Re: [R] Package MuMIn (dredge): Error in ret[, ] - cbind(x, se, rep(if (is.null(df)) NA_real_ else df, : number of items to replace is not a multiple of replacement length.
I have also reinstalled the MuMIn package as suggested at... http://r.789695.n4.nabble.com/Error-message-number-of-items-to-replace-is-not-a-multiple-of-replacement-length-td3257893.html ...however, this made no difference. any help is appreciated. thank you -- View this message in context: http://r.789695.n4.nabble.com/Package-MuMIn-dredge-Error-in-ret-cbind-x-se-rep-if-is-null-df-NA-real-else-df-number-of-items-to-re-tp4636105p4636604.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Package MuMIn (dredge): Error in ret[, ] - cbind(x, se, rep(if (is.null(df)) NA_real_ else df, : number of items to replace is not a multiple of replacement length.
Hello R community, I am attempting to run multiple logistic regressions (multinomial, via package 'nnet'), with Automated Model Selection (dredge, package 'MuMIn'). The aim is to reduce the number of predictor variables by assessing relative performance of each variable, which can be done in a coarse fashion using the Automated Model Selection option in package 'MuMIn' [dredge]. The data file is large (585000 rows) and has no NA, - or blank values (attached data file with 200 rows). Following the dredge command, I get the following error and warning (see end of message for details): Error in ret[, ] - cbind(x, se, rep(if (is.null(df)) NA_real_ else df, : number of items to replace is not a multiple of replacement length In addition: Warning message: In cbind(x, se, rep(if (is.null(df)) NA_real_ else df, length.out = n), : number of rows of result is not a multiple of vector length (arg 3). I am unclear what this means and how to resolve the issue. If anyone has any idea how to address this error, I would very much appreciate your response. Thank you in advance. Jeremy My script is as follows : ## LOAD PACKAGES library(MASS) library(MuMIn) library(nnet) library(AICcmodavg) Jdata- read.delim(/Analysis/20120709 JLittle data file.txt, header=T) attach(Jdata) names(Jdata) ##NNET ##MULTINOMIAL LOGISTIC REGRESSION ##multinom(formula, data, weights, subset, na.action, contrasts = NULL, ##Hess = FALSE, summ = 0, censored = FALSE, ##model = FALSE, ...) ##Full Model ##14 variables model1 - multinom(JVeg5~Elevation + Lat_Y_pos + Coast_dist + Coast_SE + Coast_E + Stream_dist + Subregion + Rock_Name + Slope + Aspect + Hillshade + Wind_310 + TPI + Landform, data=Jdata, maxit=600) ##with 14 variables, maximum iterations reached without convergence, therefore... ##have added maxit=600 argument, this increases maximum number of iterations ##from 100 to 600 (convergence at 550). summary(model1) ##MuMIn ##dredge analysis dredge1 - dredge(model1) Following the last line of the script, I get the following output: # weights: 10 (4 variable) initial value 44.275905 iter 10 value 573524.741778 final value 572802.916150 converged # weights: 15 (8 variable) initial value 44.275905 iter 10 value 596499.388517 iter 20 value 572607.756806 final value 572606.390789 converged Error in ret[, ] - cbind(x, se, rep(if (is.null(df)) NA_real_ else df, : number of items to replace is not a multiple of replacement length In addition: Warning message: In cbind(x, se, rep(if (is.null(df)) NA_real_ else df, length.out = n), : number of rows of result is not a multiple of vector length (arg 3) My data details: str(Jdata) 'data.frame': 552270 obs. of 17 variables: $ POINTID: int 582358 582360 582361 582359 35289 582357 582362 411225 584336 584493 ... $ Lat_Y_pos : num 19.7 19.7 19.7 19.7 16 ... $ JVeg5 : Factor w/ 5 levels 1RF,2WSFEG,..: 5 5 5 5 1 5 5 5 5 5 ... $ Subregion : Factor w/ 47 