Plotting lmer results and getting contrasts

Support Beginner Support
1

Dear all,

I just started using DataSHIELD. The purpose is to evaluate the possibility to use DataSHIELD in our upcoming medical research. Do do so I am trying to do a linear mixed model analysis.

My code looks like this:

tryCatch(
  {
    m1 <- ds.lmerSLMA(
      formula = "Var1 ~ Time * Group + (1|ID)",
      data = "D_Supine",
      datasources = conns,
      newobj = "m1"
    )
  }, error = function(e) {
    print(e)
    print(datashield.errorMessages())
  }
)

My questions:

  1. Are there any good tutorials on doing lmer analysis with DataSHIELD?
  2. How could I calculate contrasts etc using the object DataSHIELD returns?

Thanks for any help and ideas.

Best, Jonathan

2

Hi Jonathan,

Here is a tutorial I delivered on mixed effects models:

Could you give me an example of the contrasts you are looking to do, and I can have a think whether/how it is possible?

Cheers, Tim

3

Here is the markdown file:

4

Hey Tim,

thank you for the excellent video and the work you put into dsHelper!

I get it to work when my Month and Group variable are continues, but not when they are factors. It works when I run my “normal R code“ using lme4 Any tips for that?

My “preferred code“ look something like this. If the factors Months and Groups are continues they work fine.

tryCatch(
  {
    m1 <- ds.lmerSLMA(
      formula = "cont_var ~ factor_1 (Months) * factor_2 (Group) + (1|ID)",
      data = "D_Supine",
      datasources = conns,
      newobj = "m1"
    )
    m1$output.summary
  }, error = function(e) {
    print(e)
    print(datashield.errorMessages())
  }
)

Thank you.

5

Hi Jonathan, what error message do you get?

6

Hej again,

I created a markdown file and a fake dataset.

Both can be found here: Github Page

The error I get says:

Error in `select()`:
ℹ In argument: `all_of(coef_names)`.
Caused by error in `all_of()`:
! Can't subset elements that don't exist.
✖ Elements `MonthGroup12`, `MonthGroup24`, `MonthGroup3`, `MonthGroup48`, `MonthGroup6`, etc. don't exist.
Run `rlang::last_trace()` to see where the error occurred.
7

Hi Jonathan,

I tried your example and it works fine for me without any errors. The only thing I changed was the uploading of the data as a .csv file instead of .rds, but I don’t think this is the reason of the error.

Do you want to join our next drop-in session on Wednesday at 10am CET (Launch Meeting - Zoom) to have a look together?

Thanks,

Demetris

8

Hej Demetris, thank you for your reply. Currently I am trying to get my Docker Environment up and running again (on a ARM Mac) after my old computer resigned. As soon as it works I will join one of the meetings.