[R] Problem with effects package
sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid datasets splines utils stats [6] graphics grDevices methods base other attached packages: [1] effects_2.1-0 colorspace_1.1-1 [3] nnet_7.3-1 nlme_3.1-103 [5] lattice_0.20-6 reshape_0.8.4 [7] plyr_1.7.1 catdata_1.0 [9] cacheSweave_0.6-1 stashR_0.3-5 [11] filehash_2.2-1 BiocInstaller_1.4.3 [13] ctv_0.7-4 sos_1.3-1 [15] brew_1.0-6 Hmisc_3.9-3 [17] survival_2.36-12MASS_7.3-17 loaded via a namespace (and not attached): [1] cluster_1.14.2 digest_0.5.2 tools_2.15.0 # copy and paste the following: library( catdata ) data( unemployment ) unempt - unemployment unempt$durbin - unempt$durbin - 1 library( reshape ) unempt - melt( table( unempt ) ) unempw - cast( unempt, age ~ durbin ) names( unempw ) - c( 'age', 'short', 'long' ) modt - glm( durbin ~ age, weights = value, family = binomial, data = unempt ) modw - glm( cbind( short, long ) ~ age, family = binomial, data = unempw ) library( effects ) modt.ef - effect( 'age', modt ) # works! modw.ef - effect( 'age', modw ) # doesn't work! # Error in eval(expr, envir, enclos) : object 'age' not found # end __ Professor Michael Kubovy University of Virginia Department of Psychology for mail add: for FedEx or UPS add: P.O.Box 400400 Gilmer Hall, Room 102 Charlottesville, VA 22904-4400 485 McCormick Road USA Charlottesville, VA 22903 roomphone Office:B011 +1-434-982-4729 Lab:B019+1-434-982-4751 WWW:http://www.people.virginia.edu/~mk9y/ [[alternative HTML version deleted]] __ 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] Problem with effects package
Dear Michael, From ?effect (under Warnings and Limitations): Binomial generalized linear models cannot have a matrix of successes and failures on the left-hand side of the model formula; instead specify the proportion of successes (i.e., successes/(successes + failures)) as the response, and give the number of binomial trials (i.e., successes + failures) in the weights argument to glm. Best, John John Fox Sen. William McMaster Prof. of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ On Wed, 11 Apr 2012 07:20:51 -0400 Michael Kubovy kub...@virginia.edu wrote: sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid datasets splines utils stats [6] graphics grDevices methods base other attached packages: [1] effects_2.1-0 colorspace_1.1-1 [3] nnet_7.3-1 nlme_3.1-103 [5] lattice_0.20-6 reshape_0.8.4 [7] plyr_1.7.1 catdata_1.0 [9] cacheSweave_0.6-1 stashR_0.3-5 [11] filehash_2.2-1 BiocInstaller_1.4.3 [13] ctv_0.7-4 sos_1.3-1 [15] brew_1.0-6 Hmisc_3.9-3 [17] survival_2.36-12MASS_7.3-17 loaded via a namespace (and not attached): [1] cluster_1.14.2 digest_0.5.2 tools_2.15.0 # copy and paste the following: library( catdata ) data( unemployment ) unempt - unemployment unempt$durbin - unempt$durbin - 1 library( reshape ) unempt - melt( table( unempt ) ) unempw - cast( unempt, age ~ durbin ) names( unempw ) - c( 'age', 'short', 'long' ) modt - glm( durbin ~ age, weights = value, family = binomial, data = unempt ) modw - glm( cbind( short, long ) ~ age, family = binomial, data = unempw ) library( effects ) modt.ef - effect( 'age', modt ) # works! modw.ef - effect( 'age', modw ) # doesn't work! # Error in eval(expr, envir, enclos) : object 'age' not found # end __ Professor Michael Kubovy University of Virginia Department of Psychology for mail add: for FedEx or UPS add: P.O.Box 400400Gilmer Hall, Room 102 Charlottesville, VA 22904-4400485 McCormick Road USA Charlottesville, VA 22903 roomphone Office:B011 +1-434-982-4729 Lab:B019 +1-434-982-4751 WWW:http://www.people.virginia.edu/~mk9y/ __ 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] Problem with effects package
Dear List, Several times I use this package I get the error message shown below. When I work out simple examples, it turns out to be fine, but when working with real and moderate size data sets I always get the same error. Do you know what could be the cause of the problem? Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(myvariable, glm.sev1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' Thanks, Lars/ __ 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] Problem with effects package
