Using dplyr to nest or group two variables, then perform the Cronbach's alpha function or other statistics to the data

Question

In psychology, this kind of dataset presented below is pretty common

I would like to group all age (variable = quest), than group all scales (com_a4_1:com_a4_6; and gm_a4_1:gm_a4_6, etc) and then apply a reliability function to the data (psych::alpha).

I successfully create this syntax

d %>% 
  select(quest,contains("_a4_")) %>% #get the data
  group_by(quest) %>%  #group by all age interval
  do(alpha(.)$total)

However, I'm not being able to "sub" nest using the scales' items.

As far as I imagine, I'll have to pivot my data and then group or nest. However, I'm not having any success at this point. My expected result is something similar to this image below. There are "two nested results". The first result is grouped with the scale (ex: com_a4_1:com_a4_6) and the second is grouped with the age (quest)

Fake data and codes are below

library(psych)
library(tidyverse)
d %>% 
  select(quest,contains("_a4_")) %>% #get the data
  group_by(quest) %>%  #group by all age interval
  do(alpha(.)$total)


d <-structure(list(quest = c(6, 4, 2, 4, 2, 6, 2, 4, 2, 2, 4, 2, 
                             6, 4, 4, 2, 2, 4, 2, 6, 2, 2, 4, 6, 6, 4, 4, 4, 2, 6, 4, 2, 6, 
                             4, 6, 2, 2, 4, 6, 4, 2), com_a4_1 = c(10, 0, 10, 10, 5, 10, 5, 
                                                                   10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 0, 10, 
                                                                   10, 10, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 
                                                                   10, 10), com_a4_2 = c(10, 10, 5, 10, 10, 5, 10, 10, 10, 10, 10, 
                                                                                         10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10, 5, 
                                                                                         10, 10, 10, 5, 0, 10, 10, 10, 10, 0, 10, 10, 10, 10), com_a4_3 = c(10, 
                                                                                                                                                            5, 0, 5, 10, 5, 5, 10, 10, 10, 10, 10, 5, 5, 10, 10, 5, 10, 10, 
                                                                                                                                                            10, 10, 5, 5, 10, 10, 5, 5, 10, 10, 10, 10, 5, 10, 10, 10, 10, 
                                                                                                                                                            0, 10, 5, 10, 10), com_a4_4 = c(10, 0, 0, 10, 5, 10, 10, 10, 
                                                                                                                                                                                            10, 5, 5, 10, 10, 5, 10, 10, 5, 10, 10, 10, 10, 5, 10, 10, 10, 
                                                                                                                                                                                            10, 0, 10, 5, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 10, 10), 
                   com_a4_5 = c(10, 0, 0, 5, 0, 10, 5, 10, 10, 5, 10, 10, 0, 
                                10, 10, 10, 0, 10, 5, 10, 0, 0, 10, 0, 10, 10, 10, 10, 5, 
                                0, 10, 5, 5, 10, 10, 10, 0, 10, 10, 10, 10), com_a4_6 = c(5, 
                                                                                          10, 0, 10, 10, 5, 10, 10, 10, 0, 10, 10, 5, 10, 10, 10, 10, 
                                                                                          10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 5, 10, 
                                                                                          5, 10, 5, 10, 0, 10, 5, 10, 10), gm_a4_1 = c(10, 10, 10, 
                                                                                                                                       10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                       10, 10, 10, 10, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                       10, 10, 10, 10, 10, 10, 10, 10), gm_a4_2 = c(10, 10, 10, 
                                                                                                                                                                                    10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 10, 10, 10, 
                                                                                                                                                                                    10, 10, 10, 10, 10, 10, 10, 5, 5, 10, 10, 10, 0, 10, 10, 
                                                                                                                                                                                    5, 10, 10, 5, 10, 10, 10, 10), gm_a4_3 = c(10, 10, 10, 10, 
                                                                                                                                                                                                                               10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                               10, 10, 10, 10, 10, 10, 0, 0, 10, 10, 10, 0, 10, 10, 10, 
                                                                                                                                                                                                                               10, 10, 5, 10, 10, 10, 10), gm_a4_4 = c(0, 5, 10, 10, 10, 
                                                                                                                                                                                                                                                                       10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 
                                                                                                                                                                                                                                                                       10, 10, 10, 10, 10, 0, 0, 10, 10, 10, 0, 10, 5, 5, 5, 10, 
                                                                                                                                                                                                                                                                       10, 10, 10, 10, 10), gm_a4_5 = c(10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                                        10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                                        10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 10, 5, 10, 