levels AU-BF,AU-BK,..: 16 16 46 16 8 16 46 28 46 46 ... $ Rock_U_Nam : Factor w/ 607 levels Adler Hill Basalt,..: 33 33 33 33 173 33 33 585 112 112 ... $ Rock_Name : Factor w/ 32 levels ALLUVIUM,ARENITE,..: 13 13 13 13 25 13 13 10 23 23 ... $ Elevation : num 317 230 180 317 107 ... $ Slope : num 35.5 44.7 39.1 43.5 23 ... $ Aspect : num 25.3 3.68 30.83 4.02 254.66 ... $ Hillshade : int 182 211 167 212 200 218 216 245 214 27 ... $ Stream_dist: num 4241 4288 4330 4252 2160 ... $ Coast_dist : num 39497 39128 38883 39312 5601 ... $ Coast_SE : num 404751 404821 404468 404680 28426 ... $ Coast_E: int 78000 77500 77250 77750 15550 78250 77000 55650 77000 76800 ... $ Wind_310 : int 10 10 10 10 10 10 10 10 2 10 ... $ TPI: num -122.6 -109 -95.9 -94.7 -76.6 ... $ Landform : int 1 1 1 1 1 1 1 1 1 1 ... Date File Attachment (200 rows): http://r.789695.n4.nabble.com/file/n4636105/20120709_JLittle_data_file.txt 20120709_JLittle_data_file.txt -- View this message in context: http://r.789695.n4.nabble.com/Package-MuMIn-dredge-Error-in-ret-cbind-x-se-rep-if-is-null-df-NA-real-else-df-number-of-items-to-re-tp4636105.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package 'MASS' (polr): Error in svd(X) : infinite or missing values in 'x'
Dear Jessica thank you for the scale solution to my problem. I tried to manually scale my data (scaling up and removing decimals), however, this resulted in the same error message. It remains vague to me what the precise meaning of... the model matrix should be sensibly scaled with all columns having range the order of one …actually means. Regardless, the script you have supplied works for my data and looks (at this point) like a suitable solution. Many many thanks for your time in resolving this issue. Dear Rune, thank you for your valuable input. I used the package 'ordinal' originally for this ordinal logistic regression and this package was straight forward and worked fine without any errors. However, I switched to using 'MASS', as I need to run these models through an additional package 'AICcmodavg', which requires the 'MASS' inputs. Hence, I have needed the models to work in 'MASS'. The str(Jdata) call gives the following: str(Jdata) 'data.frame': 552270 obs. of 17 variables: $ POINTID: int 582358 582360 582361 582359 35289 582357 582362 411225 584336 584493 ... $ Lat_Y_pos : num 19.7 19.7 19.7 19.7 16 ... $ JVeg5 : Factor w/ 5 levels 1RF,2WSFEG,..: 5 5 5 5 1 5 5 5 5 5 ... $ Subregion : Factor w/ 47 levels AU-BF,AU-BK,..: 16 16 46 16 8 16 46 28 46 46 ... $ Rock_U_Nam : Factor w/ 607 levels Adler Hill Basalt,..: 33 33 33 33 173 33 33 585 112 112 ... $ Rock_Name : Factor w/ 32 levels ALLUVIUM,ARENITE,..: 13 13 13 13 25 13 13 10 23 23 ... $ Elevation : num 317 230 180 317 107 ... $ Slope : num 35.5 44.7 39.1 43.5 23 ... $ Aspect : num 25.3 3.68 30.83 4.02 254.66 ... $ Hillshade : int 182 211 167 212 200 218 216 245 214 27 ... $ Stream_dist: num 4241 4288 4330 4252 2160 ... $ Coast_dist : num 39497 39128 38883 39312 5601 ... $ Coast_SE : num 404751 404821 404468 404680 28426 ... $ Coast_E: int 78000 77500 77250 77750 15550 78250 77000 55650 77000 76800 ... $ Wind_310 : int 10 10 10 10 10 10 10 10 2 10 ... $ TPI: num -122.6 -109 -95.9 -94.7 -76.6 ... $ Landform : int 1 1 1 1 1 1 1 1 1 1 ... Does this provide any insight? Thank you ## Thank you both for your generous time and support, it is greatly appreciated. kind regards Jeremy -- View this message in context: http://r.789695.n4.nabble.com/Package-MASS-polr-Error-in-svd-X-infinite-or-missing-values-in-x-tp4635829p4636091.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package 'MASS' (polr): Error in svd(X) : infinite or missing values in 'x'