Dear Lars, There's not nearly enough information here to know what's wrong. I can guess (but shouldn't have to) that the model glm.sev1 is a generalized linear model of some sort, probably fit by glm(). At a minimum, it would help to know what command you used to fit the model, the history of commands leading to the error, and version and session information. Ideally you'd include a reproducible example. The size of the data set should be irrelevant to this error, so if you could supply the information I requested, along with a small subset of your data on which the model can be fit, I can try to figure out what's wrong. Best, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Lars Bishop Sent: July-30-11 3:01 PM To: r-help@r-project.org Subject: [R] Problem with effects package Dear List, Several times I use this package I get the error message shown below. When I work out simple examples, it turns out to be fine, but when working with real and moderate size data sets I always get the same error. Do you know what could be the cause of the problem? Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(myvariable, glm.sev1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' Thanks, Lars/ __ 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] Problem with effects package
Not with a description like that. You need to make a reproducible example. Try using head () or subset to make a smaller data set. Provide the data (using e.g. dput()). Provide the commands that trigger the errors. Who knows... you might even see the issue yourself then. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Lars Bishop lars...@gmail.com wrote: Dear List, Several times I use this package I get the error message shown below. When I work out simple examples, it turns out to be fine, but when working with real and moderate size data sets I always get the same error. Do you know what could be the cause of the problem? Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(myvariable, glm.sev1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' Thanks, Lars/ _ 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. [[alternative HTML version deleted]] __ 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] Problem with effects package
ok. Here's an example: R version 2.11.1 effects_2.0-10 var1 - c(25631.9392, 2521.2590, 6656.6516, 1362.5997, 6369.9818, 27253.4223, 2073.1909, 9959.3792, 3318.2500, 15323.8103, 11583.8717, 3054.5558, 625.6597, 2500., 11996.2271) var2 - as.factor(c(B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, C:750-1000, C:750-1000, B:=500, B:=500, B:=500, B:=500)) glm1 - glm(var1 ~ var2, family = Gamma(link = log)) summary(glm1) library(effects) plot(effect(var2, glm1)) Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(var2, glm1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' On Sat, Jul 30, 2011 at 3:10 PM, jim holtman jholt...@gmail.com wrote: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. We can not help unless we at least have the data that you are using. On Sat, Jul 30, 2011 at 3:01 PM, Lars Bishop lars...@gmail.com wrote: Dear List, Several times I use this package I get the error message shown below. When I work out simple examples, it turns out to be fine, but when working with real and moderate size data sets I always get the same error. Do you know what could be the cause of the problem? Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(myvariable, glm.sev1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' Thanks, Lars/ __ 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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? __ 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] Problem with effects package
Dear Lars, The problem is the : in the levels of var2, which confuses effect() about the structure of the model, since a colon indicates interaction. Try, e.g., removing the colons: var2 - as.factor(c(B=500, B=500, B=500, B=500, B=500, B=500, B=500, B=500, B=500, C750-1000, C750-1000, B=500, B=500, B=500, B=500)) Then, effect(var2, glm1) var2 effect var2 B=500 C750-1000 7947.932 13453.841 (See how helpful it can be to furnish a reproducible example?) I agree, BTW, that this is a deficiency in effect(); I'll look into it when I have a chance. Finally, there really is no advantage to making an effect display for a model with a single predictor, though perhaps this isn't what you were doing in your actual application. Best, John -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Lars