                                                                                                                                                                                                                                                                                                        5, 10, 10, 10, 10), gm_a4_6 = c(0, 10, 5, 5, 10, 5, 5, 10, 
                                                                                                                                                                                                                                                                                                                                        10, 5, 10, 10, 0, 10, 10, 10, 5, 10, 5, 10, 10, 10, 10, 0, 
                                                                                                                                                                                                                                                                                                                                        10, 10, 10, 10, 10, 0, 10, 10, 10, 10, 0, 10, 0, 10, 10, 
                                                                                                                                                                                                                                                                                                                                        10, 10), fm_a4_1 = c(10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                                                                                             10, 10, 10, 10, 10, 5, 10, 10, 10, 10, 5, 0, 10, 10, 0, 5, 
                                                                                                                                                                                                                                                                                                                                                             10, 10, 10, 10, 5, 5, 10, 10, 5, 5, 10, 10, 10, 10, 10), 
                   fm_a4_2 = c(10, 10, 10, 10, 0, 10, 10, 10, 10, 10, 10, 10, 
                               10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 10, 10, 10, 10, 5, 
                               10, 10, 5, 10, 10, 10, 10, 5, 10, 10, 10, 10, 10, 10), fm_a4_3 = c(0, 
                                                                                                  5, 10, 10, 5, 10, 5, 10, 10, 10, 10, 10, 5, 10, 5, 5, 5, 
                                                                                                  10, 10, 5, 0, 10, 5, 10, 5, 10, 10, 0, 10, 10, 5, 10, 10, 
                                                                                                  10, 0, 10, 0, 10, 10, 10, 10), fm_a4_4 = c(10, 5, 10, 10, 
                                                                                                                                             10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                             10, 10, 10, 5, 10, 10, 10, 5, 10, 10, 10, 0, 10, 10, 10, 
                                                                                                                                             10, 10, 0, 10, 10, 10, 10), fm_a4_5 = c(0, 5, 10, 10, 10, 
                                                                                                                                                                                     0, 10, 10, 10, 10, 10, 10, 0, 10, 10, 5, 10, 10, 5, 0, 10, 
                                                                                                                                                                                     10, 10, 10, 10, 10, 5, 10, 10, 0, 5, 10, 0, 10, 0, 5, 5, 
                                                                                                                                                                                     5, 10, 10, 10), fm_a4_6 = c(10, 5, 5, 0, 0, 5, 10, 10, 10, 
                                                                                                                                                                                                                 0, 10, 10, 5, 10, 10, 10, 0, 10, 0, 10, 10, 0, 10, 10, 5, 
                                                                                                                                                                                                                 0, 0, 10, 10, 10, 0, 10, 10, 5, 5, 10, 0, 0, 10, 10, 5), 
                   cg_a4_1 = c(10, 5, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 
                               10, 10, 10, 10, 10, 10, 10, 10, 0, 10, 10, 10, 10, 5, 0, 
                               10, 10, 10, 10, 5, 10, 10, 10, 10, 5, 5, 10, 10, 10), cg_a4_2 = c(5, 
                                                                                                 10, 10, 5, 10, 5, 10, 10, 10, 10, 10, 10, 5, 10, 10, 10, 
                                                                                                 10, 10, 10, 5, 10, 10, 10, 10, 10, 5, 10, 10, 10, 10, 10, 
                                                                                                 10, 10, 10, 10, 10, 10, 10, 10, 10, 10), cg_a4_3 = c(10, 
                                                                                                                                                      10, 5, 10, 10, 10, 10, 10, 10, 5, 10, 10, 5, 10, 10, 10, 
                                                                                                                                                      5, 10, 10, 10, 10, 0, 10, 10, 5, 10, 5, 10, 10, 10, 5, 10, 
                                                                                                                                                      10, 10, 10, 10, 5, 10, 10, 10, 10), cg_a4_4 = c(10, 10, 0, 
                                                                                                                                                                                                      5, 5, 5, 10, 10, 10, 5, 10, 10, 0, 5, 10, 10, 5, 10, 10, 
                                                                                                                                                                                                      10, 10, 0, 5, 10, 10, 5, 0, 0, 10, 10, 0, 10, 0, 10, 10, 
                                                                                                                                                                                                      5, 0, 5, 5, 10, 10), cg_a4_5 = c(5, 0, 0, 5, 0, 10, 5, 10, 
