Bug or intended operation of 'make_all_intermediate_trans' in ADNIMERGE in R?

[Dave Evenden]

Hi - I am trying to develop a reasonable understanding of the data manipulations in ADNIMERGE, as described in the 'Progressions' PDF, copied at the link here http://adni.bitbucket.org/Progression.html

Hopefully the following is due to my poor understanding of something, but any clarifications welcome.....

I was (and am) confused by the output object 'dd_all_int_final_3', which sometimes results in constant (and therefore overlapping) start times for different transitions, rather than what I might have expected of one transition per start/stop time period. This can be seen by inspection of 'dd_all_int_final_3' (or 'dd3'), where the same start time occurs more than once....

  id start  stop start.stage end.stage

1  2  6.03  7.05           1         3

2  2  6.03  8.00           3         1

3  2  6.03 10.04           1         0

or a more complex and perhaps better example:

     id start  stop start.stage end.stage

98  112  0.00 0.482           3         1

99  112  0.00 1.016           1         3

100 112  1.49 1.990           3         1

101 112  3.99 4.969           1         3

102 112  3.99 5.960           3         1

103 112  3.99 6.976           1         3

104 112  7.98 9.292           3         0

I attempted to 'fix' this to exemplify what I was expecting. 

The function call 'make_all_intermediate_trans' makes use of 'myFunctions.R' (part of the package download). My attempted exploratory fix is shown bold below (along with some of my added comments, and a wee bit formatting for clarity)....

  ...     

        if(subdd$stage[j] != start.stage){  ## if not same stage

          dd2 <- rbind(dd2, c(id = rid, 

                              start = start, 

                              stop = subdd$Year[j], 

                              start.stage = start.stage, 

                              end.stage = subdd$stage[j]))

          start.stage <- subdd$stage[j]     ## reset stage datum

          start <- subdd$Year[j]            ## reset time datum - DEBUG??

        }else{     

          start <- subdd$Year[j]  

        }

  ...

For my previous second case, this gives a non-overlapping time slot sequence, as shown below.

     id start  stop start.stage end.stage

98  112 0.000 0.482           3         1

99  112 0.482 1.016           1         3

100 112 1.489 1.990           3         1

101 112 3.989 4.969           1         3

102 112 4.969 5.960           3         1

103 112 5.960 6.976           1         3

104 112 7.975 9.292           3         0

Does this have any merit??

Please feel free to let me know if I have inadvertently missed any essential information needed to satisfactorily progress any discussion.

Regards and thanks,

Dave 

[Mike Donohue]

Hi Dave -

Thanks for pointing this out. I've added your fix to the package.

Thanks,

Mike