Bishop Sent: July-30-11 4:30 PM To: jim holtman; r-help@r-project.org Subject: Re: [R] Problem with effects package ok. Here's an example: R version 2.11.1 effects_2.0-10 var1 - c(25631.9392, 2521.2590, 6656.6516, 1362.5997, 6369.9818, 27253.4223, 2073.1909, 9959.3792, 3318.2500, 15323.8103, 11583.8717, 3054.5558, 625.6597, 2500., 11996.2271) var2 - as.factor(c(B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, C:750-1000, C:750-1000, B:=500, B:=500, B:=500, B:=500)) glm1 - glm(var1 ~ var2, family = Gamma(link = log)) summary(glm1) library(effects) plot(effect(var2, glm1)) Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(var2, glm1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' On Sat, Jul 30, 2011 at 3:10 PM, jim holtman jholt...@gmail.com wrote: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. We can not help unless we at least have the data that you are using. On Sat, Jul 30, 2011 at 3:01 PM, Lars Bishop lars...@gmail.com wrote: Dear List, Several times I use this package I get the error message shown below. When I work out simple examples, it turns out to be fine, but when working with real and moderate size data sets I always get the same error. Do you know what could be the cause of the problem? Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(myvariable, glm.sev1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' Thanks, Lars/ __ 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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? __ 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] Problem with effects package
Thanks for your quick response on this issue John! Yes, in my real dataset I have many predictors and more observations than in this example. I've started to remove one predictor at the time until this one was found to be causing the problem. Thanks again! Lars. On Sat, Jul 30, 2011 at 5:33 PM, John Fox j...@mcmaster.ca wrote: Dear Lars, The problem is the : in the levels of var2, which confuses effect() about the structure of the model, since a colon indicates interaction. Try, e.g., removing the colons: var2 - as.factor(c(B=500, B=500, B=500, B=500, B=500, B=500, B=500, B=500, B=500, C750-1000, C750-1000, B=500, B=500, B=500, B=500)) Then, effect(var2, glm1) var2 effect var2 B=500 C750-1000 7947.932 13453.841 (See how helpful it can be to furnish a reproducible example?) I agree, BTW, that this is a deficiency in effect(); I'll look into it when I have a chance. Finally, there really is no advantage to making an effect display for a model with a single predictor, though perhaps this isn't what you were doing in your actual application. Best, John -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Lars Bishop Sent: July-30-11 4:30 PM To: jim holtman; r-help@r-project.org Subject: Re: [R] Problem with effects package ok. Here's an example: R version 2.11.1 effects_2.0-10 var1 - c(25631.9392, 2521.2590, 6656.6516, 1362.5997, 6369.9818, 27253.4223, 2073.1909, 9959.3792, 3318.2500, 15323.8103, 11583.8717, 3054.5558, 625.6597, 2500., 11996.2271) var2 - as.factor(c(B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, B:=500, C:750-1000, C:750-1000, B:=500, B:=500, B:=500, B:=500)) glm1 - glm(var1 ~ var2, family = Gamma(link = log)) summary(glm1) library(effects) plot(effect(var2, glm1)) Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(var2, glm1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' On Sat, Jul 30, 2011 at 3:10 PM, jim holtman jholt...@gmail.com wrote: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. We can not help unless we at least have the data that you are using. On Sat, Jul 30, 2011 at 3:01 PM, Lars Bishop lars...@gmail.com wrote: Dear List, Several times I use this package I get the error message shown below. When I work out simple examples, it turns out to be fine, but when working with real and moderate size data sets I always get the same error. Do you know what could be the cause of the problem? Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds Error in plot(effect(myvariable, glm.sev1)) : error in evaluating the argument 'x' in selecting a method for function 'plot' Thanks, Lars/ __ 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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? __ 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.
