[R] error message!
Dear R-users, Can some one help me out. I tried installing some packages in R_2.5.1 but I get an error message as shown below. This is unusual since I have been installing and updatings packages in the same version of R. chooseCRANmirror() update.packages(ask='graphics') Error in .readRDS(pfile) : unknown input format or utils:::menuInstallPkgs() Error in .readRDS(pfile) : unknown input format Thanks usman ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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!
On 26/08/2007 6:13 AM, Usman Shehu wrote: Dear R-users, Can some one help me out. I tried installing some packages in R_2.5.1 but I get an error message as shown below. This is unusual since I have been installing and updatings packages in the same version of R. chooseCRANmirror() update.packages(ask='graphics') Error in .readRDS(pfile) : unknown input format or utils:::menuInstallPkgs() Error in .readRDS(pfile) : unknown input format I'd guess it's a problem with the mirror. Which one did you choose? Do you get the same error if you choose a different one? Duncan Murdoch __ R-help@stat.math.ethz.ch 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!
Usman Shehu wrote: It is not. I tried using a number of mirrors, eg Germany, Uk(Bristol), Netherlands, etc. In that case, you'll have to debug it. Run traceback after the error. .readRDS(pfile) is called in several different places; you'll need to find out where it's happening, and why it's failing. The traceback() will tell you where; you can use debug() on that function to single step through until you get to this line, and see what pfile is set to. BTW, please keep the discussion in R-help; someone else may have better contributions than me. Duncan - Original Message From: Duncan Murdoch [EMAIL PROTECTED] To: Usman Shehu [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Sunday, 26 August, 2007 12:02:13 PM Subject: Re: [R] error message! On 26/08/2007 6:13 AM, Usman Shehu wrote: Dear R-users, Can some one help me out. I tried installing some packages in R_2.5.1 but I get an error message as shown below. This is unusual since I have been installing and updatings packages in the same version of R. chooseCRANmirror() update.packages(ask='graphics') Error in .readRDS(pfile) : unknown input format or utils:::menuInstallPkgs() Error in .readRDS(pfile) : unknown input format I'd guess it's a problem with the mirror. Which one did you choose? Do you get the same error if you choose a different one? Duncan Murdoch ___ Yahoo! Answers - Got a question? Someone out there knows the answer. Try it now. http://uk.answers.yahoo.com/ __ R-help@stat.math.ethz.ch 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 when using zero-inflated count regression model in package zicounts
Dr. Stevens, I've double-checked my variable lengths. All of my variables (Total.vines, Site, Species, and DBH) came in at 549. I did correct one problem in the data entry that had escaped my previous notice: somehow the undergrad who entered all the data managed to make the Acer negundo data split into two separate categories while still appearing to use the same ACNE abbreviation. When I made that correction and re-ran zicounts, R gave me the following error messages: vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim-: dims [product 12] do not match the length of object [549] In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: eta + offset 2: longer object length is not a multiple of shorter object length in: y/mu In addition, zicounts would not run a normal poisson regression on the data, giving me the same error messages as the ZIP regression. Doing a poisson regression with glm did not show any error messages. However, the glm model with full interactions was still over-dispersed. Could the zicounts problem be that the individual sites and species had different population sizes? For instance, Site A had 149 trees, site B had 55 trees, site C had 270 trees, and site D had 75 trees. The species had similar discrepancies in population sizes, with Platanus occidentalis and Acer negundo forming the majority of the trees. Thanks for your help. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 On Aug 15, 2007, at 5:58 AM, Martin Henry H. Stevens wrote: Hi Jim, With regard to same number, I simply wanted to make sure that each variable was the same length. The error message you show is what you would get if, for instance, you misspelled one of the variables and it doesn't exist, in which case it would be NULL, while your other variables would each be 550 elements in length. Hank On Aug 14, 2007, at 4:47 PM, James Milks wrote: Dr. Stevens, Unfortunately, Poisson gives me an over-dispersed model with only 3 out of 14 variables/interactions significant. Doing a step-wise poisson regression still ended up with the same over-dispersed model. Given the high number of zeros in the response variable, Dr. Thad Tarpey (one of our statisticians on campus) suggested zero-inflated poisson regression as a possible solution to the over-dispersion problem. As for variables of the same length, there are different numbers of trees for each species and site since we ran different numbers of transects at each site (some sites were larger than others) and there were different numbers of species and trees within each transect. Acer negundo made up ~33% of all the trees we measured; Platanus occidentalis had 25%; Fraxinus americana was another 12% and ~11% was Ulmus americana. The remaining 25% was divided among 16 other species, all of which were excluded from the analysis due to singularities in the model when they were included (something about glm not liking singularities in the model). So if the zicounts requires that each species and site have the same length, then I will not be able to use it unless I can get R to randomly select x trees from each species and site combination. Thanks for your input. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 On Aug 14, 2007, at 9:37 AM, Hank Stevens wrote: Hi Jim, Two thoughts come to me, unencumbered by the thought process or knowledge of zicounts: 1. Is Poisson really NOT appropriate? (do you have to use zicounts?) 2. Are you 110% certain that all variables are the same length? Would NA's interfere? Cheers, Hank On Aug 13, 2007, at 5:10 PM, James Milks wrote: I have data on number of vines per tree for ~550 trees. Over half of the trees did not have any vines and the data is fairly skewed (median = 0, mean = 1.158, 3rd qu. = 1.000). I am attempting to investigate whether plot location (four sites), species (I'm using only the four most common species), or tree dbh has a significant influence on the number of vines per tree. When I attempted to use the zicounts function, R gave me the following error message: vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distrname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim- : dims [product 12] do not match the length of object [549] In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: x[good, ] * w 2: longer object length is not a multiple of shorter object length in: eta + offset 3: longer object
Re: [R] Error message when using zero-inflated count regression model in package zicounts
On Thu, 16 Aug 2007, James R. Milks wrote: Dr. Stevens, I've double-checked my variable lengths. All of my variables (Total.vines, Site, Species, and DBH) came in at 549. I did correct one problem in the data entry that had escaped my previous notice: somehow the undergrad who entered all the data managed to make the Acer negundo data split into two separate categories while still appearing to use the same ACNE abbreviation. When I made that correction and re-ran zicounts, R gave me the following error messages: Hmm, I don't know about the error messages in zicounts, but you could try to use the zeroinfl() implementation in package pscl: vines.zip - zeroinfl(Total.vines ~ Site + Species + DBH | Site + Species + DBH, data = sycamores.1) and see whether this produces a similar error. Z vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim-: dims [product 12] do not match the length of object [549] In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: eta + offset 2: longer object length is not a multiple of shorter object length in: y/mu In addition, zicounts would not run a normal poisson regression on the data, giving me the same error messages as the ZIP regression. Doing a poisson regression with glm did not show any error messages. However, the glm model with full interactions was still over-dispersed. Could the zicounts problem be that the individual sites and species had different population sizes? For instance, Site A had 149 trees, site B had 55 trees, site C had 270 trees, and site D had 75 trees. The species had similar discrepancies in population sizes, with Platanus occidentalis and Acer negundo forming the majority of the trees. Thanks for your help. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 On Aug 15, 2007, at 5:58 AM, Martin Henry H. Stevens wrote: Hi Jim, With regard to same number, I simply wanted to make sure that each variable was the same length. The error message you show is what you would get if, for instance, you misspelled one of the variables and it doesn't exist, in which case it would be NULL, while your other variables would each be 550 elements in length. Hank On Aug 14, 2007, at 4:47 PM, James Milks wrote: Dr. Stevens, Unfortunately, Poisson gives me an over-dispersed model with only 3 out of 14 variables/interactions significant. Doing a step-wise poisson regression still ended up with the same over-dispersed model. Given the high number of zeros in the response variable, Dr. Thad Tarpey (one of our statisticians on campus) suggested zero-inflated poisson regression as a possible solution to the over-dispersion problem. As for variables of the same length, there are different numbers of trees for each species and site since we ran different numbers of transects at each site (some sites were larger than others) and there were different numbers of species and trees within each transect. Acer negundo made up ~33% of all the trees we measured; Platanus occidentalis had 25%; Fraxinus americana was another 12% and ~11% was Ulmus americana. The remaining 25% was divided among 16 other species, all of which were excluded from the analysis due to singularities in the model when they were included (something about glm not liking singularities in the model). So if the zicounts requires that each species and site have the same length, then I will not be able to use it unless I can get R to randomly select x trees from each species and site combination. Thanks for your input. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 On Aug 14, 2007, at 9:37 AM, Hank Stevens wrote: Hi Jim, Two thoughts come to me, unencumbered by the thought process or knowledge of zicounts: 1. Is Poisson really NOT appropriate? (do you have to use zicounts?) 2. Are you 110% certain that all variables are the same length? Would NA's interfere? Cheers, Hank On Aug 13, 2007, at 5:10 PM, James Milks wrote: I have data on number of vines per tree for ~550 trees. Over half of the trees did not have any vines and the data is fairly skewed (median = 0, mean = 1.158, 3rd qu. = 1.000). I am attempting to investigate whether plot location (four sites), species (I'm using only the four most common species), or tree dbh has a significant influence on the number of vines per tree. When I attempted to use the zicounts function, R gave me the following error message: vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distrname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim- : dims [product 12] do not
Re: [R] Error message when using zero-inflated count regression model in package zicounts
No, zeroinfl() in pscl did not give me any errors when I ran the model. So there may be a bug in zicounts. Only problem now is how to interpret the zeroinfl model. Am I correct in my understanding that zeroinfl runs both the poisson and binomial models without interactions? I'm thinking along those lines since no interaction terms appear in either model. If so, how do I check for any interactions? Thanks. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 On Aug 16, 2007, at 11:19 AM, Achim Zeileis wrote: On Thu, 16 Aug 2007, James R. Milks wrote: Dr. Stevens, I've double-checked my variable lengths. All of my variables (Total.vines, Site, Species, and DBH) came in at 549. I did correct one problem in the data entry that had escaped my previous notice: somehow the undergrad who entered all the data managed to make the Acer negundo data split into two separate categories while still appearing to use the same ACNE abbreviation. When I made that correction and re-ran zicounts, R gave me the following error messages: Hmm, I don't know about the error messages in zicounts, but you could try to use the zeroinfl() implementation in package pscl: vines.zip - zeroinfl(Total.vines ~ Site + Species + DBH | Site + Species + DBH, data = sycamores.1) and see whether this produces a similar error. Z vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim-: dims [product 12] do not match the length of object [549] In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: eta + offset 2: longer object length is not a multiple of shorter object length in: y/mu In addition, zicounts would not run a normal poisson regression on the data, giving me the same error messages as the ZIP regression. Doing a poisson regression with glm did not show any error messages. However, the glm model with full interactions was still over- dispersed. Could the zicounts problem be that the individual sites and species had different population sizes? For instance, Site A had 149 trees, site B had 55 trees, site C had 270 trees, and site D had 75 trees. The species had similar discrepancies in population sizes, with Platanus occidentalis and Acer negundo forming the majority of the trees. Thanks for your help. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 when using zero-inflated count regression model in package zicounts
Hi Jim, Two thoughts come to me, unencumbered by the thought process or knowledge of zicounts: 1. Is Poisson really NOT appropriate? (do you have to use zicounts?) 2. Are you 110% certain that all variables are the same length? Would NA's interfere? Cheers, Hank On Aug 13, 2007, at 5:10 PM, James Milks wrote: I have data on number of vines per tree for ~550 trees. Over half of the trees did not have any vines and the data is fairly skewed (median = 0, mean = 1.158, 3rd qu. = 1.000). I am attempting to investigate whether plot location (four sites), species (I'm using only the four most common species), or tree dbh has a significant influence on the number of vines per tree. When I attempted to use the zicounts function, R gave me the following error message: vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distrname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim- : dims [product 12] do not match the length of object [549] In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: x[good, ] * w 2: longer object length is not a multiple of shorter object length in: eta + offset 3: longer object length is not a multiple of shorter object length in: y/mu I do not know enough about the calculations done in the function to interpret the error messages. Is there a glitch in my data and if yes, what is it? Thanks for your help. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E Pluribus Unum __ R-help@stat.math.ethz.ch 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] Error message when using zero-inflated count regression model in package zicounts
I have data on number of vines per tree for ~550 trees. Over half of the trees did not have any vines and the data is fairly skewed (median = 0, mean = 1.158, 3rd qu. = 1.000). I am attempting to investigate whether plot location (four sites), species (I'm using only the four most common species), or tree dbh has a significant influence on the number of vines per tree. When I attempted to use the zicounts function, R gave me the following error message: vines.zip-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site +Species+DBH,distrname=ZIP,data=sycamores.1) Error in ifelse(y == 0, 1, y/mu) : dim- : dims [product 12] do not match the length of object [549] In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: x[good, ] * w 2: longer object length is not a multiple of shorter object length in: eta + offset 3: longer object length is not a multiple of shorter object length in: y/mu I do not know enough about the calculations done in the function to interpret the error messages. Is there a glitch in my data and if yes, what is it? Thanks for your help. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] error message: image not found
