Imputation files not found

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amarkovitz
Posts: 7
Joined: Mon Aug 22, 2016 10:19 pm

Imputation files not found

Post by amarkovitz » Mon Aug 22, 2016 10:33 pm

Hello,

I ran what appeared to be a successful imputation procedure, but when I type realcomImputeLoad in stata, I am getting the following error:

file imputeiter100. not found

If it's helpful to diagnose this error, here is my model in stata:
realcomImpute bmi bmixsplinea1 bmixsplinea2 bmixsplinea3 bmixsplinea4 bmixsplinea5 bmiat18 ///
splinea1 splinea2 splinea3 splinea4 splinea5 parous HDL ///
parousxsplinea1 parousxsplinea2 parousxsplinea3 parousxsplinea4 parousxsplinea5 ///
post_preg_ind post_time h3 ses ///
using TestMIInput.dat, replace numresponses(7) ///
level2id(pid) cons(cons)

When I ran the MCMC, I obtained the attached log and it saved the attached impvals.txt file. It also created a storedata.mat file which as far as I can tell doesn't contain anything in it. Was there some issue in creating the imputed datasets? How were they supposed to be stored? As far as I can tell, the documentation doesn't get into this level of detail.

Thank you,
Amanda
Attachments
impvals.PNG
impvals.PNG (51.9 KiB) Viewed 1820 times
Imputation log.PNG
Imputation log.PNG (63.9 KiB) Viewed 1820 times

ChrisCharlton
Posts: 1090
Joined: Mon Oct 19, 2009 10:34 am

Re: Imputation files not found

Post by ChrisCharlton » Mon Aug 22, 2016 11:04 pm

When you run the imputation Realcom-Impute should save a file containing the imputed responses for each chosen imputation. The names of these files should correspond with the text in the fourth line of the impvals.txt file and should be in the same directory as this file. The storedata.mat file should contain the state of the software when you last used it, in theory allowing you to carry on from that point at a later date, this is not however used by external software. If the imputeiter* files are missing then it may that these was an estimation problem. The output that you posted seems to contain a lot of zeros, so it might be worth looking at the earlier output to see whether there were any further messages from when it was running the MCMC chains. It may also be worth checking the MCMC trajectories to ensure that they look okay.

amarkovitz
Posts: 7
Joined: Mon Aug 22, 2016 10:19 pm

Re: Imputation files not found

Post by amarkovitz » Tue Aug 23, 2016 1:56 pm

Hello Chris,

Thank you for the fast reply. It does seem like there might have been estimation problems, although I did not see anything in the log to indicate this. When I click "view results" I do get error messages (attached). I did monitor one of the MCMC trajectories while it was running, but could not find anywhere in the documentation that explained what to look for in these trajectories. I've attached an example of one. Is there other documentation I could use to learn more about how to evaluate these trajectories?

I've tried many different versions of this model with different predictor variables and haven't yet been able to sucessfully run it without some type of error. Are there any tips for getting the model to fit? I'm predicting a level 2 variable (BMI at age 18) and I have values for BMI at other ages, as well as other variables that will end up in my final model. There are some missing values for BMI at other ages, although not many, so I included them as response variables.

Thank you,
Amanda
Attachments
MCMC trajectory.jpg
MCMC trajectory.jpg (24.06 KiB) Viewed 1816 times
Imputation log view results.PNG
Imputation log view results.PNG (86.3 KiB) Viewed 1816 times

ChrisCharlton
Posts: 1090
Joined: Mon Oct 19, 2009 10:34 am

Re: Imputation files not found

Post by ChrisCharlton » Tue Aug 23, 2016 3:35 pm

It looks like something definitely is going wrong there, you shouldn't get any error messages while estimating and the value of the beta you are monitoring is staying extremely close to zero. I would suggest that you initially check the files that have been output from Stata for use in Realcom-Impute to ensure that they match what you expect from your data. I would also suggest checking that the value used to correspond to "missing" within these files matches that specified within Realcom-Impute before you start the iterations. For general advice on MCMC and interpreting the chains see the first chapter of the MLwiN MCMC guide (http://www.bris.ac.uk/cmm/media/softwar ... mc-web.pdf)

amarkovitz
Posts: 7
Joined: Mon Aug 22, 2016 10:19 pm

Re: Imputation files not found

Post by amarkovitz » Tue Aug 23, 2016 6:48 pm

Hello Chris,

Thank you for that information, that will be very helpful. In an effort to try to figure out what might be going wrong, I tried to simplify the problem. I ran MI again with just two variables, BMI at age 18 which is missing for about 44% of people and current BMI which I made sure was not missing for anyone. I am now getting an immediate error upon running the MCMC despite confirming that the missing value was set to 9999 in the dataset and in REALCOM. I also tried it with a few other non-missing predictors in the model as well. I feel like there must be something very basic that I'm missing, any suggestions are greatly appreciated!

Here is my stata code:
sort pid

replace bmiat18=9999 if missing(bmiat18)

drop if bmi==.

realcomImpute bmiat18 bmi ///
using TestMIInput2.dat, replace numresponses(1) ///
level2id(pid) cons(cons)
Attachments
Imputation.PNG
Imputation.PNG (42.19 KiB) Viewed 1810 times
Error in imputation.PNG
Error in imputation.PNG (53.6 KiB) Viewed 1810 times

ChrisCharlton
Posts: 1090
Joined: Mon Oct 19, 2009 10:34 am

Re: Imputation files not found

Post by ChrisCharlton » Tue Aug 23, 2016 7:49 pm

The interface for setting the missing value can sometimes be confusing. Can you confirm that you clicked the button labelled "set missing value to:" after typing in the new value, as I think that the error message you are getting is suggesting that it isn't seeing any missing data?

amarkovitz
Posts: 7
Joined: Mon Aug 22, 2016 10:19 pm

Re: Imputation files not found

Post by amarkovitz » Thu Aug 25, 2016 9:34 pm

Hello Chris,

Unfortunately, I did try that and received the same error. I've also tried a few different missing values (ex. STATA's default -9.999e+29, 9999, and 99999) and also have tried running the model with different response and auxiliary variables to see if was something wrong with the variables I'm using, but am having the same problem. Is there anything else you would suggest I try?

