I was trying to use report of the R package report to get a report of the results of 2 Wilcoxon tests, one for each Session.
I can obtain the test results but not the text report.
I couldn't find any examples of using purr and report.
library(tidyverse)
library(report)
df <- tibble(Session = c(rep("1", 10), rep("2", 10)),
scores = sample(20:70, 20),
group = c(rep("before", 5), rep("after",5),
rep("before", 5), rep("after",5)))
# function to compute Wilcoxon test
w_test <- function(df) {
wilcox.test(scores ~ group, df, paired = TRUE)
}
# testing w_test function for Session 1
dfS1 <- df %>% filter(Session == "1")
w_test(dfS1)
#>
#> Wilcoxon signed rank exact test
#>
#> data: scores by group
#> V = 4, p-value = 0.4375
#> alternative hypothesis: true location shift is not equal to 0
# this does not work because I can't map wtest to report::report
w <- df %>%
group_by(Session) %>%
nest() %>%
mutate(wtest = map(data, w_test),
result = map(wtest, report))
#> Could not compute effectsize NA.
#> Possible reason: Unable to retrieve data from htest object.
#> Try using
#> 'rb()' directly.
#> Error in `mutate()`:
#> ℹ In argument: `result = map(wtest, report)`.
#> ℹ In group 1: `Session = "1"`.
#> Caused by error in `map()`:
#> ℹ In index: 1.
#> Caused by error in `abs()`:
#> ! non-numeric argument to mathematical function
#> Backtrace:
#> ▆
#> 1. ├─df %>% group_by(Session) %>% nest() %>% ...
#> 2. ├─dplyr::mutate(...)
#> 3. ├─dplyr:::mutate.data.frame(...)
#> 4. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
#> 5. │ ├─base::withCallingHandlers(...)
#> 6. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
#> 7. │ └─mask$eval_all_mutate(quo)
#> 8. │ └─dplyr (local) eval()
#> 9. ├─purrr::map(wtest, report)
#> 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 11. │ ├─purrr:::with_indexed_errors(...)
#> 12. │ │ └─base::withCallingHandlers(...)
#> 13. │ ├─purrr:::call_with_cleanup(...)
#> 14. │ ├─report (local) .f(.x[[i]], ...)
#> 15. │ └─report:::report.htest(.x[[i]], ...)
#> 16. │ ├─report::report_table(x, model_info = model_info, ...)
#> 17. │ └─report:::report_table.htest(x, model_info = model_info, ...)
#> 18. │ ├─base::do.call(report_effectsize, args)
#> 19. │ ├─report (local) `<fn>`(`<htest>`, model_info = `<named list>`)
#> 20. │ └─report:::report_effectsize.htest(`<htest>`, model_info = `<named list>`)
#> 21. │ └─report:::.report_effectsize_wilcox(x, table, dot_args)
#> 22. │ ├─base::do.call(effectsize::interpret_r, args)
#> 23. │ └─effectsize (local) `<fn>`(NULL)
#> 24. │ └─effectsize::interpret(abs(r), rules)
#> 25. └─base::.handleSimpleError(...)
#> 26. └─purrr (local) h(simpleError(msg, call))
#> 27. └─cli::cli_abort(...)
#> 28. └─rlang::abort(...)
w$report
#> Error in eval(expr, envir, enclos): object 'w' not found
Created on 2023-10-01 with reprex v2.0.2
To make report() work with htest object, you probably need to drop data argument from wilcox.test() and change the formula accordingly (relevant github issue):
library(tidyverse)
library(report)
df <- tibble(Session = c(rep("1", 10), rep("2", 10)),
scores = sample(20:70, 20),
group = c(rep("before", 5), rep("after",5),
rep("before", 5), rep("after",5)))
# using `data`, report() fails:
wilcox.test(scores ~ group, df, paired = TRUE) |> report()
#> Could not compute effectsize NA.
#> Possible reason: Unable to retrieve data from htest object.
#> Try using
#> 'rb()' directly.
#> Error in abs(r): non-numeric argument to mathematical function
# without `data`, referring to frame in formula:
wilcox.test(df$scores ~ df$group, paired = TRUE) |> report()
#> Effect sizes were labelled following Funder's (2019) recommendations.
#>
#> The Wilcoxon signed rank exact test testing the difference in ranks between
#> df$scores and df$group suggests that the effect is negative, statistically
#> significant, and very large (W = 8.00, p = 0.049; r (rank biserial) = -0.71,
#> 95% CI [-0.92, -0.18])
With changed function:
w_test <- function(df) {
wilcox.test(df$scores ~ df$group, paired = TRUE)
}
df %>%
group_by(Session) %>%
nest() %>%
mutate(wtest = map(data, w_test),
result = map(wtest, report))
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `wtest = map(data, w_test)`.
#> ℹ In group 2: `Session = "2"`.
#> Caused by warning in `wilcox.test.default()`:
#> ! cannot compute exact p-value with ties
#> # A tibble: 2 × 4
#> # Groups: Session [2]
#> Session data wtest result
#> <chr> <list> <list> <list>
#> 1 1 <tibble [10 × 2]> <htest> <report [1]>
#> 2 2 <tibble [10 × 2]> <htest> <report [1]>
Depending on what you need to be reported, you can also extract values directly from htest object or pass it through broom::tidy() instead of report().
Another alternative would be {rstatix}, it's designed to be "pipe-friendly" and works with grouped frames:
library(rstatix, warn.conflicts = FALSE)
df %>%
group_by(Session) %>%
wilcox_test(scores ~ group, paired = TRUE, detailed = TRUE)
#> # A tibble: 2 × 13
#> Session estimate .y. group1 group2 n1 n2 statistic p conf.low
#> * <chr> <dbl> <chr> <chr> <chr> <int> <int> <dbl> <dbl> <dbl>
#> 1 1 13 scores after before 5 5 13 0.188 -13
#> 2 2 25.0 scores after before 5 5 14 0.104 4.50
#> # ℹ 3 more variables: conf.high <dbl>, method <chr>, alternative <chr>
Created on 2023-10-01 with reprex v2.0.2