Re: [R] Error message in dredge function (MuMIn package) used with binary GLM
Hi Cat, are you using some very old version of MuMIn? That would explain the missing 'QAICc'. As for the error message about 'logLik', it usually occurs when there are some misspelled arguments (that go into ... and are passed to the rank function, 'AICc' in your case). Check if there is some argument (of type logical) in your call to 'dredge' that is not its formal argument. kamil On 2013-03-30 03:13, cat.e.co...@gmail.com wrote: Hi Kamil, Thanks for your help. I do want to use rank=QAICc, but I when I try it I get the following error message: Error in get(as.character(FUN), mode = function, envir = envir) : object 'QAICc' of mode 'function' was not found Do I need to install another package that would recognise this? When I leave the script with rank=AICc (to see if it will run), and having removed chat (which I put in after previously recieving an error message about it being missing from the formula), I still get my original error message: Error in UseMethod(logLik) : no applicable method for 'logLik' applied to an object of class logical Any further thoughts? Thanks, Cat quote author='Kamil Barton' 'rank' should be QAICc. AICc does not have argument 'chat', hence the error. kamil Hi all, I'm having trouble with the model generating 'dredge' function in the MuMIn 'Multi-model Inference' package. Here's the script: globalmodel- glm(TB~lat+protocol+tested+ streams+goats+hay+cattle+deer, family=binomial) chat- deviance(globalmodel)/59 #There we 59 residual degrees of freedom in this global model. models- dredge(globalmodel, beta=FALSE, evaluate=TRUE, rank=AICc, chat=chat, fixed=NULL, trace=FALSE) And the error message is: Error in UseMethod(logLik) : no applicable method for 'logLik' applied to an object of class logical I have trawled the literature and it seems to be ok to use a binary GLM as the global model - could this be the problem? The variables are a mix of binary and continuous data. Any thoughts? Thanks, Cat /quote Quoted from: http://r.789695.n4.nabble.com/Error-message-in-dredge-function-MuMIn-package-used-with-binary-GLM-tp4662842p4662881.html The University of Aberdeen is a charity registered in Scotland, No SC013683. __ 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 in dredge function (MuMIn package) used with binary GLM
Hi Kamil, (I have replied to the forum but my posts as replies never seem to get accepted, so here is the text in an email also. Apologies if it comes through twice.) Thanks so much for the prompt reply. You've solved it! Actually I had the latest version of the package, but an older version of R that wasn't supporting the package evidently... when I updated it everything ran with the AICc rank. However, when I run it with QAICc (which i think Iwant to use), R returns the error Error in chat 1 : 'chat' is missing and does not conduct the dredge. My chat (variance inflation factor) is 0.597. As this is 1, should I just rank by AICc? I still have a small sample size necessitating AICc. For interest, I can make the dredge run with rank=QAICc, but I need to include the chat, and a error message then tells me In rank(x, chat = 0.597604265592854) : 'chat' given is 1, increased to 1. The script for this is below: ##Information Theoretic Approach globalmodel- glm(TB~lat+protocol+tested+streams+goats+hay+cattle+deer, family=binomial) chat- deviance(globalmodel)/59 #There we 59 residual degrees of freedom in this model. models- dredge(globalmodel, beta=FALSE, evaluate=TRUE, rank=QAICc, chat=chat, fixed=NULL, trace=FALSE) models warnings() I think I will use just AICc, but do let me know if you think this is wrong! Many thanks again for your help, Cat On 1 April 2013 22:19, Kamil Barton [via R] ml-node+s789695n4662958...