                                                                                                                                                                                                                                       10, 0, 10, 10, 10, 10, 5, 10, 0, 10, 0, 10, 0, 0, 10, 10, 
                                                                                                                                                                                                                                       5, 10, 5, 10, 5, 5, 5, 0, 10, 10, 5, 10, 0, 10, 10, 10, 10
                                                                                                                                                                                                      ), cg_a4_6 = c(0, 0, 5, 10, 10, 10, 10, 10, 0, 10, 5, 10, 
                                                                                                                                                                                                                     10, 10, 5, 10, 10, 10, 10, 10, 5, 10, 10, 10, 10, 5, 5, 10, 
                                                                                                                                                                                                                     5, 10, 0, 10, 10, 5, 5, 10, 5, 10, 10, 10, 10), ps_a4_1 = c(10, 
                                                                                                                                                                                                                                                                                 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                 10, 10, 5, 5, 10, 5, 10, 10, 10, 10), ps_a4_2 = c(0, 10, 
                                                                                                                                                                                                                                                                                                                                   10, 10, 5, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                                                                   10, 5, 10, 5, 10, 10, 10, 5, 10, 10, 10, 5, 0, 10, 10, 10, 
                                                                                                                                                                                                                                                                                                                                   5, 0, 10, 5, 10, 10, 10, 10), ps_a4_3 = c(10, 0, 10, 5, 5, 
                                                                                                                                                                                                                                                                                                                                                                             10, 5, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 
                                                                                                                                                                                                                                                                                                                                                                             5, 10, 10, 10, 5, 10, 10, 10, 5, 10, 10, 10, 10, 5, 0, 5, 
                                                                                                                                                                                                                                                                                                                                                                             0, 10, 5, 10, 10), ps_a4_4 = c(10, 10, 10, 10, 5, 10, 5, 
                                                                                                                                                                                                                                                                                                                                                                                                            10, 10, 0, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 
                                                                                                                                                                                                                                                                                                                                                                                                            10, 10, 10, 10, 10, 10, 5, 10, 5, 10, 10, 10, 10, 5, 5, 10, 
                                                                                                                                                                                                                                                                                                                                                                                                            10, 10, 10), ps_a4_5 = c(5, 5, 10, 5, 10, 5, 10, 10, 0, 0, 
                                                                                                                                                                                                                                                                                                                                                                                                                                     10, 10, 5, 10, 10, 10, 10, 10, 0, 10, 5, 5, 5, 10, 0, 10, 
                                                                                                                                                                                                                                                                                                                                                                                                                                     5, 10, 5, 0, 10, 10, 10, 10, 0, 5, 0, 5, 10, 10, 5), ps_a4_6 = c(5, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      5, 0, 5, 0, 10, 0, 10, 5, 5, 10, 10, 5, 10, 10, 10, 0, 10, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      5, 10, 5, 0, 5, 10, 5, 10, 5, 0, 5, 10, 0, 0, 10, 5, 0, 5, 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      0, 10, 10, 10, 10)), row.names = c(NA, -41L), class = "data.frame")