Thanks Jessi, your insights are extremely helpful. If you would indulge me one more quick question on your script. You have written... newData-data.frame(JVeg5=factor(Jdata[,JVeg5]),scale(Jdata[,c(Elevation,Lat_Y_pos,Coast_dist,Stream_dist)])) I wish to expand this analysis for all other variables in my data matrix, of which one is a factor (and therefore cannot be 'scaled'). Adding these variables to your script... newData-data.frame(JVeg5=factor(Jdata[,JVeg5]),scale(Jdata[,c(Elevation, Slope, Aspect, Hillshade, Lat_Y_pos, Coast_dist, Coast_SE, Coast_E, Wind_310, Stream_dist, TPI, Landform, Rock_Name)])) ...returns the error: Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric because Rock_Name must be numeric to be scaled. I've tried a couple of options for incorporating this factor (Rock_Name) into the script without success. For example: newData-data.frame(JVeg5=factor(Jdata[,JVeg5], Rock_Name=factor(Jdata[,Rock_Name]), scale(Jdata[,c(Elevation, Slope, Aspect, Hillshade, Lat_Y_pos, Coast_dist, Coast_SE, Coast_E, Wind_310, Stream_dist, TPI, Landform)])) Do you have a suggestion which might work for this analysis? Thank you for your support with this, I really appreciate it. kind regards -- View this message in context: http://r.789695.n4.nabble.com/Package-MASS-polr-Error-in-svd-X-infinite-or-missing-values-in-x-tp4635829p4636244.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Package 'MASS' (polr): Error in svd(X) : infinite or missing values in 'x'
Hello, I am trying to run an ordinal logistic regression (polr) using the package 'MASS'. I have successfully run other regression classes (glm, multinom) without much problem, but with the 'polr' class I get the following error: Error in svd(X) : infinite or missing values in 'x' which appears when I run the summary command. The data file is large (585000 rows) and has no NA, - or blank values. My script (in brief) is as follows, with results: library(MASS) ## ADD DATA Jdata- read.delim(/Analysis/20120709 JLittle data file.txt, header=T) attach(Jdata) names(Jdata) [1] POINTID Lat_Y_pos JVeg5 Subregion Rock_U_Nam Rock_Name Elevation Slope Aspect Hillshade Stream_dist Coast_dist Coast_SE [14] Coast_E Wind_310TPI Landform Global - polr(JVeg5 ~ Elevation + Lat_Y_pos + Coast_dist + Stream_dist, data=Jdata) summary(Global) Error in svd(X) : infinite or missing values in 'x' ##Try with omit NA command Global - polr(JVeg5 ~ Elevation + Lat_Y_pos + Coast_dist + Stream_dist, data=Jdata, na.action = na.omit, Hess = TRUE) summary(Global) Error in svd(X) : infinite or missing values in 'x' Does this imply an 'infinite value' and what would this mean? If anyone has any idea how to address this error, I would very much appreciate your response. Thank you in advance. Jeremy Date File Attachment (200 rows): http://r.789695.n4.nabble.com/file/n4635829/20120709_JLittle_data_file.txt 20120709_JLittle_data_file.txt -- View this message in context: http://r.789695.n4.nabble.com/Package-MASS-polr-Error-in-svd-X-infinite-or-missing-values-in-x-tp4635829.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package 'MASS' (polr): Error in svd(X) : infinite or missing values in 'x'
Hi Jessica, thank you for your prompt response. Yes I had deduced it had to do with the Hessian. However, I am not clear what all columns having range the order of one actually means and what this means for my data. Does this mean removing decimals (ie by shifting the decimal place)? I would have thought that the data matrix was already sensibly scaled. Any further insight greatly appreciated. Regards -- View this message in context: http://r.789695.n4.nabble.com/Package-MASS-polr-Error-in-svd-X-infinite-or-missing-values-in-x-tp4635829p4635928.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
