formula: ~1 | CL (Intercept) Residual StdDev: 0.8313193 0.5346455 Variance function: Structure: fixed weights Formula: ~invwt Number of Observations: 700 Number of Groups: 100 > fit2 Error in asMethod(object) : matrix is not symmetric [1,2] Wayne (Yanwei) Zhang Statistical Research CNA Email: Yanwei.Zhang@cna.com<mailto:Yanwei.Zhang@cna.com> NOTICE: This e-mail message, including any attachments and appended messages, is for the sole use of the intended recipients and may contain...

...Document" .x #returns *** caught segfault *** address 0x1398754, cause 'memory not mapped' Traceback: 1: .Call("RS_XML_dumpHTMLDoc", doc, as.integer(indent), as.character(encoding), as.logical(indent), PACKAGE = "XML") 2: saveXML(from) 3: saveXML(from) 4: asMethod(object) 5: as(x, "character") 6: cat(as(x, "character"), "\n") 7: print.XMLInternalDocument(<pointer: 0x11656d3e0>) 8: print(<pointer: 0x11656d3e0>) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving works...

...uous) as a function of tree density (indicated by leaf-area). Thus, I have tried to specify a Gamma distribution with a log-link function but consistently receive an error as follows: > total=glmer(total~gla4+(1|plot)+(1|year/month),data=veg,family=Gamma(link=log)) > summary(total) Error in asMethod(object) : matrix is not symmetric [1,2] I have also tried fitting glmm's with lme4 and glmer to other Gamma-distributed data but receive the same error. Has anyone had similar problems and found any solutions? Thank you for your input. Best regards, ___________________________________ Matt...

...valid dimension attribute the traceback() says: 16: stop(paste("Invalid \"", Class, "\" object: ", errors, sep = "")) 15: validObject(.Object) 14: .local(.Object, ...) 13: initialize(value, ...) 12: initialize(value, ...) 11: new("matrix.csr") 10: asMethod(object) 9: as(object, superClass) 8: validityMethod(as(object, superClass)) 7: identical(x, TRUE) 6: anyStrings(validityMethod(as(object, superClass))) 5: validObject(.Object) 4: .local(.Object, ...) 3: initialize(value, ...) 2: initialize(value, ...) 1: new("matrix.diag.csr", ra = 1:3, j...

...ination of continuous and categorical variables. After discretizing the continuous variables, I wrote the following instruiction to perform Apriori, but I obtained the following error message: > rules <- apriori(dd_new,parameter=list(supp=0.5, conf=0.9, target="rules")) Erreur dans asMethod(object) : column(s)12345679101112131415162123242553not a factor Does this have any relation with the missing values? Thanks. Cordially, Soumaya

...lmer model with na.action = na.pass, using a command in the following form: > mod = lmer(y~a+b+(1|item) + (1|subj), data=data1, na.action=na.pass) No error message is returned after this line. However, when I called the model using print(mod, corr=F), an error message showed up: > Error in asMethod(object) : matrix is not symmetric [1,2] So my question are the following: (1) am I right in using na.pass in order to maintain the size of the data set the model is based on? (2) how does lmer() function handle the option na.pass? Is there something else I need to set other than na.action? I'...

Hey everyone, I would like to develop a package using S4 classes. I have to define several S4 classes that inherits from each others as follow: # A <- B <- C <- D I also would like to define .DollarNames methods for these class so, if I have understood well, I also have to define an old class as follow: # AOld <- A <- B <- C <- D setOldClass(Classes = "AOld")

...sigma2) w=exp(s) eBLP_glimmix_quad[kk]=mean((T4+n*T3*T4*(yi1/n+yi2/n-T1-T2)/(1+T3*n*(T1+T2))-w)^2) } MSE_eBLP_quad[i3]<-mean(eBLP_glimmix_quad) } print(MSE_eBLP_quad) then you can execute fit2 again after you run my code. After that, you will find the following error message. Error in asMethod(object) : matrix is not symmetric [1,2] Please let me know how to solve this problem. Thanks a lot. -- View this message in context: http://n4.nabble.com/Matrix-is-not-symmetric-under-lme4-tp1836523p1836523.html Sent from the R help mailing list archive at Nabble.com.