user_2461552 · Answer

I followed your idea of pivoting longer, using pivot_longer() from tidyr to put the scale groups in rows but leave the items in columns. (The last two examples in the documentation for pivot_longer() are my go-to when trying to remember how to do this.)

However, this relies on you having the same number of items for each scale; I'm not sure how it will hold up for varying items per scale.

Once things are in a longer form, use a nest_by() on quest and the scales variable followed by mutate() to nest and calculate the alpha for each row.

I didn't paste all the warnings and messages here, but there were loads. You can also remove the data column at the end if you don't need it any longer.

library(psych)
library(dplyr)
library(tidyr)

d %>%
    pivot_longer(cols = -quest,
                 names_to = c("scale", ".value"),
                 names_pattern = "(\w+_\w+_)(.)") %>%
    nest_by(quest, scale) %>%
    mutate(alpha(data)$total)

#> # A tibble: 15 x 12
#> # Rowwise:  quest, name
#>    quest name       data raw_alpha std.alpha `G6(smc)` average_r    `S/N`    ase
#>                                 
#>  1     2 cg_a4_ [16 x 6]     0.619   0.594      0.728    0.226    1.46    0.141 
#>  2     2 com_a~ [16 x 6]     0.810   0.808      0.881    0.412    4.20    0.0719
#>  3     2 fm_a4_ [16 x 6]     0.400   0.421      0.546    0.108    0.728   0.221 
#>  4     2 gm_a4_ [16 x 6]     0.842   0.952      0.745    0.831   19.7     0.0592
#>  5     2 ps_a4_ [16 x 6]     0.684   0.753      0.870    0.337    3.05    0.123 
#>  6     4 cg_a4_ [15 x 6]     0.677   0.696      0.807    0.276    2.29    0.126 
#>  7     4 com_a~ [15 x 6]     0.673   0.613      0.842    0.209    1.58    0.110 
#>  8     4 fm_a4_ [15 x 6]     0.669   0.714      0.811    0.294    2.50    0.124 
#>  9     4 gm_a4_ [15 x 6]     0.811   0.759      0.873    0.386    3.15    0.0389
#> 10     4 ps_a4_ [15 x 6]     0.533   0.551      0.605    0.170    1.23    0.161 
#> 11     6 cg_a4_ [10 x 6]    -0.168  -0.00601    0.550   -0.00120 -0.00597 0.621 
#> 12     6 com_a~ [10 x 6]    -0.184   0.228      0.486    0.0686   0.295   0.644 
#> 13     6 fm_a4_ [10 x 6]     0.508   0.542      0.727    0.191    1.18    0.248 
#> 14     6 gm_a4_ [10 x 6]    -0.075  -0.492     -0.0806  -0.0582  -0.330   0.398 
#> 15     6 ps_a4_ [10 x 6]     0.844   0.879      0.903    0.592    7.26    0.0710
#> # ... with 3 more variables: mean , sd , median_r

^{Created on 2021-09-23 by the reprex package (v2.0.0)}

user_2498085 · Answer

Feels like grouping/pivoting is trying to over-engineer a solution. One approach could be to write a function that allows you to set the value that sits within contains().

library(psych)
library(tidyverse)

apply_alpha <- function(data, nest_contains) {
  
  data %>%
    select(quest, contains(nest_contains)) %>%
    group_by(quest) %>%
    do(alpha(.)$total)
  
}

apply_alpha(d, 'com_')
apply_alpha(d, 'gm_')
apply_alpha(d, 'fm_')

Important to note that with this approach I'm receiving a large number of warning messages that I'm not familiar with. They're coming from the use of the alpha() function.