I have a R version 2.4 and I installed R version 2.5(current version) on Mac OS X 10.4.10. I tried dyn.load to load a object code compiled from C source. I got the following error message: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Users/jusong/Desktop/BPM/R/group.so': dlopen(/Users/jusong/Desktop/BPM/R/group.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.4/Resources/lib/ libR.dylib Referenced from: /Users/jusong/Desktop/BPM/R/group.so Reason: image not found How can I fix this problem? Best, Jungeun Song  __ R-help@stat.math.ethz.ch 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 lmer
I do not think anyone has answered this. I'm trying to run a simple one-way ANCOVA with the lmer function in R package lme4, but have encountered some conceptual problem. The data file MyData.txt is like this: Group Subj Cov Resp A1 3.90 4.05 A 2 4.05 4.25 A 3 4.25 3.60 A 4 3.60 4.20 A 5 4.20 4.05 A 6 4.05 3.85 B 7 3.85 4.15 B 8 4.15 4.60 B 9 4.60 4.15 B 10 4.15 4.40 B 11 4.40 3.35 B 12 3.35 3.80 B 13 3.80 3.90 Since I would like to treat subject (Subj) as a random factor, my one- way ANCOVA (with covariate, Cov) is: This is a conceptual problem, indeed. To be able to estimate a subject effect, you need to have repeated measurements (several lines) per observed subject ... Cheers, Lorenz __ R-help@stat.math.ethz.ch 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 lmer
Thanks a lot for the response and explanation, Lorenz! It seems that I can run the analysis with 'lm' without treating subject as a random factor lm(Resp ~ Group*Cov, TestData) Thanks, Gang On Aug 2, 2007, at 5:09 AM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I do not think anyone has answered this. I'm trying to run a simple one-way ANCOVA with the lmer function in R package lme4, but have encountered some conceptual problem. The data file MyData.txt is like this: Group Subj Cov Resp A1 3.90 4.05 A 2 4.05 4.25 A 3 4.25 3.60 A 4 3.60 4.20 A 5 4.20 4.05 A 6 4.05 3.85 B 7 3.85 4.15 B 8 4.15 4.60 B 9 4.60 4.15 B 10 4.15 4.40 B 11 4.40 3.35 B 12 3.35 3.80 B 13 3.80 3.90 Since I would like to treat subject (Subj) as a random factor, my one- way ANCOVA (with covariate, Cov) is: TestData=read.table(MyData.txt, header=T); m1 - lmer(Resp ~ Group * Cov + (1 | Subj), TestData) This is a conceptual problem, indeed. To be able to estimate a subject effect, you need to have repeated measurements (several lines) per observed subject ... Cheers, Lorenz __ R-help@stat.math.ethz.ch 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] Error message when running lm() with na.action=NULL
Hi there, I am trying to run a liner regression using lm with na.action = NULL, but I am getting an error message. Any ideas as to why this may be happening? Please see code and error message below: reg_test-lm(yy~.,data=test,na.action=NULL) Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in foreign function call (arg 4) This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, please telephone or email the sender and delete this message and any attachment from your system. If you are not the intended recipient you must not copy this message or attachment or disclose the contents to any other person. Nothing contained in the attached email shall be regarded as an offer to sell or as a solicitation of an offer to buy any services, funds or products or an expression of any opinion or views of the firm or its employees. Nothing contained in the attached email shall be deemed to be an advise of, or recommendation by, the firm or its employees. No representation is made as to accuracy, completeness, reliability or appropriateness of the information contained in the attached email. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 when running lm() with na.action=NULL
Sorry, I forgot to reply to all. See Patrick suggestion below. I also got another idea from Julian Faraway's book on R res - rep(NA,153) res[as.numeric(row.names(na.omit(airquality)))] - gl$res where gl was a regression and airquality the data. Thanks, Fabian -Original Message- From: Patrick Burns [mailto:[EMAIL PROTECTED] Sent: Tuesday, July 31, 2007 12:55 PM To: Garavito,Fabian Subject: Re: [R] Error message when running lm() with na.action=NULL Garavito,Fabian wrote: I was trying to get a vector of residuals where NA would be assigned to the lm residual vector (in this case reg_test$residuals) whenever NA was present in the sample. For instance, Obs fitted residual O1 f1 r1 O2 f2 r2 NA NA NA All I am getting is residual vectors for Non Missing observations (i.e. the dimension of the residual vector could be different from that of the response vector) Makes sense. I think you need to do it yourself. Perhaps something like (untested): test.nona - na.omit(test) mod - lm(y | ., data=test.nona) allresids - rep(NA, nrow(test)) allresids[-attr(test.nona, 'na.action')] - residuals(mod) Putting this into a function would probably be the way to go. Thank you very much for your help. I used to use R a few years ago, but I have not used it in a long while. Moreover, I had been using SAS in the last year and going back to R has been quite difficult. I was actually looking for a good book in R. Any ideas? 'good' is questionable and not exactly about R, but S Poetry is at least free. Venables and Ripley is a common citation. Peter Dalgaard's book is given good reviews. There is a book that is aimed more towards finance (which I'm assuming you are in) but I've forgotten what it is nor have I seen it. Searching Amazon should probably show you a lot of your choices, and I haven't heard of any books that generate aversion. Pat Fabian -Original Message- From: Patrick Burns [mailto:[EMAIL PROTECTED] Sent: Tuesday, July 31, 2007 11:39 AM To: Garavito,Fabian Subject: Re: [R] Error message when running lm() with na.action=NULL Doing na.action=NULL means that you need to get rid of missing values yourself from your data, which I'm guessing you haven't done. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Garavito,Fabian wrote: Hi there, I am trying to run a liner regression using lm with na.action = NULL, but I am getting an error message. Any ideas as to why this may be happening? Please see code and error message below: reg_test-lm(yy~.,data=test,na.action=NULL) Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in foreign function call (arg 4) This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, please telephone or email the sender and delete this message and any attachment from your system. If you are not the intended recipient you must not copy this message or attachment or disclose the contents to any other person. Nothing contained in the attached email shall be regarded as an offer to sell or as a solicitation of an offer to buy any services, funds or products or an expression of any opinion or views of the firm or its employees. Nothing contained in the attached email shall be deemed to be an advise of, or recommendation by, the firm or its employees. No representation is made as to accuracy, completeness, reliability or appropriateness of the information contained in the attached email. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, please telephone or email the sender and delete this message and any attachment from your system. If you are not the intended recipient you must not copy this message or attachment or disclose the contents to any other person. Nothing contained in the attached email shall be regarded as an offer to sell or as a solicitation of an offer to buy any services, funds or products or an expression of any opinion or views of the firm or its employees. Nothing contained in the attached email shall be deemed to be an advise of, or recommendation by, the firm or its employees. No representation is made as to accuracy, completeness, reliability or appropriateness of the information contained in the attached email
[R] Error message in lmer
I'm trying to run a simple one-way ANCOVA with the lmer function in R package lme4, but have encountered some conceptual problem. The data file MyData.txt is like this: Group Subj Cov Resp A 1 3.90 4.05 A2 4.05 4.25 A3 4.25 3.60 A4 3.60 4.20 A5 4.20 4.05 A6 4.05 3.85 B7 3.85 4.15 B8 4.15 4.60 B9 4.60 4.15 B10 4.15 4.40 B11 4.40 3.35 B12 3.35 3.80 B13 3.80 3.90 Since I would like to treat subject (Subj) as a random factor, my one- way ANCOVA (with covariate, Cov) is: TestData=read.table(MyData.txt, header=T); m1 - lmer(Resp ~ Group * Cov + (1 | Subj), TestData) but I got the following error message: Error in lmerFactorList(formula, mf, fltype) : number of levels in grouping factor(s) 'Subj' is too large Do I have some misconception about the model? Thank you very much. Gang __ R-help@stat.math.ethz.ch 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] error message survreg.fit
Dear All, I am doing a parametric survival analysis with: fit - survreg(Surv(xyz$start, xyz$stop, xyz$event, type=interval) ~ 1, dist='loglogistic') At this point I do not want to look into covariates, hence the '~1' as model formulation. As event types I have exact, interval, and right censored lifetime data. Everything works fine. For reasons that are not important here now, I wanted to look for the effects of 'randomly' re-allocating event types to the lifetime data. However, when I did this (keeping everything else the same), R returned this error message: Error in survreg.fit(X, Y, weights, offset, init = init, controlvals = control, : NA/NaN/Inf in foreign function call (arg 9) I am puzzled by this error message and can't find anything in the archives etc. Your input would be greatly appreciated. Best regards, Michael Michael Drescher Ontario Forest Research Institute Ontario Ministry of Natural Resources 1235 Queen St East Sault Ste Marie, ON, P6A 2E3 Tel: (705) 946-7406 Fax: (705) 946-2030 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] error message: only first element in each line of matrix used
I have a matrix and am trying to write a code to
1. identify all neg values along each line
2. for each neg value I need to identify min(j+3)
3. end with this code: eq[i,j]- ifelse(mat.r[i,j] (0.5*mat.s[i,j]),
mat.all[i,j], 0)
This is the code I have so far. I have tried several different methods but I
keep getting the same error message that the condition has length 1 and
only the first element will be used.
Any suggestions?
int - 3
for(i in 1:nrow(mat.all)) {
start.year - min(which(is.na(mat.all[i,])==F (mat.all[i,]0)))
fin.year - max(which(is.na(mat.all[i,])==F))
for(j in start.year:fin.year) {
if(mat.all[i,(j-int):(j-1)]0){
mat.s[i,j] - ifelse((mat.all[i,(j-int):(j-1)])==pmin, mat.all[i,j], 0);
mat.r [i,j] - which.max((mat.all[i,(j+1):(j+int)]) 0) }
}}
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Re: [R] error message: only first element in each line of matrix used
your problem is in the statement:
if(mat.all[i,(j-int):(j-1)]0){
you have multiple values in the comparison and the 'if' statement can only
use a single value. Do you want the statement to read:
if(all(mat.all[i,(j-int):(j-1)]0)){
which will test for 'all' the comparisons to be true?
On 6/6/07, Melanie Ann Harsch [EMAIL PROTECTED] wrote:
I have a matrix and am trying to write a code to
1. identify all neg values along each line
2. for each neg value I need to identify min(j+3)
3. end with this code: eq[i,j]- ifelse(mat.r[i,j] (0.5*mat.s[i,j]),
mat.all[i,j], 0)
This is the code I have so far. I have tried several different methods
but I
keep getting the same error message that the condition has length 1 and
only the first element will be used.
Any suggestions?
int - 3
for(i in 1:nrow(mat.all)) {
start.year - min(which(is.na(mat.all[i,])==F (mat.all[i,]0)))
fin.year - max(which(is.na(mat.all[i,])==F))
for(j in start.year:fin.year) {
if(mat.all[i,(j-int):(j-1)]0){
mat.s[i,j] - ifelse((mat.all[i,(j-int):(j-1)])==pmin, mat.all[i,j],
0);
mat.r [i,j] - which.max((mat.all[i,(j+1):(j+int)]) 0)
}
}}
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+1 513 646 9390
What is the problem you are trying to solve?
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[R] error message
Hi, I am trying to install the package exonmap and RMySQL however I keep getting the following error: Error in library(pkg, character.only = TRUE) : 'RMySQL' is not a valid package -- installed 2.0.0? I have R version 2.4.1 so I know its not a version issue. I deleted and reinstalled the folders again and the same thing happened. Has anyone any ideas? Thanks, Karen __ R-help@stat.math.ethz.ch 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
Hi Karen -- This sounds like a Bioconductor question, and should be sent to the Bioconductor list. http://www.bioconductor.org/docs/mailList.html Likely the complaint is about RMySQL being too old, rather than R. The idea of 'reinstalling folders' doesn't sound like a good strategy for updating packages; for Bioconductor see http://www.bioconductor.org/docs/install-howto.html likely source(http://www.bioconductor.org/biocLite.R;) biocLite(exonmap) does the trick. If not and the problem seems to be RMySQL, then try biocLite(RMySQL) or in a more robust way update all of your currently installed packages with library(Biobase) update.packages(repos=biocReposList()) Finally, please provide a more informative subject line and the output of sessionInfo() so that the community can get a better understanding of the platform and packages you're using, and hence the source of your problems. Best, Martin karen power [EMAIL PROTECTED] writes: Hi, I am trying to install the package exonmap and RMySQL however I keep getting the following error: Error in library(pkg, character.only = TRUE) : 'RMySQL' is not a valid package -- installed 2.0.0? I have R version 2.4.1 so I know its not a version issue. I deleted and reinstalled the folders again and the same thing happened. Has anyone any ideas? Thanks, Karen __ R-help@stat.math.ethz.ch 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. -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-help@stat.math.ethz.ch 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
install.packages(RMySQL, dep=T) should fix it for you. b ps: The error says RMySQL is the problem... it is not complaining about R itself (although it would not be a bad idea, given that the latest R is v 2.5.0, so it would be a better idea to start by upgrading your R) On May 22, 2007, at 11:59 AM, karen power wrote: Hi, I am trying to install the package exonmap and RMySQL however I keep getting the following error: Error in library(pkg, character.only = TRUE) : 'RMySQL' is not a valid package -- installed 2.0.0? I have R version 2.4.1 so I know its not a version issue. I deleted and reinstalled the folders again and the same thing happened. Has anyone any ideas? Thanks, Karen __ R-help@stat.math.ethz.ch 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] error message when using outer function
Dear R-users,
I have two sets of code that appear to me to be equivalent, shown below, and
yet I get the error message
Error in dim(robj) - c(dX, dY) : dim- : dims [product 4] do not match the
length of object [1]
after executing the assignment to logdens2. Both functions post.a1 and
post.a2 return the same values when run alone and not embedded in the
function outer. I would appreciate help in understanding the differences
between these two sets of code.
The code in post.a1 is from Gelman, Carlin, Stern, and Rubin's Bayesian Data
Analysis solutions, problem 3.5. I was trying to modify this code in
post.a2 when I ran into this error.
post.a1 - function(mu,sd,y){
ldens - 0
for (i in 1:length(y)) ldens - ldens + log(dnorm(y[i],mu,sd))
ldens}
y - c(10,10,12,11,9)
mugrid - c(10,11)
sdgrid - c(1,1.2)
logdens1 - outer (mugrid, sdgrid, post.a1, y)
#*** no error messages ***
post.a2 - function(mu,sd,y)
{
ldens - sum(log(dnorm(y,mu,sd)))
ldens
}
y - c(10,10,12,11,9)
mugrid - c(10,11)
sdgrid - c(1,1.2)
logdens2 - outer (mugrid, sdgrid, post.a2, y)
#***error message occurs here ***
Thank You!
Grant Reinman
e-mail:[EMAIL PROTECTED]
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Re: [R] error message when using outer function
Comments inside.
Reinman, Grant napsal(a):
Dear R-users,
I have two sets of code that appear to me to be equivalent, shown below, and
yet I get the error message
Error in dim(robj) - c(dX, dY) : dim- : dims [product 4] do not match the
length of object [1]
after executing the assignment to logdens2. Both functions post.a1 and
post.a2 return the same values when run alone and not embedded in the
function outer. I would appreciate help in understanding the differences
between these two sets of code.
