multi-level imputation error #293

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1. stefvanbuuren commented on Dec 9, 2020

   

   stefvanbuuren

   on Dec 9, 2020

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   Sorry I can't do magic. Please provide a reproducible example in a really simplified case.
2. bryorsnef commented on Dec 9, 2020

   

   bryorsnef

   on Dec 9, 2020

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   Appologies for not posting right away with an example - I was hoping this was a known issue or if I broke something obvious. I'm waiting for confirmation from a collaborator that I can share the original data, because I'm having issues reproducing the issue on my own.
3. gerkovink commented on Dec 9, 2020

   

   gerkovink

   on Dec 9, 2020

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   There is a pipe symbol | in your code. I believe the language interpreter reads this as a conditional and expects some input, but instead finds a closing parenthesis ). I believe your error will disappear if you adjust the following part in your code:

   (1+subid+itemid|)

   All the best,

   Gerko
4. gerkovink commented on Dec 9, 2020

   

   gerkovink

   on Dec 9, 2020

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   I can't even reprex your error because the above code breaks the reprex()

   > reprex()
   Rendering reprex...
   Error: callr subprocess failed: <text>:24:43: unexpected ')'
   23: imp <- mice(boys, m = 3, maxit = 2) # proof of concept
   24: with(imp, lmer(age ~ hgt + (1 + bmi + tv |)
                                                 ^
   Type .Last.error.trace to see where the error occured

   But in mice the following code also breaks, which proves my point.

   > imp <- mice(boys, m = 3, maxit = 2) # proof of concept
   
    iter imp variable
     1   1  hgt  wgt  bmi  hc  gen  phb  tv  reg
     1   2  hgt  wgt  bmi  hc  gen  phb  tv  reg
     1   3  hgt  wgt  bmi  hc  gen  phb  tv  reg
     2   1  hgt  wgt  bmi  hc  gen  phb  tv  reg
     2   2  hgt  wgt  bmi  hc  gen  phb  tv  reg
     2   3  hgt  wgt  bmi  hc  gen  phb  tv  reg
   > with(imp, lmer(age ~ hgt + (1 + bmi + tv|)))
   Error: unexpected ')' in "with(imp, lmer(age ~ hgt + (1 + bmi + tv|)"
5. bryorsnef commented on Dec 9, 2020

   

   bryorsnef

   on Dec 9, 2020

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   Thanks for the help. The error isn't happening in the analysis step though, it's happening when I call mice() to do the imputation step. I don't explicitly state an lmer formula anywhere. I've been searching around for any resources on multi-level imputation in mice or other packages or functions to use. I see the mice.impute.ml.lmer in miceadds, but I'm having a hell of a time getting that set up. I'd like to stick to an FCS approach because the analyses I want to do eventually involve random slopes, so joint modelling seems less appealing. But finding clear guidance with good documentation hasn't been easy. Any suggestions on good tutorials or resources for multi-level imputation would be helpful.
6. stefvanbuuren commented on Dec 10, 2020

   

   stefvanbuuren

   on Dec 10, 2020

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   @gerkovink Thanks, R expects a variable name after |. It does not make sense to leave it empty. @bryorsnef did you already try specify your class variable?
7. gerkovink commented on Dec 15, 2020

   

   gerkovink

   on Dec 15, 2020

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   finding clear guidance with good documentation hasn't been easy. Any suggestions on good tutorials or resources for multi-level imputation would be helpful.

   Have a look at the Multilevel Imputation Vignette

   Can't help you any further without a proper reprex since the error seems to be dependent on your imputation specification.

   All the best,

   Gerko
8. gerkovink commented on Dec 23, 2020

   

   gerkovink

   on Dec 23, 2020

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   Closing as the issue is not reproducible.
9. gerkovink

   closed this as completedon Dec 23, 2020
10. amices

    locked and limited conversation to collaborators on Apr 1, 2021