fisher.test() not compatible with D2()

[stefvanbuuren]

Function fisher.test() does not produce estimate and std.error components in the return value. D2() relies on pool(), and hence fails. Would be useful to have a work-around.

require(mice)
#> Loading required package: mice
#> 
#> Attaching package: 'mice'
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> The following objects are masked from 'package:base':
#> 
#>     cbind, rbind
data <- nhanes2
data$chl <- cut(data$chl, breaks = 2)
imp <- mice(data, print = FALSE)
fit <- with(imp, fisher.test(xtabs(~ hyp + chl)))
names(fit$analyses[[1]])
#> [1] "p.value"     "conf.int"    "estimate"    "null.value"  "alternative"
#> [6] "method"      "data.name"
D2(fit, fit0 = NULL, use = "wald")
#> Error in `summarize()`:
#> ! Problem while computing `ubar = mean(.data$std.error^2)`.
#> Caused by error in `.data$std.error`:
#> ! Column `std.error` not found in `.data`.

#> Backtrace:
#>      ▆
#>   1. ├─mice::D2(fit, fit0 = NULL, use = "wald")
#>   2. │ └─mice::pool(fit1)
#>   3. │   └─mice:::pool.fitlist(getfit(object), dfcom = dfcom, rule = rule)
#>   4. │     └─w %>% group_by(!!!syms(grp)) %>% ...
#>   5. ├─dplyr::summarize(...)
#>   6. ├─dplyr:::summarise.data.frame(...)
#>   7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), caller_env = caller_env())
#>   8. │   ├─base::withCallingHandlers(...)
#>   9. │   └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
#>  10. │     └─base::lapply(.x, .f, ...)
#>  11. │       └─dplyr (local) FUN(X[[i]], ...)
#>  12. │         └─mask$eval_all_summarise(quo)
#>  13. ├─base::mean(.data$std.error^2)
#>  14. ├─std.error
#>  15. ├─rlang:::`$.rlang_data_pronoun`(.data, std.error)
#>  16. │ └─rlang:::data_pronoun_get(...)
#>  17. └─rlang:::abort_data_pronoun(x, call = y)
#>  18.   └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)

^{Created on 2022-10-25 with reprex v2.0.2}