user_13321647 · Answer

You could to something like this: Let me know to explain if this is what you are looking for:

library(tidyverse)
library(psych)

reg_fm_a4_ <- "^fm_a4_.*"
reg_com_a4_ <- "^com_a4_.*"
reg_gm_a4_ <- "^gm_a4_.*"
reg_cg_a4_ <- "^cg_a4_.*"
reg_ps_a4_ <- "^ps_a4_.*"

regs <- c(reg_fm_a4_, reg_com_a4_, reg_gm_a4_, reg_cg_a4_, reg_ps_a4_) %>% 
    set_names(c("fm_a4_", "com_a4_", "gm_a4_", "cg_a4_", 
                "ps_a4_"))


cronbachs_alpha <- 
    map_df(regs, ~ 
               d %>% 
               select(dplyr::matches(.x)) %>% 
               psych::alpha(check.keys = TRUE) %>% .$total %>% 
               tibble::rownames_to_column()
           ,.id = "scale"
    )

    scale rowname raw_alpha std.alpha   G6(smc) average_r       S/N        ase     mean       sd   median_r
1  fm_a4_         0.4655172 0.4841889 0.5081686 0.1352840 0.9386944 0.12722395 8.008130 1.716728 0.16047102
2 com_a4_         0.7246145 0.7294824 0.7367755 0.3100766 2.6966174 0.06440378 8.130081 2.056329 0.32419199
3  gm_a4_         0.6285083 0.6818823 0.7360522 0.2632152 2.1434909 0.08701602 7.337398 1.516341 0.09958706
4  cg_a4_         0.5260735 0.5134628 0.5966499 0.1495805 1.0553414 0.10814655 6.524390 1.737080 0.12196703
5  ps_a4_         0.7173328 0.7486200 0.7597498 0.3317028 2.9780417 0.06479382 7.906504 1.990620 0.36281243

user_2725773 · Answer

You could do your reshaping and then work with nested data. Of course, if you don't want to keep the nested data in your results, you can just unselect the data column.

The advantage of this solution (if you see it as such) is that you a) don't need to create extra objects nor b) specific functions.

d %>%
  mutate(id = 1:n()) %>%
  pivot_longer(cols = c(-id, -quest)) %>%
  separate(col = name,
           into = c("scale", "item"),
           sep = "_",
           extra = "merge") %>%
  pivot_wider(names_from = item) %>%
  select(-id) %>%
  group_by(quest, scale) %>%
  nest() %>%
  mutate(alpha_results = map(data, ~alpha(.)$total)) %>%
  unnest_wider(alpha_results) %>%
  arrange(scale, quest)

which gives:

# Groups:   quest, scale [15]
   quest scale data              raw_alpha std.alpha `G6(smc)` average_r    `S/N`    ase  mean    sd median_r
                                                
 1     2 cg         0.619   0.594      0.728    0.226    1.46    0.141   7.60 1.90    0.157 
 2     4 cg         0.677   0.696      0.807    0.276    2.29    0.126   8    1.88    0.368 
 3     6 cg        -0.168  -0.00601    0.550   -0.00120 -0.00597 0.621   8.42 1.07    0.102 
 4     2 com        0.810   0.808      0.881    0.412    4.20    0.0719  7.24 2.63    0.457 
 5     4 com        0.673   0.613      0.842    0.209    1.58    0.110   8.83 1.60    0.201 
 6     6 com       -0.184   0.228      0.486    0.0686   0.295   0.644   8.5  0.946   0.0970
 7     2 fm         0.4     0.421      0.546    0.108    0.728   0.221   8.12 1.62    0.0953
 8     4 fm         0.669   0.714      0.811    0.294    2.50    0.124   8.28 1.82    0.366 
 9     6 fm         0.508   0.542      0.727    0.191    1.18    0.248   7.42 1.73    0.279 
10     2 gm         0.842   0.952      0.745    0.831   19.7     0.0592  9.48 1.05    0.831 
11     4 gm         0.811   0.759      0.873    0.386    3.15    0.0389  8.83 1.94    0.511 
12     6 gm        -0.075  -0.492     -0.0806  -0.0582  -0.330   0.398   8.33 1.11   -0.111 
13     2 ps         0.684   0.753      0.870    0.337    3.05    0.123   7.08 1.97    0.316 
14     4 ps         0.533   0.551      0.605    0.170    1.23    0.161   8.83 1.29    0.150 
15     6 ps         0.844   0.879      0.903    0.592    7.26    0.0710  7.83 2.43    0.604

Using dplyr to nest or group two variables, then perform the Cronbach's alpha function or other statistics to the data

4 Answers