Hello!
I am having an issue running Amelia to impute missing
dichotomous variables (listed under "ords" below). My data set has n=2628 and 69 variables with
missing data. For about half of the variables, the missingness is less
than 20%. For the other half of the variables, the missingness is
between 30% and 40%. I have updated R & Amelia on my Mac: R 2.11.0
and Amelia 1.2-17.
This is the code I'm running:
az.out<-amelia(x=dat, m=5, p2s=2,ords=c("recid","gender","bin_race","pf2_1","pf2_7","pf3_1","pf3_4","pf3_6","pf4_5","pf4_16","pf5_1","pf5_10","r2_2","r2_3","r2_4","r2_5","r2_8","r3_2","r3_3","r4_1","r4_3","r4_9","r4_10","r4_12","r4_14","r4_15","r5_2","r5_3","r5_4","r5_6","r5_7","r5_8","r6_1","r6_2","r6_3","r6_4","ipf2_1","ipf2_7","ipf3_1","ipf3_4","ipf3_6","ipf4_5","ipf4_16","ipf5_1","ipf5_10","ir2_2","ir2_3","ir2_4","ir2_5","ir2_8","ir3_2","ir3_3","ir4_1","ir4_3","ir4_9","ir4_10","ir4_12","ir4_14","ir4_15","ir5_2","ir5_3","ir5_4","ir5_6","ir5_7","ir5_8","ir6_1","ir6_2","ir6_3","ir6_4"),
idvars=c("recidcount"))
And this is the error it results in:
amelia starting
beginning prep functions
Variables
used: recid age gender bin_race pf2_1 pf2_7 pf3_1 pf3_4 pf3_6 pf4_5
pf4_16 pf5_1 pf5_10 r2_2 r2_3 r2_4 r2_5 r2_8 r3_2 r3_3 r4_1 r4_3 r4_9
r4_10 r4_12 r4_14 r4_15 r5_2 r5_3 r5_4 r5_6 r5_7 r5_8 r6_1 r6_2 r6_3
r6_4 ipf2_1 ipf2_7 ipf3_1 ipf3_4 ipf3_6 ipf4_5 ipf4_16 ipf5_1 ipf5_10
ir2_2 ir2_3 ir2_4 ir2_5 ir2_8 ir3_2 ir3_3 ir4_1 ir4_3 ir4_9 ir4_10
ir4_12 ir4_14 ir4_15 ir5_2 ir5_3 ir5_4 ir5_6 ir5_7 ir5_8 ir6_1 ir6_2
ir6_3 ir6_4
running bootstrap
-- Imputation 1 --
setting up EM chain indicies
1Error in eigen(thetanew[2:nrow(thetanew), 2:ncol(thetanew)], only.values = TRUE, :
infinite or missing values in 'x'
I
was concerned about collinearity, so I calculated the VIFs and removed
the variables with high VIFs. Now all the variables have VIF < 10.
I've also tried a ridge prior of up to 300 to account for the high
missingness rate. I've looked in the listserv archives and of course
"googled" my error as well.
Any guidance on what might be causing this error would be appreciated. Thank you!
Wendy Nuzzo
soon-to-be M.S. Stat
Portland State University
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Good Afternoon,
My name is Mitzi Lewis and I'm working with Amelia for the first time to
help deal with missing data for my dissertation. I've been able to use
Amelia to get the five imputed files, outdata_. However, I'm running into
problems pooling the results of subsequent regression analysis run on each
of these files. Some of the results can be manually pooled, but not all (at
least I don't know how to do it; e.g., calculating a pooled p value for 5
Wald statistics or pooled confidence intervals for odds ratios). When I
called a research and statistical support center at my university, it was
suggested that all I need to do is run the statistical analysis on the last
of the imputed files (outdata5 in this case) as each of the imputed data
files holds increasingly better imputed data. Is this correct? If so, is
there some sort of documentation I could cite to support this decision? The
information I've found (before making this call) has centered around how to
pool the data. My next step was going to be exploring Zelig, but if the last
imputed file from Amelia would be appropriate for analysis, that would save
some time (and I'm pressed for time on this particular project).
Thanks so much for any guidance you can provide.
Mitzi
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Hi, perhaps I'm doing something wrong, but ask=FALSE doesn't seem to
stop the ask in plot.amelia. Example call:
png(file =
paste("/home/james/repos/bdp/doc/images/",fname,"_a_withbounds_%03d.png",sep=""),
width=1200, height=850, bg="transparent")
plot(df.amelia,ask=FALSE)
dev.off()
I always see:
Hit <Return> to see next plot:
Regards,
James Marca
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