R help - Jul 2012 - 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, -9999 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_310"    "TPI"        
"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 


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Since its something about the Hessian, and occurs in the vcov() call, have you
thought about the note:

"The vcov method uses the approximate Hessian: for reliable results the
model matrix should be sensibly scaled with all columns having range the order
of one. "

?

I'm sorry i can't help you much further here, no idea about ordinal
logistic regression ;)

On 09.07.2012, at 11:55, Jeremy Little wrote:
> 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, -9999 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_310"    "TPI"       
"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.

	[[alternative HTML version deleted]]

Hi Jeremy,

newData<-data.frame(JVeg5=factor(Jdata[,"JVeg5"]),scale(Jdata[,c("Elevation","Lat_Y_pos","Coast_dist","Stream_dist")]))
Global <- polr(JVeg5 ~  Elevation +  Lat_Y_pos + Coast_dist + Stream_dist,
		data=newData, na.action = na.omit, Hess = TRUE)

summary(Global)

Does this still do what you want? At least it doesn't produce the error like
this.

greetings Jessi


On 09.07.2012, at 11:55, Jeremy Little wrote:
> 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, -9999 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_310"    "TPI"       
"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.

	[[alternative HTML version deleted]]

Hi Jeremy,

I think Jessica is right that probably you could make polr converge
and produce a Hessian if the data are better scaled, but there might
also be other things not allowing you to get the Hessian/vcov. Could
be insightful if you showed us the result of
str(Jdata)

Also, I am thinking that perhaps the another implementation of ordinal
regression models might avoid the problem. You could try the ordinal
package (of which I am the author) -- the following should reproduce
the MASS::polr results:

install.packages(ordinal)
library(ordinal)
Global <- clm(JVeg5 ~  Elevation +  Lat_Y_pos + Coast_dist +
Stream_dist, data=Jdata)
summary(Global)

Another option would be Frank Harrell's lrm function in the rms package.

HTH,
Rune

On 9 July 2012 11:55, Jeremy Little <jeremy.little at my.jcu.edu.au>
wrote:
> 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, -9999 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_310"    "TPI"       
"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 at 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.


-- 
Rune Haubo Bojesen Christensen

Ph.D. Student, M.Sc. Eng.
Phone: (+45) 45 25 33 63
Mobile: (+45) 30 26 45 54

DTU Informatics, Section for Statistics
Technical University of Denmark, Build. 305, Room 122,
DK-2800 Kgs. Lyngby, Denmark