Thank you,
Amanda

ChrisCharlton
Posts: 1090
Joined: Mon Oct 19, 2009 10:34 am

Re: Imputation files not found

Post by ChrisCharlton » Thu Aug 25, 2016 10:28 pm

If you have access to MLwiN you could try working through the example in the Realcom-Impute manual (http://www.bris.ac.uk/media-library/sit ... tation.pdf) to see whether you get the same problems there. If not then if you are able to replicate the problem using a publicly available dataset then we can look into it further and see whether there is an undiscovered bug in the software.

amarkovitz
Posts: 7
Joined: Mon Aug 22, 2016 10:19 pm

Re: Imputation files not found

Post by amarkovitz » Wed Aug 31, 2016 1:57 pm

Hello Chris,

I tried to use a publicly available dataset and I did not receive the error about missing data, but it is having the estimation problem that I initially wrote about:
. realcomImputeLoad
file impvals.txt not found

Perhaps it just isn't a very good example and if so please let me know an example that should run (I tried having less missing data and it was still a problem). Here is the STATA code I used:

/*Use a publicly available multilevel STATA dataset*/
use http://www.stata-press.com/data/r12/productivity.dta

/*Create a level-2 (state-level) variable with missing data*/
/*Mean unemployment by state*/
by state, sort: egen meanunemp = mean(unemp)

/*Missing at random conditional on "public" variable*/
replace meanunemp=. if public>50000

/*Create dataset for REALCOM-Impute*/
gen cons = 1
sort state
cd "H:\HUNT\Datasets_intermediate" //Same folder that REALCOM-Impute starts in
realcomImpute meanunemp public gsp ///
using TestMIInput.dat, replace numresponses(1) ///
level2id(state) cons(cons)

realcomImputeLoad

Thank you,
Amanda
Attachments
Monitor Graphs.PNG
Monitor Graphs.PNG (27.26 KiB) Viewed 1797 times
REALCOM window.PNG
REALCOM window.PNG (48.91 KiB) Viewed 1797 times

ChrisCharlton
Posts: 1090
Joined: Mon Oct 19, 2009 10:34 am

Re: Imputation files not found

Post by ChrisCharlton » Wed Aug 31, 2016 3:25 pm

I just tried replicating your example and it seemed to work for me:

Code to set up imputation in Stata:

Code: Select all

. /*Use a publicly available multilevel STATA dataset*/
. use http://www.stata-press.com/data/r12/productivity.dta
(Public Capital Productivity)

. 
. /*Create a level-2 (state-level) variable with missing data*/
. /*Mean unemployment by state*/
. by state, sort: egen meanunemp = mean(unemp)

. 
. /*Missing at random conditional on "public" variable*/
. replace meanunemp=. if public>50000
(113 real changes made, 113 to missing)

. 
. /*Create dataset for REALCOM-Impute*/
. gen cons = 1

. sort state

. cd "O:\Realcom-stata" //Same folder that REALCOM-Impute starts in
O:\Realcom-stata

. realcomImpute meanunemp public gsp ///
> using TestMIInput.dat, replace numresponses(1) ///
> level2id(state) cons(cons)
1 responses: meanunemp
2 auxiliary variables: public gsp
(note: file TestMIInput.dat not found)
Data saved to TestMIInput.dat
(note: file TestMIInput_wts.dat not found)
Realcom-Impute output:

Code: Select all

User selected O:\Realcom-stata\TestMIInput.dat

c_nimpute =

     1


c_naux =

     4


c_vartype =

     1


ans =

     2


c_betaconstraint =

     0
     1


fid =

     3


Imputation_method =

     0


Multivariate estimation using Gibbs  and MH sampling - Normal/probit models

Independence assumed with standard probit model for unordered categories

 Nov 14 2006

Two-level responses version

NRTYPE =

     1


BETASTART =

     0
     0
     0


BETASTART_2 =

   Empty matrix: 1-by-0


SIGMASTART =

    1.3530


 Burn in =    100        Sample =   1000

       no level 1, level 2 units =    816,      48

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Error using save
Unable to write file storedata: permission denied.

Error in mcmcdriver (line 1192)



Error in gui_2levmixresp>pushbutton16_RunMCMC_Callback (line 264)



Error in gui_mainfcn (line 96)



Error in gui_2levmixresp (line 46)



Error in @(hObject,eventdata)gui_2levmixresp('pushbutton16_RunMCMC_Callback',hObject,eventdata,guidata(hObject))



Error while evaluating uicontrol Callback
Code to load imputed data into Stata:

Code: Select all

. realcomImputeLoad

10 multiple imputations successfully loaded

  Style:  wide
          last mi update 31aug2016 16:19:12, 0 seconds ago

  Obs.:   complete          703
          incomplete        113  (M = 10 imputations)
          ---------------------
          total             816

  Vars.:  imputed:  1; meanunemp(113)

          passive:  0

          regular:  0

          system:   1; _mi_miss

         (there are 12 unregistered variables)
Can you confirm that you are setting the output directory (via the Impute button in Realcom) to be the same as Stata is using?

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