The code in post.a1 is from Gelman, Carlin, Stern, and Rubin's Bayesian Data
Analysis solutions, problem 3.5. I was trying to modify this code in
post.a2 when I ran into this error.
post.a1 - function(mu,sd,y){
ldens - 0
for (i in 1:length(y)) ldens - ldens + log(dnorm(y[i],mu,sd))
ldens}
y - c(10,10,12,11,9)
mugrid - c(10,11)
sdgrid - c(1,1.2)
logdens1 - outer (mugrid, sdgrid, post.a1, y)
#*** no error messages ***
Actually pretty ugly coding (for a textbook) in my opinion... Try what
you get with
y - c(10,10,12,11,9)
mugrid - c(10,11)
sdgrid - c(1,1.2)
log(dnorm(y[1],mean=mugrid,sd=sdgrid))
[1] -0.9189385 -1.4484823
This is in a perfect accordance with help(dnorm), which says you are
allowed to specify a vector of means and SDs. Here 2 values were
specified, so you obtain 2 density values.
Now, adding a vector of length 2 to a constant:
#not run here# ldens - ldens + log(dnorm(y[i],mu,sd))
is again a vector of length 2.
However, using sum() in your code below gives you just a single number
and R starts complaining because the dimensions don't match.
Petr
post.a2 - function(mu,sd,y)
{
ldens - sum(log(dnorm(y,mu,sd)))
ldens
}
y - c(10,10,12,11,9)
mugrid - c(10,11)
sdgrid - c(1,1.2)
logdens2 - outer (mugrid, sdgrid, post.a2, y)
#***error message occurs here ***
Thank You!
Grant Reinman
e-mail:[EMAIL PROTECTED]
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--
Petr Klasterecky
Dept. of Probability and Statistics
Charles University in Prague
Czech Republic
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[R] Error message when building a package
I'm trying to build a package. The machine is PowerPC G4 with Mac OS 10.4.8, and I'm using R2.4.1. I get R CMD build roots working, and it created roots.tar.gz. But I get the following message when I run R CMD INSTALL -l ../myrlibrary roots.tar.gz == * Installing *source* package 'roots' ... ** libs ** arch - ppc gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include-fPIC -g -O2 -c fifrt.c -o fifrt.o gfortran-4.0 -arch ppc -fPIC -g -O2 -c fthrt.f -o fthrt.o gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o roots.so fifrt.o fthrt.o -lgfortran -lgcc_s -lSystemStubs -lmx -lSystem -L/Library/Frameworks/R.framework/Resources/lib/ppc -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dy lib /usr/bin/libtool: unknown option character `m' in: -macosx_version_min Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile[,dirname]] [-arch_only arch] [-sacLT] Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile[,dirname]] [-arch_only arch] [-o output] [-install_name name] [-compatibility_version #] [-current_version #] [-seg1addr 0x#] [-segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table filename] [-seg_addr_table_filename file_system_path] [-all_load] [-noall_load] make: *** [roots.so] Error 1 chmod: /../myrlibrary/roots/libs/ppc/*: No such file or directory ERROR: compilation failed for package 'roots' ** Removing '/../myrlibrary/roots' One thing I can see from above is the message /usr/bin/libtool: unknown option character `m' in: -macosx_version_min, which I got when compiling other c programs to be called by R. How can I fix it or get around it? I appreciate your time and help very much. Lillian Yau __ R-help@stat.math.ethz.ch 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 when building a package
Please update your Xcode tools. According to http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html 2.2 or later is needed, and 2.4.1 is current. On Tue, 30 Jan 2007, C. Lillian Yau wrote: I'm trying to build a package. The machine is PowerPC G4 with Mac OS 10.4.8, and I'm using R2.4.1. I get R CMD build roots working, and it created roots.tar.gz. But I get the following message when I run R CMD INSTALL -l ../myrlibrary roots.tar.gz == * Installing *source* package 'roots' ... ** libs ** arch - ppc gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include-fPIC -g -O2 -c fifrt.c -o fifrt.o gfortran-4.0 -arch ppc -fPIC -g -O2 -c fthrt.f -o fthrt.o gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o roots.so fifrt.o fthrt.o -lgfortran -lgcc_s -lSystemStubs -lmx -lSystem -L/Library/Frameworks/R.framework/Resources/lib/ppc -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dy lib /usr/bin/libtool: unknown option character `m' in: -macosx_version_min [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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 using normality test in vars
I'm running a vector-time series model with the vars package. When I
test the univariate and multivariate normality of the residuals using
normality(), I get the results, but also this warning
Warning messages:
1: longer object length
is not a multiple of shorter object length in: b2 - rep(3, 4)
2: longer object length
is not a multiple of shorter object length in: b2 - rep(3, 4)
What does this mean and do I need to worry about it.
Dear David,
thanks for pointing this out. The warning is caused in the calculation
of the kurtosis in function .jb.multi which is contained in
R/internal.R. The relevant expression should be 'rep(3, K)'. An updated
version of package 'vars' will be submitted in due course. I will ship
you version of the corrected package off list.
Best,
Bernhard
*
Confidentiality Note: The information contained in this mess...{{dropped}}
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[R] Error message using normality test in vars
Hi all, I'm running a vector-time series model with the vars package. When I test the univariate and multivariate normality of the residuals using normality(), I get the results, but also this warning Warning messages: 1: longer object length is not a multiple of shorter object length in: b2 - rep(3, 4) 2: longer object length is not a multiple of shorter object length in: b2 - rep(3, 4) What does this mean and do I need to worry about it. Thanks in advance, David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] Web: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 Fax: 608-262-0843 __ R-help@stat.math.ethz.ch 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] Error Message saying .Call(R_lazyLoadDBfetch, etc.
Hi, I got the following error message when running a function of mine doing intensive computations: Erreur dans .Call(R_lazyLoadDBfetch, key, file, compressed, hook, PACKAGE = base) : référence d'argument par défaut récursive I haven't found neither where the problem lies nor what could be recursive. Besides, I wonder whether it might or not be a problem of memory size. Could you please give me any suggestion on how to interpret this message? Thanks in advance, jacques --- Jacques VESLOT CNRS UMR 8090 I.B.L (2ème étage) 1 rue du Professeur Calmette B.P. 245 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 http://www-good.ibl.fr __ R-help@stat.math.ethz.ch 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 saying .Call(R_lazyLoadDBfetch, etc.
Jacques VESLOT [EMAIL PROTECTED] writes: Hi, I got the following error message when running a function of mine doing intensive computations: Erreur dans .Call(R_lazyLoadDBfetch, key, file, compressed, hook, PACKAGE = base) : référence d'argument par défaut récursive I haven't found neither where the problem lies nor what could be recursive. Besides, I wonder whether it might or not be a problem of memory size. Could you please give me any suggestion on how to interpret this message? The prototypical situation is this f-function(a=a)a f(2) [1] 2 f() Error in f() : recursive default argument reference The default for argument a ends up needing the value of a. This can also happens more indirectly when multiple arguments refer to eachother. BTW: Is that error message proper French? Should it not be référence récursive d'argument par défaut or so. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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 for row names
On Wed, 8 Nov 2006, Taka Matzmoto wrote: Hi R users - I got an error message when reading in a saved file (a list structure) dget(REPLICATION001) Error in attributes(.Data) - c(attributes(.Data), attrib) : row names must be 'character' or 'integer', not 'double' I don't need row names and didn't even specify row names when I saved the file. What do I need to do for reading in the file successfully? You haven't told us how you wrote the file, but my guess is that you used dput(). If so, consult the help page and note it says Deparsing an object is difficult, and not always possible. With the default 'control = c(showAttributes)', 'dput()' attempts to deparse in a way that is readable, but for more complex or unusual objects, not likely to be parsed as identical to the original. Use 'control = all' for the most complete deparsing; use 'control = NULL' for the simplest deparsing, not even including attributes. so your problem is described right there on the help page. And please don't sent multiple messages on the same topic: your second message is about an inaccurate dput of the file, and not about an actual object in R. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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 Documentation
cjkogan111 wrote:
Hello,
I am new to R, and trying to work with it. I have a couple of quick
questions. First, I made a program and got the following error message.
--
Error in if (DatMdFile$Time.Value[NmRecord] VBinTimesMinTop[NmCounter]) {
:
missing value where TRUE/FALSE needed
In addition: Warning message:
not meaningful for factors in: Ops.factor(DatMdFile$Time.Value[NmRecord],
VBinTimesMinTop[NmCounter])
-
I noticed that one of the values had decimal places, while the other didn't,
so the comparison would be 11.00 10
I don't know if that might have anything to do with my problem.
Well, not really the decimal places, but the data type.
Anyway, I don't have much idea what the error means, and I don't know how to
check what data type the different vectors are.
So time to start looking at the documentation?
class() is your friend, you might also want to try str().
I was wondering if anyone could help me out, and also, I was wondering if
there is any error documentation (stuff that tells what the error means.)
Probably one of your objects is a factor rather than a numeric value.
Thanks!
- cjkogan111
ujligges1234
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[R] Error Message Documentation
Hello,
I am new to R, and trying to work with it. I have a couple of quick
questions. First, I made a program and got the following error message.
--
Error in if (DatMdFile$Time.Value[NmRecord] VBinTimesMinTop[NmCounter]) {
:
missing value where TRUE/FALSE needed
In addition: Warning message:
not meaningful for factors in: Ops.factor(DatMdFile$Time.Value[NmRecord],
VBinTimesMinTop[NmCounter])
-
I noticed that one of the values had decimal places, while the other didn't,
so the comparison would be 11.00 10
I don't know if that might have anything to do with my problem.
Anyway, I don't have much idea what the error means, and I don't know how to
check what data type the different vectors are.
I was wondering if anyone could help me out, and also, I was wondering if
there is any error documentation (stuff that tells what the error means.)
Thanks!
- cjkogan111
--
View this message in context:
http://www.nabble.com/Error-Message-Documentation-tf2283899.html#a6344607
Sent from the R help forum at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] error message from lm.ridge() in MASS ***package***
jz7 == jz7 [EMAIL PROTECTED] on Tue, 22 Aug 2006 17:10:42 -0400 (EDT) writes: jz7 Dear all, jz7 I got a wierd problem when using lm.ridge() in MASS library. there is MASS the book and MASS the package, and there is even a MASS library (namely the file MASS.so or MASS.dll depending on your platform) but you are really talking about the MASS *package* ! jz7 When my X matrix has few columns, there is no jz7 problem. But when my X matrix gets larger (over 1000 jz7 columns), I got the following error: and where is the selfcontained reproducible code which we ask you for, explicitly in the posting guide and at the footer of every R-help message ??? jz7 Error in Xs$v %*% a : non-conformable arguments jz7 In addition: Warning messages: jz7 1: longer object length jz7 is not a multiple of shorter object length in: d^2 + rep(lambda, jz7 rep(p, k)) jz7 2: longer object length jz7 is not a multiple of shorter object length in: drop(d * rhs)/div jz7 The R code I use for the calculation is lm.ridge( y ~ x,lambda=seq(1,15,1)). jz7 Please advice. jz7 Thanks a lot! jz7 Jeny __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error message from lm.ridge() in MASS library
Dear all, I got a wierd problem when using lm.ridge() in MASS library. When my X matrix has few columns, there is no problem. But when my X matrix gets larger (over 1000 columns), I got the following error: Error in Xs$v %*% a : non-conformable arguments In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: d^2 + rep(lambda, rep(p, k)) 2: longer object length is not a multiple of shorter object length in: drop(d * rhs)/div The R code I use for the calculation is lm.ridge( y ~ x,lambda=seq(1,15,1)). Please advice. Thanks a lot! Jeny __ R-help@stat.math.ethz.ch 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 when using optim
(Subject changed to something less perjorative. This is not `optim error'.) On Wed, 9 Aug 2006, Frank Black wrote: Dear all, There have been one or two questions posted to the list regarding the optim error non-finite finite-difference value [4]. The error apparently means that the 4th element of the gradient is non-finite. (Without an example of the optim usage, we have little to go on. This does not occur in the default method, so we don't even know which method was asked for. Please do study the posting guide: we ask to information for good reasons.) It means that the finite-difference approximation to the gradient is non-finite (as it says). Most likely this occurs when the user-supplied function is returning Inf (so the finite difference is Inf - Inf) or returning NA/NaN. My question is what part(s) of my program should I fiddle with in an attempt to fix it? Starting values? Something in the log-likelihood itself? Perhaps the data (which is generated)? Any thoughts would be greatly appreciated. If the function you are optimizing never returns Inf or NA/NaN, the message will not occur. Nor will it occur if you supply a gradient function. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] error message
Hello, we work in nlme, with R version 2.2.1. We ran the follwing sentence, a growth function, formula(my data.gd) L.gd ~ Largo | ID Rich- function(Largo, Linf, K, t0, m) Linf *(1-exp(-K(edad-t0)))^(1/(1-m)) Rich.nlme - nlme(Largo ~ Rich(edad, Linf, K, t0, m), + data = L.gd, + fixed = Linf + K +t0 +m~ 1, + start = list(fixed = c(800, 0.3,-0.5,0.3))) And the program gave us this error message, Error: Singularity in backsolve at level 0, block 1 In addition: Warning messages: 1: NaNs produced in: log(x) 2: NaNs produced in: log(x) Does anyone know what this means? We would apreciate if you could point us to a reference Lic. Gabriela Escati Peñaloza Biología y Manejo de Recursos Acuáticos Centro Nacional Patagónico(CENPAT). CONICET Bvd. Brown s/nº. (U9120ACV)Pto. Madryn Chubut Argentina Tel: 54-2965/451301/451024/451375/45401 (Int:277) Fax: 54-29657451543 _ Horóscopos, Salud y belleza, Chistes, Consejos de amor: el contenido más divertido para tu celular está en Yahoo! Móvil. Obtenelo en http://movil.yahoo.com.ar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message with nmds
On Tue, 2006-05-16 at 13:25 -0700, Jonathan Hughes wrote: I am trying to apply nmds to a data matrix but I receive the following error message: Error in isoMDS(dis, y = y, k = k, maxit = maxit) : zero or negative distance between objects 5 and 7 The data are in a vegetation cover-class matrix (species in columns, plots in rows, classes 1-8 with lots of zero values) converted to a dissimilarity matrix (bray curtis). I assumed that objects 5 and 7 refer to rows of my original data; and they do have the same species with the same cover classes. I deleted one of these rows but I received the same error message with a rerun of nmds. As it turns out, the new rows 5 and 7 are the same. How do I avoid this problem? Jonathan, this is a FAQ in the proper sense of the word: this is frequently asked. Last thread was on April, 2006. See https://stat.ethz.ch/pipermail/r-help/2006-April/092598.html and answers. You may also use RSiteSearch with keyword isoMDS to find other (and older) threads. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message with nmds
