impvar parameter for pool_performance in psfmi package

[Haruharuka.H]

I am trying to use pool_performance to do calibration plot and also AUC for ROC for model performance in R.
I don't get impvar parameter in the function though the description says that Name of the variable that distinguishes the imputed datasets.
What does it mean? could you give me any example?

[technocrat]

Here is the example from help("pool_performance"). It gives "Impnr"as theimpvarargument. As you note, theargument` section for the function specifies it as

A character vector. Name of the variable that distinguishes the imputed datasets.

And that is a variable within the data argument. Using the example that is lbpmilr, which has as its variables

> colnames(lbpmilr)
 [1] "Impnr"         "ID"            "Chronic"       "Gender"       
 [5] "Carrying"      "Pain"          "Tampascale"    "Function"     
 [9] "Radiation"     "Age"           "Smoking"       "Satisfaction" 
[13] "JobControl"    "JobDemands"    "SocialSupport" "Duration"     
[17] "BMI" 

and the first is given as the impvar argument, which is typeof integer and contains unique values in the range 1:10. help("ibpmilr") describes the data set as 10 imputed data set and so it appears that Impnr` is an identifier relating each observation (row) to one of the imputed data sets identified by the integers 1:10.

library(psfmi)
perf <- pool_performance(
  data = lbpmilr, nimp = 5, impvar = "Impnr",
  formula = Chronic ~ Gender + Pain + Tampascale +
    Smoking + Function + Radiation + Age + factor(Carrying),
  cal.plot = TRUE, plot.method = "mean",
  groups_cal = 10, model_type = "binomial"
)

perf$ROC_pooled
#>                     95% Low C-statistic 95% Up
#> C-statistic (logit)  0.8005      0.8714 0.9197
perf$R2_pooled
#> [1] 0.5060599

^{Created on 2023-06-28 with reprex v2.0.2}

[Haruharuka.H]

Thank you for the answer! So what I have to do now is

1. add one column with Impnr for each imputed data set
   (for imputed_1 all impnr is 1, for imputed_2 all impnr is 2...etc)
2. put impnr in the parameter of impvar
3. do pool_performance

Is it correct?

Then I was wondering how I can do that in r...

[technocrat]

That's it. Might be easier just to add s column to each of the imputed datasets before combining them.