Re: [R] Re strict AIC comparison to succesful models?
Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? -- View this message in context: http://www.nabble.com/Restrict-AIC-comparison-to-succesful-models--tp23985797p23987185.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.
Re: [R] Re strict AIC comparison to succesful models?
On Thu, 2009-06-11 at 12:08 -0700, Ben Bolker wrote: Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? Good idea but unfortunately I get an error message with: models - list(m1,m2,m3) test - function(x) length(x)1 is.OK - sapply(models,test) do.call(AIC,models[is.OK]) I think the issue is that AIC is expecting a ... of model objects (not a list or a vector) and I'm not sure how to construct that. Manuel __ 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] Re strict AIC comparison to succesful models?
Manuel Morales wrote: On Thu, 2009-06-11 at 12:08 -0700, Ben Bolker wrote: Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? Good idea but unfortunately I get an error message with: models - list(m1,m2,m3) test - function(x) length(x)1 is.OK - sapply(models,test) do.call(AIC,models[is.OK]) I think the issue is that AIC is expecting a ... of model objects (not a list or a vector) and I'm not sure how to construct that. Manuel The problem is that when your fitting function fails, NOTHING gets created. Try this: # resp - c(1,1,2) pred - c(1,2,3) m1 - try(lm(resp~pred)) m2 - try(lm(resp~poly(pred,2))) m3 - try(lm(resp~poly(pred,3))) # Fails, obviously models - list(m1,m2,m3) test - function(x) !inherits(x,try-error) is.OK - sapply(models,test) AIC(m1,m2) ## works ## all these work but lead to objects with ugly row names do.call(AIC,models[is.OK]) do.call(AIC,models[is.OK]) do.call(stats:::AIC.default,models[is.OK]) dd - do.call(AIC,list(m1,m2)) rownames(dd) - NULL dd -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bol...@ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc signature.asc Description: OpenPGP digital signature __ 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] Re strict AIC comparison to succesful models?
On Thu, 2009-06-11 at 16:10 -0400, Ben Bolker wrote: Manuel Morales wrote: On Thu, 2009-06-11 at 12:08 -0700, Ben Bolker wrote: Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? Good idea but unfortunately I get an error message with: models - list(m1,m2,m3) test - function(x) length(x)1 is.OK - sapply(models,test) do.call(AIC,models[is.OK]) I think the issue is that AIC is expecting a ... of model objects (not a list or a vector) and I'm not sure how to construct that. Manuel The problem is that when your fitting function fails, NOTHING gets created. Try this: # resp - c(1,1,2) pred - c(1,2,3) m1 - try(lm(resp~pred)) m2 - try(lm(resp~poly(pred,2))) m3 - try(lm(resp~poly(pred,3))) # Fails, obviously models - list(m1,m2,m3) test - function(x) !inherits(x,try-error) is.OK - sapply(models,test) AIC(m1,m2) ## works ## all these work but lead to objects with ugly row names do.call(AIC,models[is.OK]) do.call(AIC,models[is.OK]) do.call(stats:::AIC.default,models[is.OK]) dd - do.call(AIC,list(m1,m2)) rownames(dd) - NULL dd I see, it wasn't an error message just a very ugly output. Reassigning the row names works great! Thanks, Manuel -- http://mutualism.williams.edu __ 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.