I am trying to apply nmds to a data matrix but I receive the following error message: Error in isoMDS(dis, y = y, k = k, maxit = maxit) : zero or negative distance between objects 5 and 7 The data are in a vegetation cover-class matrix (species in columns, plots in rows, classes 1-8 with lots of zero values) converted to a dissimilarity matrix (bray curtis). I assumed that objects 5 and 7 refer to rows of my original data; and they do have the same species with the same cover classes. I deleted one of these rows but I received the same error message with a rerun of nmds. As it turns out, the new rows 5 and 7 are the same. How do I avoid this problem? Any advice for this neophyte would be greatly appreciated. Thanks! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message explanation for lmer
I don't know how to get that particular error message from lmer, but I can guess that it might occur when you are trying to estimate more parameters than the data will support. To overcome this, I would try the following: First, have you tried experimenting with different models and / or data sets to create very simple example examples, one that gives the error you don't understand and another slighly different that seems to work fine? That may be the easiest and most sensible thing to do. If you get that far and still can't figure it out, I suggest you send that simple, self-contained, reproducible example to this list. This is something suggested in the posting guide! (www.R-project.org/posting-guide.html). It can help you find the problem and failing that can make it easier for someone else to understand your problem. Without that, I'm just guessing, and I know that some frequent contributors to this list are less likely to respond to a question without something like that. Beyond this, I could make other suggestions. For example, have you tried method = PQL and AGQ? If both of these work, then I would think there might be something strange with Laplace at least for this example. Also, I don't know what family you are using, but if it's normal, have you tried running the same model using lme in library(nlme)? (At one time, I think you may have had to quit R and restart in changing from lme4 to nlme or vice versa, I don't remember now, but I always do that to avoid potential conflicts between the two packages.) If it's NOT normal, I might still try the same model in lme ignoring the nonnormality. If you get similar convergence problems or if intervals dies on you or give extremely wide confidence intervals, that suggests you may be trying to estimate too many effects. Is it convenient to make tables to find out how many combinations of factors you have? If you slice things too thinly, the model can't be estimated; you can get convergence problems from that. If it were me, I might try to make a local copy of the code and walk through it line by line using debug until I figured out the problem. However, this might not be feasible if you're not familiar enough with the algorithm to almost write your own code. hope this helps, spencer graves Bill Shipley wrote: I am getting the following error message using the lmer function for mixed models with method=Laplace: nlminb returned message false convergence (8) in: LMEopt(x=mer,value=cv) Could anyone explain what this means, and how I might overcome (or track down) the problem? Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message explanation for lmer
I got strange error messages when I had other packages opened the same time as lme4 (e.g. as nlme). Try to not have other libraries loaded. /A __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message explanation for lmer
I am getting the following error message using the lmer function for mixed models with method=Laplace: nlminb returned message false convergence (8) in: LMEopt(x=mer,value=cv) Could anyone explain what this means, and how I might overcome (or track down) the problem? Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message
Yes, the author of the message does :) Your fit is exactly collinear. From ?predict.lm If the fit is rank-deficient, some of the columns of the design matrix will have been dropped. Prediction from such a fit only makes sense if 'newdata' is contained in the same subspace as the original data. That cannot be checked accurately, so a warning is issued. (in fact predict.lm is being called here.) On Tue, 28 Mar 2006, stephenc wrote: Hi Does anyone know what this means: glm.model = glm(formula = as.factor(nextDay) ~ ., family=binomial, data=spi[1:1000,]) pred - predict(glm.model, spi[1001:1250,-9], type=response) Warning message: prediction from a rank-deficient fit may be misleading in: predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type == 9 is my determinant and I still get this message even when I remove the 9. Stephen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message
Hi Does anyone know what this means: glm.model = glm(formula = as.factor(nextDay) ~ ., family=binomial, data=spi[1:1000,]) pred - predict(glm.model, spi[1001:1250,-9], type=response) Warning message: prediction from a rank-deficient fit may be misleading in: predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type == 9 is my determinant and I still get this message even when I remove the 9. Stephen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message with stats package fx cor R aqua v1.14
Hello, Sorry if this is somewhere in the archives but i couldn't find it. I am using the funtion cor() and inputting a large matrix with a column of 0, for which i get NA's for. I'm looking for a way to overcome that divide by 0 error btw but my real issue is this: I specify the method as pearson but the error messages always say kendall ex) read.csv(ncatest.csv, header = FALSE, sep = ,, dec=.)-ncatest ncatest- ncatest[,-1] rownames(ncatest2)- ncatest[,1] ncatest2-as.matrix(ncatest2) dim(ncatest2) [1] 1048211 cornca-cor(ncatest2, method=pearson) Warning message: the standard deviation is zero in: cor(x, y, na.method, method == kendall) I would like to confirm that i am using the metric I specified and that its not defaulting to kendall for some weird reason. Thanks for any assistance. Sincerely, betty -- [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message from Variogram.lme Example
On Tue, 14 Mar 2006, Prof Brian Ripley wrote: So this is most likely a bug in package nlme. However, we need a reproducible example to be able to do anything about it, and without even the traceback() we cannot be sure that it is in nlme. Please follow the bug-reporting procedure. It does seem to be a bug in Variogram.lme (assuming this is the BodyWeight dataset from package nlme). The lines val - na.omit(val) val$n.pairs - as.vector(table(na.omit(cutDist))) need to be interchanged since one bin has a zero count and gets omitted. On Mon, 13 Mar 2006, Rick Bilonick wrote: When I try to run the example from Variogram with an lme object, I get an error (although summary works): R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) ISBN 3-900051-07-0 ... fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Error: couldn't find function lme Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error: couldn't find function Variogram library(nlme) fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error in $-.data.frame(`*tmp*`, n.pairs, value = c(160, 0, 160, 16, : replacement has 10 rows, data has 9 [...] Information on package 'nlme' Description: Package: nlme Version: 3.1-68.1 Date: 2006-01-05 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error Message from Variogram.lme Example
When I try to run the example from Variogram with an lme object, I get an error (although summary works): R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) ISBN 3-900051-07-0 ... fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Error: couldn't find function lme Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error: couldn't find function Variogram library(nlme) fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error in $-.data.frame(`*tmp*`, n.pairs, value = c(160, 0, 160, 16, : replacement has 10 rows, data has 9 summary(fm1) Linear mixed-effects model fit by REML Data: BodyWeight AIC BIClogLik 1171.720 1203.078 -575.8599 Random effects: Formula: ~Time | Rat Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 36.9390723 (Intr) Time 0.2484113 -0.149 Residual 4.4436052 Fixed effects: weight ~ Time * Diet Value Std.Error DF t-value p-value (Intercept) 251.65165 13.094025 157 19.218816 0. Time 0.35964 0.091140 157 3.946019 0.0001 Diet2 200.66549 22.679516 13 8.847873 0. Diet3 252.07168 22.679516 13 11.114509 0. Time:Diet20.60584 0.157859 157 3.837858 0.0002 Time:Diet30.29834 0.157859 157 1.889903 0.0606 Correlation: (Intr) Time Diet2 Diet3 Tm:Dt2 Time -0.160 Diet2 -0.577 0.092 Diet3 -0.577 0.092 0.333 Time:Diet2 0.092 -0.577 -0.160 -0.053 Time:Diet3 0.092 -0.577 -0.053 -0.160 0.333 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -3.25558796 -0.42196874 0.08229384 0.59933559 2.78994477 Number of Observations: 176 Number of Groups: 16 Information on package 'nlme' Description: Package: nlme Version: 3.1-68.1 Date: 2006-01-05 Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message from Variogram.lme Example
So this is most likely a bug in package nlme. However, we need a reproducible example to be able to do anything about it, and without even the traceback() we cannot be sure that it is in nlme. Please follow the bug-reporting procedure. On Mon, 13 Mar 2006, Rick Bilonick wrote: When I try to run the example from Variogram with an lme object, I get an error (although summary works): R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) ISBN 3-900051-07-0 ... fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Error: couldn't find function lme Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error: couldn't find function Variogram library(nlme) fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error in $-.data.frame(`*tmp*`, n.pairs, value = c(160, 0, 160, 16, : replacement has 10 rows, data has 9 [...] Information on package 'nlme' Description: Package: nlme Version: 3.1-68.1 Date: 2006-01-05 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message from Variogram.lme Example
Rick Bilonick rab45+ at pitt.edu writes: When I try to run the example from Variogram with an lme object, I get an error (although summary works): library(nlme) fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) Error in $-.data.frame(`*tmp*`, n.pairs, value = c(160, 0, 160, 16, : replacement has 10 rows, data has 9 The example is does not run, but if you leave out nint=10 (giving default nint=20), or use any number nint =12, it works. The example has a don't run in the docs, but it could easily be cleaned up. If it should serve as documentation of the error message, it's a bit confusing. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message in cph
[EMAIL PROTECTED] wrote: Hi, List, I am using function 'cph' in package 'Design'. I have run into this error message but could not find documentation after looking for a long time. Could someone help me out? What kind of problem it is in my data set and how to fix it? Thanks a lot! Auston Error in fitter(X, Y, strata = Strata, offset = offset, weights = weights, :NA/NaN/Inf in foreign function call (arg 6) Please try again with recent versions of R and Design. Please specify a *reproducible* example, otherwise we cannot help that much. If this is a bug in a package, please report to the package maintainer. Uwe Ligges platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor2.0 year 2005 month10 day 06 svn rev 35749 language R Auston Wei Statistical Analyst Department of Biostatistics and Applied Mathematics The University of Texas MD Anderson Cancer Center Tel: 713-563-4281 Email: [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message in cph
Hi, List, I am using function 'cph' in package 'Design'. I have run into this error message but could not find documentation after looking for a long time. Could someone help me out? What kind of problem it is in my data set and how to fix it? Thanks a lot! Auston Error in fitter(X, Y, strata = Strata, offset = offset, weights = weights, :NA/NaN/Inf in foreign function call (arg 6) platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor2.0 year 2005 month10 day 06 svn rev 35749 language R Auston Wei Statistical Analyst Department of Biostatistics and Applied Mathematics The University of Texas MD Anderson Cancer Center Tel: 713-563-4281 Email: [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message in cox regression cph()
Hi,
I have been trying to get the cph() function of the Design package to work but
get an error message I don't understand:
Error in if (!length(fname) || !any(fname == zname)) { :
missing value where TRUE/FALSE needed
I have tried the same for a dummy dataset I made, and than it seems to work
fine. However, it doesn't do it for my own data. Does anyone have a clue as to
what this message means, whether I have made a mistake somewhere(although it
seems ok to me?) and especially how to solve this problem. I know I could have
used coxph() instead, but I'd like to predict the outcome on another dataset
and coxph() does not allow for interaction terms...
I hope anyone can help me here. Underneath is the code I used for my data, if
it's of any use...
Thanks, cheers Roel
Roel May
NINA, Norway
modeldata - as.data.frame(modeldata)
survchoice-Surv(2-modeldata$USED,is.element(modeldata$USED,1))
d -
datadist(modeldata$ID,modeldata$ASP_NW,modeldata$ALT,modeldata$SLOPE,modeldata$PLACEMENT,modeldata$DTL,modeldata$TRACK,modeldata$PRIVATE,modeldata$BUSH,modeldata$ROCK,modeldata$GRASS,modeldata$WATER,modeldata$RUGGED,modeldata$CABIN,data=modeldata)
options(datadist=d)
options(contrasts=c(contr.treatment,contr.treatment))
interactmodel -
cph(survchoice~(ASP_NW+RUGGED+SLOPE+GRASS:PLACEMENT+PRIVATE+BUSH:ROCK+RUGGED:ROCK+DTL)+strat(ID),data=modeldata,method=breslow,y=TRUE,x=TRUE,surv=TRUE)
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Re: [R] error message in cox regression cph()
May, Roel wrote:
Hi,
I have been trying to get the cph() function of the Design package to work
but get an error message I don't understand:
Error in if (!length(fname) || !any(fname == zname)) { :
missing value where TRUE/FALSE needed
I have tried the same for a dummy dataset I made, and than it seems to work
fine. However, it doesn't do it for my own data. Does anyone have a clue as
to what this message means, whether I have made a mistake somewhere(although
it seems ok to me?) and especially how to solve this problem. I know I could
have used coxph() instead, but I'd like to predict the outcome on another
dataset and coxph() does not allow for interaction terms...
I hope anyone can help me here. Underneath is the code I used for my data, if
it's of any use...
Thanks, cheers Roel
Roel May
NINA, Norway
modeldata - as.data.frame(modeldata)
survchoice-Surv(2-modeldata$USED,is.element(modeldata$USED,1))
d -
datadist(modeldata$ID,modeldata$ASP_NW,modeldata$ALT,modeldata$SLOPE,modeldata$PLACEMENT,modeldata$DTL,modeldata$TRACK,modeldata$PRIVATE,modeldata$BUSH,modeldata$ROCK,modeldata$GRASS,modeldata$WATER,modeldata$RUGGED,modeldata$CABIN,data=modeldata)
Don't use $ in input arguments to datadist. Use the whole data frame or
use with( ).
options(datadist=d)
options(contrasts=c(contr.treatment,contr.treatment))
Remove. This is the default.
interactmodel -
cph(survchoice~(ASP_NW+RUGGED+SLOPE+GRASS:PLACEMENT+PRIVATE+BUSH:ROCK+RUGGED:ROCK+DTL)+strat(ID),data=modeldata,method=breslow,y=TRUE,x=TRUE,surv=TRUE)
Use * for interactions and to make sure your model follows the hierarchy
principle.
Next time please also give the version of Design you are using.