@n4.nabble.com wrote: Hi Cat, are you using some very old version of MuMIn? That would explain the missing 'QAICc'. As for the error message about 'logLik', it usually occurs when there are some misspelled arguments (that go into ... and are passed to the rank function, 'AICc' in your case). Check if there is some argument (of type logical) in your call to 'dredge' that is not its formal argument. kamil On 2013-03-30 03:13, [hidden email]http://user/SendEmail.jtp?type=nodenode=4662958i=0wrote: Hi Kamil, Thanks for your help. I do want to use rank=QAICc, but I when I try it I get the following error message: Error in get(as.character(FUN), mode = function, envir = envir) : object 'QAICc' of mode 'function' was not found Do I need to install another package that would recognise this? When I leave the script with rank=AICc (to see if it will run), and having removed chat (which I put in after previously recieving an error message about it being missing from the formula), I still get my original error message: Error in UseMethod(logLik) : no applicable method for 'logLik' applied to an object of class logical Any further thoughts? Thanks, Cat quote author='Kamil Barton' 'rank' should be QAICc. AICc does not have argument 'chat', hence the error. kamil Hi all, I'm having trouble with the model generating 'dredge' function in the MuMIn 'Multi-model Inference' package. Here's the script: globalmodel- glm(TB~lat+protocol+tested+ streams+goats+hay+cattle+deer, family=binomial) chat- deviance(globalmodel)/59 #There we 59 residual degrees of freedom in this global model. models- dredge(globalmodel, beta=FALSE, evaluate=TRUE, rank=AICc, chat=chat, fixed=NULL, trace=FALSE) And the error message is: Error in UseMethod(logLik) : no applicable method for 'logLik' applied to an object of class logical I have trawled the literature and it seems to be ok to use a binary GLM as the global model - could this be the problem? The variables are a mix of binary and continuous data. Any thoughts? Thanks, Cat /quote Quoted from: http://r.789695.n4.nabble.com/Error-message-in-dredge-function-MuMIn-package-used-with-binary-GLM-tp4662842p4662881.html The University of Aberdeen is a charity registered in Scotland, No SC013683. __ [hidden email] http://user/SendEmail.jtp?type=nodenode=4662958i=1mailing 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. -- If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/Error-message-in-dredge-function-MuMIn-package-used-with-binary-GLM-tp4662842p4662958.html To unsubscribe from Error message in dredge function (MuMIn package) used with binary GLM, click herehttp://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4662842code=Y2F0LmUuY293aWVAZ21haWwuY29tfDQ2NjI4NDJ8MTMyMDc2OTMxNw== .
[R] Error message in dredge function (MuMIn package) used with binary GLM
Hi all, I'm having trouble with the model generating 'dredge' function in the MuMIn 'Multi-model Inference' package. Here's the script: globalmodel- glm(TB~lat+protocol+tested+ streams+goats+hay+cattle+deer, family=binomial) chat- deviance(globalmodel)/59 #There we 59 residual degrees of freedom in this global model. models- dredge(globalmodel, beta=FALSE, evaluate=TRUE, rank=AICc, chat=chat, fixed=NULL, trace=FALSE) And the error message is: Error in UseMethod(logLik) : no applicable method for 'logLik' applied to an object of class logical I have trawled the literature and it seems to be ok to use a binary GLM as the global model - could this be the problem? The variables are a mix of binary and continuous data. Any thoughts? Thanks, Cat __ 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 in dredge function (MuMIn package) used with binary GLM
'rank' should be QAICc. AICc does not have argument 'chat', hence the error. kamil CatCowie wrote Hi all, I'm having trouble with the model generating 'dredge' function in the MuMIn 'Multi-model Inference' package. Here's the script: globalmodel- glm(TB~lat+protocol+tested+ streams+goats+hay+cattle+deer, family=binomial) chat- deviance(globalmodel)/59 #There we 59 residual degrees of freedom in this global model. models- dredge(globalmodel, beta=FALSE, evaluate=TRUE, rank=AICc, chat=chat, fixed=NULL, trace=FALSE) And the error message is: Error in UseMethod(logLik) : no applicable method for 'logLik' applied to an object of class logical I have trawled the literature and it seems to be ok to use a binary GLM as the global model - could this be the problem? The variables are a mix of binary and continuous data. Any thoughts? Thanks, Cat -- View this message in context: http://r.789695.n4.nabble.com/Error-message-in-dredge-function-MuMIn-package-used-with-binary-GLM-tp4662842p4662881.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.
