Re: [R] Error message glmer using R: “ 'what' must be a character string or a function”
You can reproduce the problem by having a data.frame (or anything else) in your environment: new - data.frame(ï..VAR1 = rep(c(TRUE,NA,FALSE), c(10,2,8)), random=rep(1:3,len=20), clustno=rep(c(1:5),len=20), validatedRS6=rep(0:1,len=20)) model1- glmer(validatedRS6 ~ random + (1|clustno), data=new, family=binomial(), nAGQ=3) # Error in do.call(new, c(list(Class = glmResp, family = family), ll[setdiff(names(ll), : # 'what' must be a character string or a function The problem is in the call do.call(new, list()) It finds your dataset 'new' (in .GlobalEnv), which is not a function or the name of a function, not the function 'new' from the 'methods' package. Rename your dataset, so you do not have anything called 'new' masking the one in package:methods, and things should work. Write to the maintainer of the package (use maintainer(lme4) for the address) about the problem. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of EmmaB Sent: Tuesday, November 05, 2013 4:48 PM To: r-help@r-project.org Subject: Re: [R] Error message glmer using R: “ 'what' must be a character string or a function” str(new) 'data.frame': 1214 obs. of 4 variables: $ ï..VAR1 : logi NA NA NA NA NA NA ... $ random : int 1 1 1 1 1 1 1 1 1 1 ... $ clustno : int 1 1 1 1 1 1 1 1 1 1 ... $ validatedRS6: int 0 0 0 0 0 0 0 0 0 0 ... -- View this message in context: http://r.789695.n4.nabble.com/Error-message-glmer- using-R-what-must-be-a-character-string-or-a-function-tp4679829p4679836.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message glmer using R: “ 'what' must be a character string or a function”
You can reproduce the problem by having a data.frame (or anything else) in your environment: I left out called 'new' in the above statement. The example is correct. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of William Dunlap Sent: Wednesday, November 06, 2013 8:04 AM To: EmmaB; r-help@r-project.org Subject: Re: [R] Error message glmer using R: “ 'what' must be a character string or a function” You can reproduce the problem by having a data.frame (or anything else) in your environment: new - data.frame(ï..VAR1 = rep(c(TRUE,NA,FALSE), c(10,2,8)), random=rep(1:3,len=20), clustno=rep(c(1:5),len=20), validatedRS6=rep(0:1,len=20)) model1- glmer(validatedRS6 ~ random + (1|clustno), data=new, family=binomial(), nAGQ=3) # Error in do.call(new, c(list(Class = glmResp, family = family), ll[setdiff(names(ll), : # 'what' must be a character string or a function The problem is in the call do.call(new, list()) It finds your dataset 'new' (in .GlobalEnv), which is not a function or the name of a function, not the function 'new' from the 'methods' package. Rename your dataset, so you do not have anything called 'new' masking the one in package:methods, and things should work. Write to the maintainer of the package (use maintainer(lme4) for the address) about the problem. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of EmmaB Sent: Tuesday, November 05, 2013 4:48 PM To: r-help@r-project.org Subject: Re: [R] Error message glmer using R: “ 'what' must be a character string or a function” str(new) 'data.frame': 1214 obs. of 4 variables: $ ï..VAR1 : logi NA NA NA NA NA NA ... $ random : int 1 1 1 1 1 1 1 1 1 1 ... $ clustno : int 1 1 1 1 1 1 1 1 1 1 ... $ validatedRS6: int 0 0 0 0 0 0 0 0 0 0 ... -- View this message in context: http://r.789695.n4.nabble.com/Error-message-glmer- using-R-what-must-be-a-character-string-or-a-function-tp4679829p4679836.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message glmer using R: “ 'what' must be a character string or a function”
William Dunlap wdunlap at tibco.com writes: You can reproduce the problem by having a data.frame (or anything else) in your environment: I left out called 'new' in the above statement. The example is correct. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- [snip] You can reproduce the problem by having a data.frame (or anything else) in your environment: new - data.frame(ï..VAR1 = rep(c(TRUE,NA,FALSE), c(10,2,8)), random=rep(1:3,len=20), clustno=rep(c(1:5),len=20), validatedRS6=rep(0:1,len=20)) model1- glmer(validatedRS6 ~ random + (1|clustno), data=new, family=binomial(), nAGQ=3) # Error in do.call(new, c(list(Class = glmResp, family = family), ll[setdiff(names(ll), : # 'what' must be a character string or a function The problem is in the call do.call(new, list()) It finds your dataset 'new' (in .GlobalEnv), which is not a function or the name of a function, not the function 'new' from the 'methods' package. Rename your dataset, so you do not have anything called 'new' masking the one in package:methods, and things should work. Write to the maintainer of the package (use maintainer(lme4) for the address) about the problem. For what it's worth, I saw this on StackOverflow: [broken URL] http://stackoverflow.com/questions/19801070/ error-message-glmer-using-r-what-must-be-a-character-string-or-a-function answered it there, and have fixed it on Github: https://github.com/lme4/lme4/commit/9c12f002821f9567d5454e2ce3b78076dabffb54 While it is not officially forbidden in http://www.r-project.org/posting-guide.html (to my surprise, I can't even find any proscription against cross-posting to R mailing lists, although there is a section about which list to post to), posting to both r-help and Stack Overflow tends to lead to duplicated effort/ frustration. Please choose one or the other (in my opinion it's OK to cross-post after a few days if you don't get any responses in one place, provided that you say that you've cross-posted and ideally provide a reference link to the cross-post). Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message glmer using R: “ 'what' must be a character string or a function”
On Nov 5, 2013, at 3:36 PM, EmmaB wrote: I am running a multi-level model. I use the following commands with validatedRS6 as the outcome, random as the predictor and clustno as the random effects variable. new-as.data.frame(read.delim(BABEX.dat, header=TRUE)) install.packages(lme4) library(lme4) model1- glmer(validatedRS6 ~ random + (1|clustno), data=new, family=binomial(logit), nAGQ) However, I get the following error Error in do.call(new, c(list(Class = glmResp, family = family), ll[setdiff(names(ll), : 'what' must be a character string or a function I have absolutely no idea what has gone wrong and have searched the internet. I am sorry but I cannot provide the data as it is from an intervention which has yet to be published. You at least need to post the output of str(new). -- View this message in context: http://r.789695.n4.nabble.com/Error-message-glmer-using-R-what-must-be-a-character-string-or-a-function-tp4679829.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message glmer using R: “ 'what' must be a character string or a function”
str(new) 'data.frame': 1214 obs. of 4 variables: $ ï..VAR1 : logi NA NA NA NA NA NA ... $ random : int 1 1 1 1 1 1 1 1 1 1 ... $ clustno : int 1 1 1 1 1 1 1 1 1 1 ... $ validatedRS6: int 0 0 0 0 0 0 0 0 0 0 ... -- View this message in context: http://r.789695.n4.nabble.com/Error-message-glmer-using-R-what-must-be-a-character-string-or-a-function-tp4679829p4679836.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