Frank
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--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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[R] error message from building R in Mac
Following the instruction in R website and downloading gcc and g77, I am trying to configure and build R in my Mac laptop, but got some error message that I do not know how to resolve. Do any of you know how to solve this problem? After type ./configure, I got the following message. R is now configured for powerpc-apple-darwin8.3.0 Source directory: . Installation directory:/Library/Frameworks C compiler:gcc -g -O2 C++ compiler: g++ -g -O2 Fortran compiler: gfortran -g -O2 Interfaces supported: X11, aqua, tcltk External libraries:readline, BLAS(generic), LAPACK(in blas) Additional capabilities: iconv, MBCS, NLS Options enabled: framework, R profiling Recommended packages: yes But after typing make, I got the following error message. make[1]: Nothing to be done for `R'. make[1]: Nothing to be done for `R'. make[2]: Nothing to be done for `R'. creating src/scripts/R.fe config.status: creating src/include/config.h config.status: src/include/config.h is unchanged Rmath.h is unchanged make[3]: Nothing to be done for `R'. make[4]: `libbz2.a' is up to date. make[4]: `libpcre.a' is up to date. make[4]: `libz.a' is up to date. make[3]: Nothing to be done for `R'. make[3]: `stamp-lo' is up to date. make[3]: `stamp-lo' is up to date. make[3]: `stamp-lo' is up to date. /Users/fang-yichiou/tmp/R-2.2.0/lib/libR.dylib is unchanged /Users/fang-yichiou/tmp/R-2.2.0/bin/exec/R is unchanged make[4]: `R_X11.so' is up to date. make[4]: `internet.so' is up to date. make[4]: `lapack.so' is up to date. make[4]: `vfonts.so' is up to date. building system startup profile building package 'base' all.R is unchanged building package 'tools' all.R is unchanged make[5]: `Makedeps' is up to date. ../../../../library/tools/libs/tools.so is unchanged building package 'utils' all.R is unchanged building package 'grDevices' all.R is unchanged ../../../library/grDevices/R/grDevices is unchanged make[5]: `Makedeps' is up to date. ../../../../library/grDevices/libs/grDevices.so is unchanged Error in solve.default(rgb) : lapack routines cannot be loaded In addition: Warning message: unable to load shared library '/Users/fang-yichiou/tmp/R-2.2.0/ modules/lapack.so': dlopen(/Users/fang-yichiou/tmp/R-2.2.0/modules/lapack.so, 6): Symbol not found: _rcblas_zdotc_sub__ Referenced from: /Users/fang-yichiou/tmp/R-2.2.0/modules/lapack.so Expected in: flat namespace Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[2]: *** [R] Error 1 make[1]: *** [R] Error 1 make: *** [R] Error 1 Thanks for your advice in advance. Fang-Yi __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message in polr
Dear members of the list, I'm fitting ordinal regressions using polr, and in some models I get the error copied below. Dependent variable is an ordered factor of bird abundance categories, and predictors are continuous habitat variables. ro6 - polr(formula = abun ~ InOmbrot + Oliva.OC + ToCultAr + DivCulArb + AltitMax + COORXY) summary(ro6) Re-fitting to get Hessian Error in La.svd(x, nu, nv, method) : error code 8 from Lapack routine dgesdd In addition: Warning messages: 1: NaNs produced in: dlogis(x, location, scale, log) 2: NaNs produced in: dlogis(x, location, scale, log) But if I call for the ro6 object I get the coefficients but without standard errors: ro6 Call: polr(formula = abun ~ InOmbrot + Oliva.OC + ToCultAr + DivCulArb + AltitMax + COORXY) Coefficients: InOmbrot Oliva.OC ToCultAr DivCulArb AltitMax -2.721242e-01 2.590153e-02 2.098157e-02 7.908437e-01 2.088895e- 03 COORXY 5.937940e-06 Intercepts: 0|1 1|2 2|3 18.16425 18.97070 20.94103 Residual Deviance: 817.667 AIC: 835.667 It seems that the error is related to the number of predictors involved since if I use a lower number, say five predictors, polr does not produce this error message in summary. I have been looking at previous messages concerning errors in polr but I haven't found the solution. I would ackowledge very much any help. Germán López __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message: The following object(s) are masked
Ettinger, Nicholas wrote:
Hello!
First time posting here:
Here is my code:
x - c(1:22)
finaloutput=cidrm=NULL
finaldiversityoutput=diversitym=NULL
diversityinfo=read.table(Diversity_info.txt, header=T, sep=\t,
row.names=NULL)
attach(diversityinfo)
diversitynr=nrow(diversityinfo)
diversitytemp - matrix(0,nrow=diversitynr,ncol=1)
for(j in 1:length(x))
{
diversitym=read.table(paste(paste(Div-Chr,x[j],
sep=),_corr.txt,sep=), header=T, sep=\t, row.names=NULL)
attach(diversitym)
diversitytemp - cbind(diversitytemp,diversitym)
print(paste(paste(Diversity-Chrom,x[j], sep=),.txt,sep=))
print(dim(diversitytemp))
}
I am essentially trying to combine several tab-delimited text data files
together into one big file.
I recently upgraded to R 2.2.0. I now get multiple error messages of
the form:
The following object(s) are masked from diversitym ( position 4 ) :
X X.1 X.2
These are *Warning* messges, not errors.
You are using attach but never detach in your loop. Each attach masks
the objects you have attached formerly, because there are the same names
in it, obviously.
Your code works as before, but you should not use attach without
detaching. I'd suggest not to use attach() at all unless you know what
you are doing and it really improved convenience in interactive analyses.
Uwe Ligges
I searched on masked and read the manual about conflicts but I don't
really understand what the issue is. I didn't get this error message,
using the same code with R 2.1.0. Can somebody help (I'm not a
programmer).
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[R] Error message: The following object(s) are masked
Hello!
First time posting here:
Here is my code:
x - c(1:22)
finaloutput=cidrm=NULL
finaldiversityoutput=diversitym=NULL
diversityinfo=read.table(Diversity_info.txt, header=T, sep=\t,
row.names=NULL)
attach(diversityinfo)
diversitynr=nrow(diversityinfo)
diversitytemp - matrix(0,nrow=diversitynr,ncol=1)
for(j in 1:length(x))
{
diversitym=read.table(paste(paste(Div-Chr,x[j],
sep=),_corr.txt,sep=), header=T, sep=\t, row.names=NULL)
attach(diversitym)
diversitytemp - cbind(diversitytemp,diversitym)
print(paste(paste(Diversity-Chrom,x[j], sep=),.txt,sep=))
print(dim(diversitytemp))
}
I am essentially trying to combine several tab-delimited text data files
together into one big file.
I recently upgraded to R 2.2.0. I now get multiple error messages of
the form:
The following object(s) are masked from diversitym ( position 4 ) :
X X.1 X.2
I searched on masked and read the manual about conflicts but I don't
really understand what the issue is. I didn't get this error message,
using the same code with R 2.1.0. Can somebody help (I'm not a
programmer).
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[R] Error Message - Error: symbol print-name too long
Dear All, I write to ask for information regarding the error message: Error: symbol print-name too long. I am afraid that I can't include any code to help with any further diagnosis of the problem as the code is far too long to be of any use, and I have not been able to re-create the problem in shorter example codes. I have searched the R manual and help pages and found no mention of this error message. All help appreciated, Carl A Anderson. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message - Error: symbol print-name too long
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You aren't giving us much to go on, so I can only make a very wild guess. Check that your file doesn't have a stray ` character in it. R will start reading from that point on and try to make this an internal symbol. If it doesn't find the closing ` for too many characters, it gives the error message you see. I have seen this once before and that is what the cause was - a stray ` put in by hitting the ` key rather than Esc. Carl Anderson wrote: Dear All, I write to ask for information regarding the error message: Error: symbol print-name too long. I am afraid that I can't include any code to help with any further diagnosis of the problem as the code is far too long to be of any use, and I have not been able to re-create the problem in shorter example codes. I have searched the R manual and help pages and found no mention of this error message. All help appreciated, Carl A Anderson. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html - -- Duncan Temple Lang[EMAIL PROTECTED] Department of Statistics work: (530) 752-4782 371 Kerr Hall fax: (530) 752-7099 One Shields Ave. University of California at Davis Davis, CA 95616, USA -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2 (Darwin) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFDOAYs9p/Jzwa2QP4RAhtAAJ97sqWdUTOPjtZ2RMJR0qcfyjIAZgCfZLF1 IXTk0bY5RQUD2e+8VlzLpw4= =+pim -END PGP SIGNATURE- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message - Error: symbol print-name too long
Duncan, Thank you for your help. I am pleased to say your 'very wild guess' was exactly correct. Can't believe I missed it! Carl - Original Message - From: Duncan Temple Lang [EMAIL PROTECTED] To: Carl Anderson [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch; [EMAIL PROTECTED] Sent: Tuesday, September 27, 2005 12:31 AM Subject: Re: [R] Error Message - Error: symbol print-name too long -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You aren't giving us much to go on, so I can only make a very wild guess. Check that your file doesn't have a stray ` character in it. R will start reading from that point on and try to make this an internal symbol. If it doesn't find the closing ` for too many characters, it gives the error message you see. I have seen this once before and that is what the cause was - a stray ` put in by hitting the ` key rather than Esc. Carl Anderson wrote: Dear All, I write to ask for information regarding the error message: Error: symbol print-name too long. I am afraid that I can't include any code to help with any further diagnosis of the problem as the code is far too long to be of any use, and I have not been able to re-create the problem in shorter example codes. I have searched the R manual and help pages and found no mention of this error message. All help appreciated, Carl A Anderson. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html - -- Duncan Temple Lang[EMAIL PROTECTED] Department of Statistics work: (530) 752-4782 371 Kerr Hall fax: (530) 752-7099 One Shields Ave. University of California at Davis Davis, CA 95616, USA -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2 (Darwin) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFDOAYs9p/Jzwa2QP4RAhtAAJ97sqWdUTOPjtZ2RMJR0qcfyjIAZgCfZLF1 IXTk0bY5RQUD2e+8VlzLpw4= =+pim -END PGP SIGNATURE- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message running R2WinBUGS
This is a question related to WinBUGS, not to R nor to the R2WinBUGS
interface. Please ask on the appropriate lists/forums related to
WinBUGS (with plain WinBUGS code, rather than R's interface code).
BTW: Let's answer your question before:
You have specified x[1,28] to be 127, but it is from a Binomial
distribution with n=100 (hence impossible!).
And that's what the WinBUGS (NOT R!) error message tells you.
Uwe Ligges
qi zhang wrote:
*Dear R-user,
*
I try to run Winbugs from R using bugs function in R2WinBUGS.My model works
well in Winbugs except that I can't get DIC. Since I don't need DIC, when I
try to run Winbugs from R , I set DIC=FALSE. My model is as following:
model {
for (i in 1:N) {
for(j in 1 : T ) {
x[i, j] ~ dbin(p[i, j],n[i])
#Hier.prior
p[i, j] ~ dbeta(alpha[i, j], beta[i, j])
alpha[i, j] - pi[ j]*(1-theta[i])/theta[i]
beta[i, j] -(1-pi[ j])*(1-theta[i])/theta[i]
}
}
for(j in 1 : T ) {
pi[ j ] ~dbeta(0.1,0.1)I(0.1,0.9)
}
for (i in 1:N) {
theta[i] ~dbeta(2,10)
}
}
And my R code is as followings:
initials1-list(theta=c(0.2,0.01), pi=rbeta(50, 0.1, 0.1)*0.8+0.1
, p=matrix(rbeta(100, 2, 10)*0.8+0.1,nr=2,nc=50,byrow=TRUE))
inits-list(initials1 initials1)
data-list(N=2,T=50 ,n=c(100,150),x = structure(.Data = c(
3, 47, 8, 19, 87, 69,
2, 4, 75, 24, 16, 81,
10, 78, 87, 44, 17, 56,
23, 75, 55, 85, 84, 69,
6, 36, 8, 90, 47, 6,
87, 61, 49, 57, 28, 56,
31, 54, 75, 79, 67, 38,
28, 13, 89, 63, 32, 68,
70, 7,
24, 95, 8, 14, 127, 134,
7, 8, 133, 40, 76, 126,
0, 132, 120, 137, 9, 91,
3, 130, 18, 80, 134, 95,
12, 34, 19, 111, 34, 25,
127, 79, 132, 84, 72, 134,
67, 44, 95, 69, 80, 51,
57, 12, 138, 137, 64, 80,
130, 58), .Dim = c(2, 50)))
#run winbugs
library(R2WinBUGS)
structure-bugs(data,inits,model.file=S:/Common/zhangqi/ebayes/for
R/model.txt,
parameters=c(p,pi,theta),n.chains=2,n.iter=2000,n.burnin=500,
debug=TRUE,DIC=FALSE,bugs.directory=c:/Program Files/WinBUGS14/,
working.directory = NULL )
Even if I changed initial values several times, I still keep geting the
following error message in Winbugs:
display(log)
check(S:/Common/zhangqi/ebayes/for R/model.txt)
model is syntactically correct
data(C:/Program Files/R/rw2011/data.txt)
data loaded
compile(2)
model compiled
inits(1,C:/Program Files/R/rw2011/inits1.txt)
value of binomial x[1,28] must be between zero and order of x[1,28]
I really have no clue about what I can do to fix it.
Could any of your please take a look at my problem, I truely appreciate any
suggestions.
