rdplyrgroup-bynest
Using dplyr to nest or group two variables, then perform the Cronbach's alpha function or other statistics to the data
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")
Solution
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
#> <dbl> <chr> <list<t> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 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 <dbl>, sd <dbl>, median_r <dbl>
Created on 2021-09-23 by the reprex package (v2.0.0)
- How to add a hover-over tooltip to rhandonstable header cell?
- How to detect the right encoding for read.csv?
- Rcpp Rf_warningcall compiler warnings
- Modify the name of factor variables in lm function(summary function)
- Extreme value analysis and quantile estimation using log Pearson type 3 (Pearson III) distribution - R vs Python
- How to hide NAs when using xlsx::saveWorkbook?
- How do I retrieve a simple numeric value from a named numeric vector in R?
- Adding an image in navbar and adjusting alignment in Rmarkdown
- Matching pair-wise columns from left to right across rows in one dataframe to another dataframe and adding new columns with matching values
- Income to outcome flow chart in Sankey plotly R
- color mapping in geom_conn_bundle not showing correctly
- Print R package startup message AFTER automatic package conflict messages instead of before
- Summing a set of R dataframe rows (column-wise), while retaining the first n columns
- Added variable / partial regression plots for groups in an interaction?
- how to make a topoplot in R with coordinates variable distribution
- List of all functions in base R?
- Plotting multiple plots for different initial conditions in one graph
- Printing repetitively on the same line in R
- Generating UI/Server based on initial selection
- Subset dataframe based on pickerInput
- How to let user pick the data in R-shiny?
- Couldn't show my simple bar charts separately on Shiny R dashboardBody
- How to programmatically filter contents of a second shiny app displayed via iframe
- How to select specific interesting groups for the boxplot in R Shiny app?
- Crosstable and Plot grouping with reactive values
- Is there a way to make multiple Shiny picker inputs where the selections must be disjoint?
- Delay/avoid duplication of shiny server side functions until after credentials
- Predictions only returns value "1"
- How to display a busy indicator in a shiny app?
- Append doesn't work when writing to CSV in R