I have a dataframe with columns Time_points_secs, Treatment and Pellet.
I want to test for normality before running statistics and then produce a line graph. I am creating a function so that i can repeat the same code for other columns within the dataframe (e.g. Pellet_count, etc.).
My function is:
line_graph<-function(var){
Normality<- df %>%
group_by(Treatment, Time_point_secs) %>%
filter(n_distinct(.data[[var]]) > 1) %>%
shapiro_test(.data[[var]]) #rstatix package
return(Normality)
}
line_graph("Pellet")
But i get an error saying:
Error in `mutate()`:
ℹ In argument: `data = map(.data$data, .f, ...)`.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `select()`:
! Can't subset columns that don't exist.
✖ Column `.data[["Pellet"]]` doesn't exist.
I've tried [[var]],{{var}} but neither works.
Embracing ({{var}}) should work without any issues, though you might have called the function with a character vector as in your example (line_graph("Pellet")) instead of using unquoted data-variable (line_graph(Pellet)).
And shapiro_test(.data[[var]]) fails as it expects "/../ One or more unquoted expressions (or variable names) separated by commas /../" for ..., but shapiro_test(.data[[var]]) apparently gets parsed as shapiro_test(vars = '.data[[var]]').
So either use embrace and pass the argument without quotes or adjust shapiro_test() to use vars parameter:
library(rstatix)
library(dplyr)
# use env-variable, call with character vector: f_envvar("var")
f_envvar<-function(var){
mtcars %>%
group_by(am, gear) %>%
filter(n_distinct(.data[[var]]) > 1) %>%
shapiro_test(vars = var) #rstatix package
}
# use data-variable, call with unquoted promise: f_embrace(var)
f_embrace<-function(var){
mtcars %>%
group_by(am, gear) %>%
filter(n_distinct({{var}}) > 1) %>%
shapiro_test({{var}}) #rstatix package
}
norm_envvar <- f_envvar("vs")
norm_embrce <- f_embrace(vs)
norm_envvar
#> # A tibble: 3 × 5
#> am gear variable statistic p
#> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 0 3 vs 0.499 0.00000348
#> 2 1 4 vs 0.566 0.0000632
#> 3 1 5 vs 0.552 0.000131
# check if identical:
identical(norm_envvar, norm_embrce)
#> [1] TRUE
tibble(mtcars)
#> # A tibble: 32 × 11
#> mpg cyl disp hp drat wt qsec vs am gear carb
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 21 6 160 110 3.9 2.62 16.5 0 1 4 4
#> 2 21 6 160 110 3.9 2.88 17.0 0 1 4 4
#> 3 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1
# ...
#> # ℹ 22 more rows
Backtrace for original approach with shapiro_test(.data[[var]]):
line_graph<-function(var){
Normality<- mtcars %>%
group_by(am, gear) %>%
filter(n_distinct(.data[[var]]) > 1) %>%
shapiro_test(.data[[var]]) #rstatix package
return(Normality)
}
line_graph("vs")
#> Error in `mutate()`:
#> ℹ In argument: `data = map(.data$data, .f, ...)`.
#> Caused by error in `map()`:
#> ℹ In index: 1.
#> Caused by error in `select()`:
#> ! Can't subset columns that don't exist.
#> ✖ Column `.data[["vs"]]` doesn't exist.
#> Backtrace:
#> ▆
#> 1. ├─global line_graph("vs")
#> 2. │ └─... %>% shapiro_test(.data[[var]])
#> 3. ├─rstatix::shapiro_test(., .data[[var]])
#> 4. │ └─data %>% doo(shapiro_test, ..., vars = vars)
#> 5. ├─rstatix::doo(., shapiro_test, ..., vars = vars)
#> 6. │ └─... %>% mutate(data = map(.data$data, .f, ...))
#> 7. ├─dplyr::mutate(., data = map(.data$data, .f, ...))
#> 8. ├─dplyr:::mutate.data.frame(., data = map(.data$data, .f, ...))
#> 9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
#> 10. │ ├─base::withCallingHandlers(...)
#> 11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
#> 12. │ └─mask$eval_all_mutate(quo)
#> 13. │ └─dplyr (local) eval()
#> 14. ├─purrr::map(.data$data, .f, ...)
#> 15. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 16. │ ├─purrr:::with_indexed_errors(...)
#> 17. │ │ └─base::withCallingHandlers(...)
#> 18. │ ├─purrr:::call_with_cleanup(...)
#> 19. │ └─rstatix (local) .f(.x[[i]], ...)
#> 20. │ └─data %>% select(!!!syms(vars))
#> 21. ├─dplyr::select(., !!!syms(vars))
#> 22. ├─dplyr:::select.data.frame(., !!!syms(vars))
#> 23. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
#> 24. │ └─tidyselect:::eval_select_impl(...)
#> 25. │ ├─tidyselect:::with_subscript_errors(...)
#> 26. │ │ └─rlang::try_fetch(...)
#> 27. │ │ └─base::withCallingHandlers(...)
#> 28. │ └─tidyselect:::vars_select_eval(...)
#> 29. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
#> 30. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
#> 31. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
#> 32. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
#> 33. │ └─tidyselect:::as_indices_sel_impl(...)
#> 34. │ └─tidyselect:::as_indices_impl(...)
#> 35. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
#> 36. │ └─vctrs::vec_as_location(...)
#> 37. └─vctrs (local) `<fn>`()
#> 38. └─vctrs:::stop_subscript_oob(...)
#> 39. └─vctrs:::stop_subscript(...)
#> 40. └─rlang::abort(...)
Created on 2023-06-27 with reprex v2.0.2