Qi Zhang
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[R] error message running R2WinBUGS
*Dear R-user,
*
I try to run Winbugs from R using bugs function in R2WinBUGS.My model works
well in Winbugs except that I can't get DIC. Since I don't need DIC, when I
try to run Winbugs from R , I set DIC=FALSE. My model is as following:
model {
for (i in 1:N) {
for(j in 1 : T ) {
x[i, j] ~ dbin(p[i, j],n[i])
#Hier.prior
p[i, j] ~ dbeta(alpha[i, j], beta[i, j])
alpha[i, j] - pi[ j]*(1-theta[i])/theta[i]
beta[i, j] -(1-pi[ j])*(1-theta[i])/theta[i]
}
}
for(j in 1 : T ) {
pi[ j ] ~dbeta(0.1,0.1)I(0.1,0.9)
}
for (i in 1:N) {
theta[i] ~dbeta(2,10)
}
}
And my R code is as followings:
initials1-list(theta=c(0.2,0.01), pi=rbeta(50, 0.1, 0.1)*0.8+0.1
, p=matrix(rbeta(100, 2, 10)*0.8+0.1,nr=2,nc=50,byrow=TRUE))
inits-list(initials1 initials1)
data-list(N=2,T=50 ,n=c(100,150),x = structure(.Data = c(
3, 47, 8, 19, 87, 69,
2, 4, 75, 24, 16, 81,
10, 78, 87, 44, 17, 56,
23, 75, 55, 85, 84, 69,
6, 36, 8, 90, 47, 6,
87, 61, 49, 57, 28, 56,
31, 54, 75, 79, 67, 38,
28, 13, 89, 63, 32, 68,
70, 7,
24, 95, 8, 14, 127, 134,
7, 8, 133, 40, 76, 126,
0, 132, 120, 137, 9, 91,
3, 130, 18, 80, 134, 95,
12, 34, 19, 111, 34, 25,
127, 79, 132, 84, 72, 134,
67, 44, 95, 69, 80, 51,
57, 12, 138, 137, 64, 80,
130, 58), .Dim = c(2, 50)))
#run winbugs
library(R2WinBUGS)
structure-bugs(data,inits,model.file=S:/Common/zhangqi/ebayes/for
R/model.txt,
parameters=c(p,pi,theta),n.chains=2,n.iter=2000,n.burnin=500,
debug=TRUE,DIC=FALSE,bugs.directory=c:/Program Files/WinBUGS14/,
working.directory = NULL )
Even if I changed initial values several times, I still keep geting the
following error message in Winbugs:
display(log)
check(S:/Common/zhangqi/ebayes/for R/model.txt)
model is syntactically correct
data(C:/Program Files/R/rw2011/data.txt)
data loaded
compile(2)
model compiled
inits(1,C:/Program Files/R/rw2011/inits1.txt)
value of binomial x[1,28] must be between zero and order of x[1,28]
I really have no clue about what I can do to fix it.
Could any of your please take a look at my problem, I truely appreciate any
suggestions.
Qi Zhang
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Re: [R] Error message NA/NaN/Inf in foreign function call (arg 6) when using knn()
Kerri-Ann Norton wrote: I am trying to use knn to do a nearest neighbor classification. I tried using my dataset and got an error message so I used a simple example to try and understand what I was doing wrong and got the same message. Here is what I typed into R: try [,1] [,2] [,3] [,4] r A A T G r A A T G f A A c G f A A c G f A A c G cl2 -factor(c(rep(1,2), rep(2,3))) cl2 [1] 1 1 2 2 2 Levels: 1 2 knn(try, try, cl2, k = 2) Error in knn(try, try, cl2, k = 2) : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning messages: 1: NAs introduced by coercion 2: NAs introduced by coercion I used try as test and train because I thought the error might be that the size of test and train data were different. If someone could explain what the error means or how to fix it, I would greatly appreciate it. Kerri-Ann Norton __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html What is the euclidean distance between c and T? I think this is a user error which the code does not intercept with a nice error message. Uwe Ligges __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message NA/NaN/Inf in foreign function call (arg 6) when using knn()
I am trying to use knn to do a nearest neighbor classification. I tried using my dataset and got an error message so I used a simple example to try and understand what I was doing wrong and got the same message. Here is what I typed into R: try [,1] [,2] [,3] [,4] r A A T G r A A T G f A A c G f A A c G f A A c G cl2 -factor(c(rep(1,2), rep(2,3))) cl2 [1] 1 1 2 2 2 Levels: 1 2 knn(try, try, cl2, k = 2) Error in knn(try, try, cl2, k = 2) : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning messages: 1: NAs introduced by coercion 2: NAs introduced by coercion I used try as test and train because I thought the error might be that the size of test and train data were different. If someone could explain what the error means or how to fix it, I would greatly appreciate it. Kerri-Ann Norton __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message from pamr
Hi, I got the fowllowing error message when I run pamr. Could you please advise me what does this error mean? Many thanks -- mydata - pamr.from.excel(datgrp4, 352, sample.labels=TRUE) Read 812768 items Read in 2307 genes Read in 350 samples Read in 350 sample labels Make sure these figures are correct!! mytrain - pamr.train(mydata) Error in if (from == to || length.out 2) by - 1 : missing value where logical needed - Rekindle the Rivalries. Sign up for Fantasy Football [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message from pamr
luk wrote: Hi, I got the fowllowing error message when I run pamr. Could you please advise me what does this error mean? Many thanks -- mydata - pamr.from.excel(datgrp4, 352, sample.labels=TRUE) Read 812768 items Read in 2307 genes Read in 350 samples Read in 350 sample labels Make sure these figures are correct!! mytrain - pamr.train(mydata) Error in if (from == to || length.out 2) by - 1 : missing value where logical needed There is no reproducible example given, hence we can only guess. Might be a bug in package pamr or user error, if the first, you want to contact the package maintainer rather than R help. Uwe Ligges - Rekindle the Rivalries. Sign up for Fantasy Football [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message glmmPQL
Hi, I'm fitting a model for two-nested binay data in glmmPQL function but I have this error message: Error in solve.default(estimates[dimE[1] - (p:1), dimE [2] - (p:1), drop = FALSE]) : system is computationally singular: reciprocal condition number = 1.14416e-018. How do I can solve this problem? Or the problem are the data? Thanks, Pedro A. Torres S. Graduate Student - Statistics Department of Mathematics University of Puerto Rico at Mayaguez (1 787) 832-4040 X 2537 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message from vignette strucchange-intro example
Hello, I am just studying the following example from vignette: strucchange-intro, contineousely ending up in an error. This is the given code: 1. library(strucchange) 2. data(USIncExp) 3. if (!package:stats %in% search()) library(ts) 4. USIncExp2 - window(USIncExp, start = c(1985, 12)) A.Modelling: coint.res - residuals(lm(expenditure ~ income, data = USIncExp2)) coint.res - lag(ts(coint.res, start = c(1985, 12), freq = 12),k = -1) USIncExp2 - cbind(USIncExp2, diff(USIncExp2), coint.res) USIncExp2 - window(USIncExp2, start = c(1986, 1), end = c(2001,2)) #here is what eval is looking for in vain: diff.expenditure colnames(USIncExp2) - c(income,expenditure,diff.income,diff.expenditure,coint.res) B. Error correction formula ecm.model - diff.expenditure ~ coint.res + diff.income C. Using EFP (OLS) test function ocus - efp(ecm.model, type = OLS-CUSUM, data = USIncExp2) or me - efp(ecm.model, type = ME, data = USIncExp2, h = 0.2) Both commads under C give me : --- Error in eval(expr, envir, enclos) : Object diff.expenditure not found --- Since quite some time I am sitting here and wonder whether there is an error in the given code or if it my simple inability to catch up with a self-breed error (???) -- platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor0.0 year 2004 month10 day 04 language R Maybe someone to direct my delusion to something helpful, so far I've looked for typos and alike, as far I can say the code should work, isn't it? Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message from vignette strucchange-intro example
Thomas: I am just studying the following example from vignette: strucchange-intro, With problems like this, please contact the package maintainer, or at least Cc. contineousely ending up in an error. This is the given code: 1. library(strucchange) 2. data(USIncExp) 3. if (!package:stats %in% search()) library(ts) 4. USIncExp2 - window(USIncExp, start = c(1985, 12)) A.Modelling: coint.res - residuals(lm(expenditure ~ income, data = USIncExp2)) coint.res - lag(ts(coint.res, start = c(1985, 12), freq = 12),k = -1) USIncExp2 - cbind(USIncExp2, diff(USIncExp2), coint.res) USIncExp2 - window(USIncExp2, start = c(1986, 1), end = c(2001,2)) #here is what eval is looking for in vain: diff.expenditure colnames(USIncExp2) - c(income,expenditure,diff.income,diff.expenditure,coint.res) But until here the code is working, right? You've got a multivariate time series object now with the above column names, haven't you? B. Error correction formula ecm.model - diff.expenditure ~ coint.res + diff.income C. Using EFP (OLS) test function ocus - efp(ecm.model, type = OLS-CUSUM, data = USIncExp2) Both commads under C give me : --- Error in eval(expr, envir, enclos) : Object diff.expenditure not found --- Since quite some time I am sitting here and wonder whether there is an error in the given code or if it my simple inability to catch up with a self-breed error (???) Looks like the latter. I tried this with the CRAN versions of strucchange, sandwich and zoo with R --vanilla (in 2.0.0) and had no problems. Also the daily CRAN checks don't indicate that something went wrong: http://cran.r-project.org/src/contrib/checkSummary.html I suggest that you have another thorough look. If you find something str(ucch)ange, you can also contact me off-list. Z -- platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor0.0 year 2004 month10 day 04 language R Maybe someone to direct my delusion to something helpful, so far I've looked for typos and alike, as far I can say the code should work, isn't it? Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message: MCMCpack and coda
Robin, This is a problem with coda's mcmc summary method. I suspect it is in the spectrum0() call therein, but I don't know for sure. For your immediate purposes you could extract the posterior density sample as a matrix from the mcmc object and manually compute quantities of interest. Best, ADM On Oct 31, 2004, at 3:15 PM, [EMAIL PROTECTED] wrote: Hello All, I'm trying to run a one-dimenional irt model using the packages MCMC and coda on a rather large set of roll-call voting data with many missing observations. Here's a sample of the code: Post10- MCMCirt1d (Italy10, burnin = 1000, mcmc=5, thin=100, verbose=TRUE, theta.constraints = list(V549=1, V443=-1)) The MCMCirt1d command seems to work fine, but when I try to summarize the output I get the following error message(s): summary(Post10) Error: NA/NaN/Inf in foreign function call (arg 1) In addition: Warning message: Step size truncated due to divergence My understanding is that this has something to do with the missing data, though I don't know how to address this issue. Any help would be greatly appreciated. Thank you, Robin Best __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Andrew D. Martin, Ph.D. Department of Political Science Washington University Campus Box 1063 One Brookings Drive St. Louis, MO 63130 (314) 935-5863 (Office) (314) 753-8377 (Cell) (314) 935-5856 (Fax) Office: Eliot Hall 326 Email: [EMAIL PROTECTED] WWW: http://adm.wustl.edu __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error Message: MCMCpack and coda
Hello All, I'm trying to run a one-dimenional irt model using the packages MCMC and coda on a rather large set of roll-call voting data with many missing observations. Here's a sample of the code: Post10- MCMCirt1d (Italy10, burnin = 1000, mcmc=5, thin=100, verbose=TRUE, theta.constraints = list(V549=1, V443=-1)) The MCMCirt1d command seems to work fine, but when I try to summarize the output I get the following error message(s): summary(Post10) Error: NA/NaN/Inf in foreign function call (arg 1) In addition: Warning message: Step size truncated due to divergence My understanding is that this has something to do with the missing data, though I don't know how to address this issue. Any help would be greatly appreciated. Thank you, Robin Best __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message: MCMCpack and coda
On Sun, 31 Oct 2004 [EMAIL PROTECTED] wrote: Hello All, I'm trying to run a one-dimenional irt model using the packages MCMC and coda on a rather large set of roll-call voting data with many missing observations. Here's a sample of the code: Post10- MCMCirt1d (Italy10, burnin = 1000, mcmc=5, thin=100, verbose=TRUE, theta.constraints = list(V549=1, V443=-1)) The MCMCirt1d command seems to work fine, but when I try to summarize the output I get the following error message(s): summary(Post10) Error: NA/NaN/Inf in foreign function call (arg 1) In addition: Warning message: Step size truncated due to divergence My understanding is that this has something to do with the missing data, though I don't know how to address this issue. Any help would be greatly appreciated. Your understanding is not correct: NaN and Inf result from numeric overflow, divide by zero and similar. When you get an error message, try traceback() to see where it came from. This came from a `foreign', that is .C or .Fortran, call, passing in a NaN or Inf or NA, and probably one of the first two given the warning on divergence. But without a tracebacl() we don't know which call. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message in mclust
I keep on receiving the message below after submitting the following line using the mclust package. m2 is a 99 X 1 column vector. * em(modelName = E, m2, mu = c(25, 50), sigmasq=10, pro = c(0.4, 0.6)) Error in as.double.default(data) : (list) object cannot be coerced to double. Why do I receive this error? Thank, Brian C. Newquist Research Statistician Constella Health Sciences 2605 Meridian Parkway, Suite 200 Durham, NC 27713 Tel: (919) 313-7588 Fax: (919) 544-7507 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] www.constellagroup.com http://www.constellagroup.com [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message in mclust
Brian Newquist wrote: I keep on receiving the message below after submitting the following line using the mclust package. m2 is a 99 X 1 column vector. * em(modelName = E, m2, mu = c(25, 50), sigmasq=10, pro = c(0.4, 0.6)) Error in as.double.default(data) : (list) object cannot be coerced to double. Why do I receive this error? Brian, Are you sure m2 is a vector and not a data.frame or list? I can replicate your error message as follows: library(mclust) # from ?em data(iris) irisMatrix - as.matrix(iris[, 1:4]) irisClass - iris[, 5] msEst - mstep(modelName = EEE, data = irisMatrix, z = unmap(irisClass)) iris.em1 - em(modelName = msEst$modelName, data = irisMatrix, mu = msEst$mu, Sigma = msEst$Sigma, pro = msEst$pro) # not from ?em iris.em2 - em(modelName = msEst$modelName, data = iris[, 1:4], mu = msEst$mu, Sigma = msEst$Sigma, pro = msEst$pro) The second call to em produces: Error in as.double.default(data) : (list) object cannot be coerced to double That said, it shouldn't matter that `data' is a data.frame since the help page says explicitly that data.frames are allowed as long as the variables are not categorical. The first for columns of iris are `numeric'. R-2.0.0Patched with MCLUST 2.1-6 --sundar __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message in function mars() in package mda
Jude == Jude Ryan [EMAIL PROTECTED]
on Tue, 10 Aug 2004 15:56:38 -0400 writes:
Jude Hi, I am using function mars() in package mda to find
Jude knots in a whole bunch of predictor variables. I hope
Jude to be able to replicate all or some of the basis
Jude functions that the MARS software from Salford Systems
Jude creates. When I ran mars() on a small dataset, I was
Jude able to get the knots. However, when I tried running
Jude mars() on a larger dataset (145 predictor variables),
Jude for a different project, I get the following error
Jude message:
fit1 - mars(disney2[,-146], disney2[,146])
Jude Error in mars(disney2[, -146], disney2[, 146]) :
Jude NA/NaN/Inf in foreign function call (arg 5)
Jude In addition: Warning messages:
Jude 1: NAs introduced by coercion
Jude 2: NAs introduced by coercion
Jude Does arg 5 refer to the 5th column in my dataset?
no.
