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I am teaching myself to use tidyverse more, as I'm hoping to be able to make cleaner code in the future.

I have data that looks like this:

data <- as_tibble(data.frame(x = c(1,2,3,3,4),
          y = c(3,4,4,2,5),
          z = c(1,1,5,5,3)))

And I would like to get the mean, sd, and confidence intervals for all 3 columns.

The code I am hoping to use is this:

data %>%
summarize_at(vars(x:z), list(mean=mean, sd=sd, cilow = ci[2], cihigh = ci[3]))

where the ci() function is from the gmodels package. When passing a single variable through ci, you can pick which output column to view, but when it's part of a list of functions, I get the error

Error in ci[2] : object of type 'closure' is not subsettable

Any advice/suggestions are appreciated! I am trying not to manually calculate all the CIs (my actual data has many more variables to calculate)

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1 Answer 1

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We can use lambda function. In addition, _at/_all are deprecated in favor of across

library(dplyr)
library(gmodels)
data %>% 
   summarise(across(x:z, list(mean = ~ mean(.x, na.rm = TRUE),
      sd = ~ sd(.x, na.rm = TRUE), 
    cilow = ~ ci(.x)[2], cihigh = ~ ci(.x)[3])))

-output

# A tibble: 1 × 12
  x_mean  x_sd x_cilow x_cihigh y_mean  y_sd y_cilow y_cihigh z_mean  z_sd z_cilow z_cihigh
   <dbl> <dbl>   <dbl>    <dbl>  <dbl> <dbl>   <dbl>    <dbl>  <dbl> <dbl>   <dbl>    <dbl>
1    2.6  1.14    1.18     4.02    3.6  1.14    2.18     5.02      3     2   0.517     5.48

Or with summarise_at

data %>%
 summarize_at(vars(x:z), list(mean=mean, sd=sd, cilow = ~ ci(.)[2], cihigh = ~ ci(.x)[3]))
# A tibble: 1 × 12
  x_mean y_mean z_mean  x_sd  y_sd  z_sd x_cilow y_cilow z_cilow x_cihigh y_cihigh z_cihigh
   <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl>   <dbl>   <dbl>   <dbl>    <dbl>    <dbl>    <dbl>
1    2.6    3.6      3  1.14  1.14     2    1.18    2.18   0.517     4.02     5.02     5.48
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10 Comments

with summarize across I was getting the error Error in dots[[.index]] : subscript out of bounds but keeping with summarize_at, it worked!
@GabrielleMacklin please check your packageVersion('dplyr'). If it is an old version, across maynot work
It's the most recent version
@GabrielleMacklin i used 1.0.8 and it didn't show an error though
@GabrielleMacklin i wouldn't install tidyverse package as the dependencies may have broken. I always install individual packages
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