Jude This seems to be a data problem, is this correct?
we cannot know with the little information you give.
Please read (and follow!!) the posting guide!
- reproducible example !
- contact the maintainer of the package in question!
The following reproducible example doesn't show the problem you
mentioned:
library(mda)
set.seed(101)
X - matrix(rnorm(200 * 150), 200, 150)
fX - mars(X[,-146], X[,146])
str(fX)
List of 15
$ call : language mars(x = X[, -146], y = X[, 146])
$ all.terms : int [1:93] 1 2 3 4 5 6 7 8 9 10 ...
$ selected.terms: int [1:25] 1 2 3 4 5 10 12 13 14 16 ...
$ penalty : num 2
$ degree: num 1
$ nk: num 299
$ thresh: num 0.001
$ gcv : num 0.72
$ factor: num [1:99, 1:149] 0 0 0 0 0 0 0 0 0 0 ...
..- attr(*, dimnames)=List of 2
.. ..$ : NULL
.. ..$ : NULL
$ cuts : num [1:99, 1:149] 0 0 0 0 0 0 0 0 0 0 ...
$ residuals : num [1:200, 1] 0.789 0.111 -0.212 1.017 -0.391 ...
$ fitted.values : num [1:200, 1] -0.216 -0.249 -0.116 -0.274 -0.353 ...
$ lenb : int 99
$ coefficients : num [1:25, 1] 0.696 0.491 1.013 -1.043 -0.409 ...
$ x : num [1:200, 1:25] 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, class)= chr mars
BTW (as a note to the maintainer of mda):
print.mars() {and maybe summary.mars()} is severly lacking...
Jude Are there any other functions in R that will give me
Jude the knots for a set of predictor variables?
maybe, quite probably. This question is too vague [the knots?]
Regards,
Martin Maechler
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[R] Error message in function mars() in package mda
Hi, I am using function mars() in package mda to find knots in a whole bunch of predictor variables. I hope to be able to replicate all or some of the basis functions that the MARS software from Salford Systems creates. When I ran mars() on a small dataset, I was able to get the knots. However, when I tried running mars() on a larger dataset (145 predictor variables), for a different project, I get the following error message: fit1 - mars(disney2[,-146], disney2[,146]) Error in mars(disney2[, -146], disney2[, 146]) : NA/NaN/Inf in foreign function call (arg 5) In addition: Warning messages: 1: NAs introduced by coercion 2: NAs introduced by coercion Does arg 5 refer to the 5th column in my dataset? This seems to be a data problem, is this correct? Are there any other functions in R that will give me the knots for a set of predictor variables? Any help is greatly appreciated. Thanks, Jude __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message handling
On Wed, 23 Jun 2004 [EMAIL PROTECTED] wrote: Dear, R experts. Does anybody have experience with 'optim' function? Yes. I have an error message as the following. Error in optim(transcoefs, fn = hfdeviance, gr = hfdeviance.grad, method = BFGS, : initial value in vmmin is not finite I want to make a comment when this happen. Function 'fn' can return 'NA' or 'Inf' if the function cannot be evaluated at the supplied value, but the initial value must have a computable finite value of 'fn'. (Except for method 'L-BFGS-B' where the values should always be finite.) It's your error so you can control it (by not making the error). Is there way I can put *my* message after this error occur? You can use try/tryCatch and similar constructs. But it would be better to use a valid starting value as optim asks, and you can so that by calling hfdeviance(transcoefs) and checking it is finite. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message handling
Dear, R experts. Does anybody have experience with 'optim' function? I have an error message as the following. Error in optim(transcoefs, fn = hfdeviance, gr = hfdeviance.grad, method = BFGS, : initial value in vmmin is not finite I want to make a comment when this happen. Is there way I can put *my* message after this error occur? Thanks in advance + Changku Kang National Center for Environmental Assessment EPA (B211F) 919-541-1396 919-541-0245 (fax) [EMAIL PROTECTED] Graduate Student Department of Statistics, NCSU [EMAIL PROTECTED] 919-513-2956 + __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message
I received the below error using UNIX R. Could someone instruct me on helpful batch options to avoid this please? ERROR: cannot allocate vector of size 32kb __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] error message
The message says at some point in the calculation, R tries to get about 312MB of memory and was not able to. Maybe try increasing the amount of virtual (or physical) memory in your system? Andy From: Tim York I received the below error using UNIX R. Could someone instruct me on helpful batch options to avoid this please? ERROR: cannot allocate vector of size 32kb __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message in help.search
Hello, I looked around but couldn't find solutions for my problem. I downloaded v.1.9 and the patched version for windows. I use Windows XP professional with AMD Athlon XP. When I use help.search() function, I get the following error message: Error in .readRDS(contentsFile) : can't read workspace version 167772160 written by R 512.1.7; need R 256.1.4 or newer What does this mean? More importantly, how can I fix it? Thanks, Tomo * Tomoharu Eguchi Protected Resources Division Southwest Fisheries Science Center 8604 La Jolla Shores Dr. La Jolla, CA 92037 858.546.5615 Voice 858.546.5657 FAX __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message during debug
In R 1.9.0 on Windows XP Pro I get an error if I try to debug the identity function f shown: f - function(x)x debug(f) f(1) debugging in: f(1) Error in f(1) : Unimplemented feature in eval R.version.string [1] R version 1.9.0, 2004-04-12 Without debuggging its ok. ___ Make My Way your home on the Web - http://www.myway.com __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message during debug
Gabor Grothendieck wrote:
In R 1.9.0 on Windows XP Pro I get an error if I try to
debug the identity function f shown:
f - function(x)x
debug(f)
f(1)
debugging in: f(1)
Error in f(1) : Unimplemented feature in eval
R.version.string
[1] R version 1.9.0, 2004-04-12
Without debuggging its ok.
Try
f - function(x) { x }
--sundar
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Re: [R] Error message during debug
Sundar Dorai-Raj sundar.dorai-raj at PDF.COM writes:
:
: Gabor Grothendieck wrote:
:
: In R 1.9.0 on Windows XP Pro I get an error if I try to
: debug the identity function f shown:
:
:f - function(x)x
:debug(f)
:f(1)
: debugging in: f(1)
: Error in f(1) : Unimplemented feature in eval
:R.version.string
: [1] R version 1.9.0, 2004-04-12
:
: Without debuggging its ok.
:
:
:
:
: Try
:
: f - function(x) { x }
:
: --sundar
That made the error go away. Note that
f - function(x)sin(x)
does NOT produce the error under debugging. Don't know why
x and sin(x) would act differently in the above respect.
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[R] error message in mle function
I am getting an error message concerning the estimation of confidence intervals when fitting a mixed model and don't know what the problem is, or its solution. Just to provide context: the model is describing the effects of age, exp(age), harvest age, and climate variables on bighorn horn annular length. The data structure is repeated measures (between individuals, within individuals over time). Id is a random effect (there are between 3-11 horn measurements per ram, one horn measurement per age, over the 25 year period in the dataset). The mixed effect results is unable to provide confidence intervals for the fixed and random effects because: of an error in the variance-covariance structure. The error says that the intervals are non-positive definitive. Bill Shipley [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message in mle function
Is one of your variance components essentially estimating zero? If you check the numbers, delete the smallest one, and then do anova comparing the two fits, you might find that the one you deleted was not statistically significant. If I'm not mistaken, lme estimates the logarithms of the variance components. When one of them is zero, the logarithm wants to go to (-Inf). In that case, lme will still return an answer. However, intervals complains, because the observed information matrix for the parameter estimates is singular in the direction of log(variance component) that wants to go to (-Inf). Doug Bates, the developer of lme has taught many people about how to fix that problem using profile likelihood. I have not seen lme4 yet, so the problem may already have been fixed. If any if this is inaccurate, I hope Doug will correct me. hope this helps. Spencer Graves Bill Shipley wrote: I am getting an error message concerning the estimation of confidence intervals when fitting a mixed model and don't know what the problem is, or its solution. Just to provide context: the model is describing the effects of age, exp(age), harvest age, and climate variables on bighorn horn annular length. The data structure is repeated measures (between individuals, within individuals over time). Id is a random effect (there are between 3-11 horn measurements per ram, one horn measurement per age, over the 25 year period in the dataset). The mixed effect results is unable to provide confidence intervals for the fixed and random effects because: of an error in the variance-covariance structure. The error says that the intervals are non-positive definitive. Bill Shipley [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message - what does it mean???
Hi, I am trying to calculate mahalanobis distances for a matrix x with n*p variables. I am getting the following error: md2 - mahalanobis(x, center, cov) Error in solve.default(cov, tol = tol.inv) : system is computationally singular: reciprocal condition number = 2.11165e-009 What does it means? Thank you so much for any help, Monica __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error message - what does it mean???
On Tue, 9 Mar 2004, Monica Palaseanu-Lovejoy wrote: Hi, I am trying to calculate mahalanobis distances for a matrix x with n*p variables. I am getting the following error: md2 - mahalanobis(x, center, cov) Error in solve.default(cov, tol = tol.inv) : system is computationally singular: reciprocal condition number = 2.11165e-009 What does it means? Error messages usually mean what they say, and it hard to see what you mind to understand here. Whatever you supplied for `cov' is a singular matrix to the default tolerance, described on the help page. If you know what is going on with your data, you could reduce the argument `tol.inv'. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message from regsubsets
Hi, I'm using regsubsets and it works fine when nvmax = 4. However when I go for any value above 4, I get the error: Warning message: XHAUST returned error code -999 in: leaps.exhaustive(a, really.big = really.big) I'm calling regsubsets as: lp - regsubsets(x,y,nbest=1,nvmax=5,intercept=T,really.big=T, method=exhaustive) x is a data.frame with 40 variables and 277 observations (in the rows) and y is a vector of length 277. The manual mentions that really.big should be TRUE when there are more than 50 variables. But even if when I set it to FALSE in the above command it still fails with the error mesage. Thanks Could anybody explain what this error means? --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Enzymes are things invented by biologists that explain things which otherwise require harder thinking. -- Jerome Lettvin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message
I am trying to calculate n, using power.t.test power.t.test(n=NULL,delta=delta, sd=sigmaEins, sig.level= alpha, power=power, type=c(two.sample), alternative=c(two.sided)) The values of the parameter are read in from a file. I have no idea what the error message means. --- Peter Dalgaard [EMAIL PROTECTED] wrote: forkusam [EMAIL PROTECTED] writes: Hi, Can someone please tell me what such an error message could mean. i.e where a problem must have arised. Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07)) : f() values at end points not of opposite sign Looks like the innards of one of the power calculations, finding n to achieve a given power. You'd likely get an error like that if the power is not between 0 and 1, but how about telling us what you were trying to do? -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 = = Sylvie B. Forkusam Eppelheimer Str.52/A2-5-2 69115 Heidelberg, Germany Tel: (0049)-06221/346913 Mobile: 0179-6816276 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message
On Sat, 24 Jan 2004, forkusam wrote: I am trying to calculate n, using power.t.test power.t.test(n=NULL,delta=delta, sd=sigmaEins, sig.level= alpha, power=power, type=c(two.sample), alternative=c(two.sided)) The values of the parameter are read in from a file. I have no idea what the error message means. Peter Dalgaard asked you to specify a *reproducible* example. So, please specify some values for delta, sigmaEins, alpha, power. Uwe Ligges --- Peter Dalgaard [EMAIL PROTECTED] wrote: forkusam [EMAIL PROTECTED] writes: Hi, Can someone please tell me what such an error message could mean. i.e where a problem must have arised. Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07)) : f() values at end points not of opposite sign Looks like the innards of one of the power calculations, finding n to achieve a given power. You'd likely get an error like that if the power is not between 0 and 1, but how about telling us what you were trying to do? -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 = = Sylvie B. Forkusam Eppelheimer Str.52/A2-5-2 69115 Heidelberg, Germany Tel: (0049)-06221/346913 Mobile: 0179-6816276 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message
Hi, Can someone please tell me what such an error message could mean. i.e where a problem must have arised. Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07)) : f() values at end points not of opposite sign Thank you cilver = = Sylvie B. Forkusam Eppelheimer Str.52/A2-5-2 69115 Heidelberg, Germany Tel: (0049)-06221/346913 Mobile: 0179-6816276 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message
forkusam [EMAIL PROTECTED] writes: Hi, Can someone please tell me what such an error message could mean. i.e where a problem must have arised. Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07)) : f() values at end points not of opposite sign Looks like the innards of one of the power calculations, finding n to achieve a given power. You'd likely get an error like that if the power is not between 0 and 1, but how about telling us what you were trying to do? -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message in plot(aov-object) -- repost
Hi all, I posted this question several days ago, but did not get any answer until now. Since I still have no clue about the source of this error message, I repost a description of the problem including some code: A student at our institute fitted an aov model, and got the following error message: plot(p.aov) Hit Return to see next plot: Hit Return to see next plot: Error in plot.window(xlim, ylim, log, asp, ...) : need finite ylim values The second plot was not produced. I then tried to produced the plot manually, which worked, and checked the range of the residuals: qqnorm(resid(p.aov)) range(resid(p.aov)) [1] -0.2428688 0.2020649 Her data set and the model are as follows: Data: http://www.bot.unibas.ch/~pascal/ParzJan.csv Model (I don't understand the model, but that's not the issue here) p - read.csv(ParzJan.csv,header=T) p.aov -aov(terms(JI~SP+Ex+Neig+pH+K/G+H+D+tN+br+aN:br+tN:D +br:D+aN:br:D+br:tN+aN:br:D + aN:br:tN+ K:D+ K:tN+ K:br +K:aN:br+ G:K:D+ G:K:tN+ G:K:br+G:K:aN:br+ D:H+ tN:H+ br:H + aN:br:H, keep.order=T), data=p) Any help regarding the source of this plot() error message is appreciated. Pascal P.S.: She used R 1.7.1 on a Mac, but the problem was reproducible on R 1.8.1 under Linux. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message in plot(aov-object) -- repost
Pascal A. Niklaus wrote: Hi all, I posted this question several days ago, but did not get any answer until now. Since I still have no clue about the source of this error message, I repost a description of the problem including some code: A student at our institute fitted an aov model, and got the following error message: plot(p.aov) Hit Return to see next plot: Hit Return to see next plot: Error in plot.window(xlim, ylim, log, asp, ...) : need finite ylim values The second plot was not produced. I then tried to produced the plot manually, which worked, and checked the range of the residuals: qqnorm(resid(p.aov)) range(resid(p.aov)) [1] -0.2428688 0.2020649 Her data set and the model are as follows: Data: http://www.bot.unibas.ch/~pascal/ParzJan.csv Model (I don't understand the model, but that's not the issue here) p - read.csv(ParzJan.csv,header=T) p.aov -aov(terms(JI~SP+Ex+Neig+pH+K/G+H+D+tN+br+aN:br+tN:D +br:D+aN:br:D+br:tN+aN:br:D + aN:br:tN+ K:D+ K:tN+ K:br +K:aN:br+ G:K:D+ G:K:tN+ G:K:br+G:K:aN:br+ D:H+ tN:H+ br:H + aN:br:H, keep.order=T), data=p) Any help regarding the source of this plot() error message is appreciated. Without the data nobody was able to reproduce your problem .. plot.lm() produces the error message, in particular the lines hii - lm.influence(x, do.coef = FALSE)$hat which appears to be 1 in some cases, and rs - r.w/(s * sqrt(1 - hii)) (you get a division by zero and the outcome is Inf, hence it's not possible to scale the plot any more). I'd call it a bug, but I don't know what the bug really is. I'll think about it... Uwe Ligges Pascal P.S.: She used R 1.7.1 on a Mac, but the problem was reproducible on R 1.8.1 under Linux. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error message in plot(aov-object) -- repost
Uwe Ligges [EMAIL PROTECTED] writes: plot.lm() produces the error message, in particular the lines hii - lm.influence(x, do.coef = FALSE)$hat which appears to be 1 in some cases, and rs - r.w/(s * sqrt(1 - hii)) (you get a division by zero and the outcome is Inf, hence it's not possible to scale the plot any more). I'd call it a bug, but I don't know what the bug really is. I'll think about it... If the $hat is 1, then the residual is theoretically zero and you should get 0/0 == NA which would be much less trouble. Apparently, floating poing arithmetic makes it not quite so and you get Inf in some cases. I'd expect that rs[hii==1] - NA would fix things up, although you might possibly need a fuzz factor (hii 1-1e-10 or so). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message in plot(aov-object)
Hi all, A student at our institute asked me for help with the following problem: After fitting an aov model, she wanted diagnostic plots, and got the following error message: plot(p.aov) Hit Return to see next plot: Hit Return to see next plot: Error in plot.window(xlim, ylim, log, asp, ...) : need finite ylim values In addition: Warning message: X11 used font size 8 when 9 was requested The second plot was not produced. I then tried to produced the plot manually, which worked, and checked the range of the residuals: qqnorm(resid(p.aov)) range(resid(p.aov)) [1] -0.2428688 0.2020649 She used R 1.7.1 on a Mac, but I reproduced the problem on R 1.8.1 under Linux. Any help regarding the source of this problem is appreciated Pascal __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message in simulation
Dear R-users,
I am a dentist (so forgive me if my question looks stupid) and came across
a problem when I did simulations to compare a few single level and two
level regressions.
The simulations were interrupted and an error message came out like 'Error
in MEestimate(lmeSt, grps) : Singularity in backsolve at level 0, block 1'.
My collegue suggested that this might be due to my codes was not efficient
and ran out of memory. If this is the reason, could you please help me
improve my codes writing.
However, as I slightly changed the parameters, it ran well. So I suspect
memory is problem.
I use R 1.8.0 and Windows XP professional. My computer has a Pentium 4 2.4
with 512 MB memory.
Thanks in advance.
best regards,
Yu-Kang Tu
Clinical Research Fellow
Leeds Dental Institute
University of Leeds
## change scores simulation
close.screen(all=TRUE)
split.screen(c(3,3))
nitns-1
nsims-100
r-0.1
param1-c(1:nitns)
param2-c(1:nitns)
param3-c(1:nitns)
param4-c(1:nitns)
param5-c(1:nitns)
param6-c(1:nitns)
param7-c(1:nitns)
param8-c(1:nitns)
param9-c(1:nitns)
param10-c(1:nitns)
param11-c(1:nitns)
param12-c(1:nitns)
param13-c(1:nitns)
param14-c(1:nitns)
for(itn in 1:nitns){
g-rbinom(nsims,1,0.5)
b-rnorm(nsims,0,1)*10
rn-rnorm(nsims,0,1)*10
a-b*r+rn*(1-r^2)^0.5
a-round(a)+50
a-a-g*5
b-round(b)+50
abs.2-function(x) ifelse(x1,1,x)
b-abs.2(b)
c-b-a
p-c/b
lm1-lm(a~g)
lm2-lm(c~g)
lm3-lm(p~g)
lm4-lm(a~b+g)
gr-c(g,g)
occasion-rep(0:1,c(nsims,nsims))
occ-occasion-0.5
ppd-c(b,a)
h-rep(0,nsims)
mb-mean(b)
bppd-b-mb
bappd-c(h,bppd)
occgr-occ*gr
subject-c(1:nsims)
sub-c(subject,subject)
library(nlme)
lm5-lme(ppd~occ+gr+occgr,random=~1|sub)
lm5f-fixed.effects(lm5)
lm5c-as.matrix(lm5f)
lm5a-anova(lm5)
lm6-lme(ppd~occ+gr+occgr,random=~1|sub,method=ML)
lm6f-fixed.effects(lm6)
lm6c-as.matrix(lm6f)
lm6a-anova(lm6)
lm7-lme(ppd~occ+gr+occgr+bappd,random=~1|sub,method=ML)
lm7f-fixed.effects(lm7)
lm7c-as.matrix(lm7f)
lm7a-anova(lm7)
param1[itn]-coef(summary(lm1))[2,1]
param2[itn]-coef(summary(lm2))[2,1]
param3[itn]-coef(summary(lm3))[2,1]
param4[itn]-coef(summary(lm4))[3,1]
param5[itn]-lm5c[4,1]
param6[itn]-lm6c[4,1]
param7[itn]-lm7c[4,1]
param8[itn]-coef(summary(lm1))[2,4]
param9[itn]-coef(summary(lm2))[2,4]
param10[itn]-coef(summary(lm3))[2,4]
param11[itn]-coef(summary(lm4))[3,4]
param12[itn]-lm5a[4,4]
param13[itn]-lm6a[4,4]
param14[itn]-lm7a[4,4]
}
#the error message came out here.
#But if I change some of the variables to:
b-rnorm(nsims,0,1)*2
rn-rnorm(nsims,0,1)*2
a-b*r+rn*(1-r^2)^0.5
a-round(a)+7
a-a-g*2
b-round(b)+9
abs.1-function(x) ifelse(x5,5,x)
b-abs.1(b)
abs.2-function(x) ifelse(x1,1,x)
a-abs.2(a)
There is no poblem to complete the simulations.
_
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http://msn.com.tw
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Re: [R] error message in simulation
Yu-Kang -
Simulations by their nature use randomly generated data.
Sometimes the random data doesn't contain enough information
to fully determine the parameter estimates for one iteration
or another. It seems likely that that is what happened here.
The design matrix is singular for one iteration (maybe there
are NO simulated subjects in one arm of the trial) and
backsolve() very properly returns an error message. On the
very next iteration, with a different randomly-generated data
set, everything should work, again.
The function try() allows you to get past these problematic
iterations. It's better, of course, to figure out what the
requirements for a fully-specified data set are, and arrange
the random generator so that these are guaranteed to be met.
- tom blackwell - u michigan medical school - ann arbor -
On Tue, 28 Oct 2003, Tu Yu-Kang wrote:
Dear R-users,
I am a dentist (so forgive me if my question looks stupid) and came across
a problem when I did simulations to compare a few single level and two
level regressions.
The simulations were interrupted and an error message came out like 'Error
in MEestimate(lmeSt, grps) : Singularity in backsolve at level 0, block 1'.
My collegue suggested that this might be due to my codes was not efficient
and ran out of memory. If this is the reason, could you please help me
improve my codes writing.
However, as I slightly changed the parameters, it ran well. So I suspect
memory is problem.
I use R 1.8.0 and Windows XP professional. My computer has a Pentium 4 2.4
with 512 MB memory.
Thanks in advance.
best regards,
Yu-Kang Tu
Clinical Research Fellow
Leeds Dental Institute
University of Leeds
## change scores simulation
close.screen(all=TRUE)
split.screen(c(3,3))
nitns-1
nsims-100
r-0.1
param1-c(1:nitns)
param2-c(1:nitns)
param3-c(1:nitns)
param4-c(1:nitns)
param5-c(1:nitns)
param6-c(1:nitns)
param7-c(1:nitns)
param8-c(1:nitns)
param9-c(1:nitns)
param10-c(1:nitns)
param11-c(1:nitns)
param12-c(1:nitns)
param13-c(1:nitns)
param14-c(1:nitns)
for(itn in 1:nitns){
g-rbinom(nsims,1,0.5)
b-rnorm(nsims,0,1)*10
rn-rnorm(nsims,0,1)*10
a-b*r+rn*(1-r^2)^0.5
a-round(a)+50
a-a-g*5
b-round(b)+50
abs.2-function(x) ifelse(x1,1,x)
b-abs.2(b)
c-b-a
p-c/b
lm1-lm(a~g)
lm2-lm(c~g)
lm3-lm(p~g)
lm4-lm(a~b+g)
gr-c(g,g)
occasion-rep(0:1,c(nsims,nsims))
occ-occasion-0.5
ppd-c(b,a)
h-rep(0,nsims)
mb-mean(b)
bppd-b-mb
bappd-c(h,bppd)
occgr-occ*gr
subject-c(1:nsims)
sub-c(subject,subject)
library(nlme)
lm5-lme(ppd~occ+gr+occgr,random=~1|sub)
lm5f-fixed.effects(lm5)
lm5c-as.matrix(lm5f)
lm5a-anova(lm5)
lm6-lme(ppd~occ+gr+occgr,random=~1|sub,method=ML)
lm6f-fixed.effects(lm6)
lm6c-as.matrix(lm6f)
lm6a-anova(lm6)
lm7-lme(ppd~occ+gr+occgr+bappd,random=~1|sub,method=ML)
lm7f-fixed.effects(lm7)
lm7c-as.matrix(lm7f)
lm7a-anova(lm7)
param1[itn]-coef(summary(lm1))[2,1]
param2[itn]-coef(summary(lm2))[2,1]
param3[itn]-coef(summary(lm3))[2,1]
param4[itn]-coef(summary(lm4))[3,1]
param5[itn]-lm5c[4,1]
param6[itn]-lm6c[4,1]
param7[itn]-lm7c[4,1]
param8[itn]-coef(summary(lm1))[2,4]
param9[itn]-coef(summary(lm2))[2,4]
param10[itn]-coef(summary(lm3))[2,4]
param11[itn]-coef(summary(lm4))[3,4]
param12[itn]-lm5a[4,4]
param13[itn]-lm6a[4,4]
param14[itn]-lm7a[4,4]
}
#the error message came out here.
#But if I change some of the variables to:
b-rnorm(nsims,0,1)*2
rn-rnorm(nsims,0,1)*2
a-b*r+rn*(1-r^2)^0.5
a-round(a)+7
a-a-g*2
b-round(b)+9
abs.1-function(x) ifelse(x5,5,x)
b-abs.1(b)
abs.2-function(x) ifelse(x1,1,x)
a-abs.2(a)
There is no poblem to complete the simulations.
_
MSN
http://msn.com.tw
__
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Re: [R] Error message in non linear regression model
anne [EMAIL PROTECTED] writes: Hello! Trying to fit a non linear regression model modF-nlsModel(kf~3*alpha*epsilon^P, dat, list(alpha=ALPHA)) You should use nls, not nlsModel. Also, if P is fixed then this is a linear regression model. Why use nonlinear regression. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] error message in nlm()
Johannes - There's something special about the way control parameters are accepted by nlm() and nlme(). Try searching very recent help archives for nlme() or control. Try duplicating exactly one of the examples at the bottom of the help page help(nlm). My recollection is that the parameter that you actually pass has to be literally a function, maybe one with a specific name. But that's jsut vague recollection. Others will have better information. - tom blackwell - u michigan medical school - ann arbor - On Mon, 1 Sep 2003, [iso-8859-1] Hüsing, Johannes wrote: I have been trying the nlm function but received an error message which reads: Error in nlm(intensities ~ f, c(epsilon.spec.start, epsilon.unspec.start, : invalid function value in 'nlm' optimizer The error message is issued after the second call to the function that nlm minimizes over. Could you give any suggestions on what I could be mishandling? Johannes __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] error message in fitdistr
Hi R lovers
Here is a numerical vector test
test
[1] 206 53 124 112 92 77 118 75 48 176 90 74 107 126 99 84 114
147 99 114 99 84 99 99 99 99 99 104 1 159 100 53
[33] 132 82 85 106 136 99 110 82 99 99 89 107 99 68 130 99 99
110 99 95 153 93 136 51 103 95 99 72 99 50 110 37
[65] 102 104 92 90 94 99 76 81 109 91 98 96 104 104 93 99 125
89 99 99 108 90 105 92 106 103 99 99 99 94 102 103
[97] 97 99 118 91 110 99 99 99 98 105 99 97 99 101 95 98 99
102 99 99 99 99 95 93 86 96 113 87 112 120 71 99
[129] 99 81 96 113 85 116 112 84 120 88 97 104 99 105 153 103 92
99 99 99 90 108 104 99 105 97 94 93 99 85 91 99
[161] 118 99 91 99 103 101 102 96 99 123 85 101 88 99 93 73 97
89 94 69 74 99 97 91 92
Assuming it follows a lognormal distribution I'd like to determine the mean
and the sd thanks to maximum likelihood estimation
fitdistr(test,lognormal,start=list(200,10))
Error in print.fitdistr(structure(list(estimate = c(4.54666263736726, :
more elements supplied than there are to replace
I chose the parameter start randomly
I don't understand the error message. Has anybody ever encountered such
one?
thanks for the help
have a wonderful day
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