When using dplyr to create a table of summary statistics that is organized by levels of a variable, I cannot figure out the syntax for calculating quartiles without having to repeat the column name. That is, using calls, such as vars() and list() work with other functions, such as mean() and median() but not with quantile()
Searches have produced antiquated solutions that no longer work because they use deprecated calls, such as do() and/or funs().
data(iris)
library(tidyverse)
#This works: Notice I have not attempted to calculate quartiles yet
summary_stat <- iris %>%
group_by(Species) %>%
summarise_at(vars(Sepal.Length),
list(min=min, median=median, max=max,
mean=mean, sd=sd)
)
A tibble: 3 x 6
Species min median max mean sd
<fct> <dbl> <dbl> <dbl> <dbl> <dbl>
1 setosa 4.3 5 5.8 5.01 0.352
2 versicolor 4.9 5.9 7 5.94 0.516
3 virginica 4.9 6.5 7.9 6.59 0.636
##########################################################################
#Does NOT work:
five_number_summary <- iris %>%
group_by(Species) %>%
summarise_at(vars(Sepal.Length),
list(min=min, Q1=quantile(.,probs = 0.25),
median=median, Q3=quantile(., probs = 0.75),
max=max))
Error: Must use a vector in `[`, not an object of class matrix.
Call `rlang::last_error()` to see a backtrace
###########################################################################
#This works: Remove the vars() argument, remove the list() argument,
#replace summarise_at() with summarise()
#but the code requires repeating the column name (Sepal.Length)
five_number_summary <- iris %>%
group_by(Species) %>%
summarise(min=min(Sepal.Length),
Q1=quantile(Sepal.Length,probs = 0.25),
median=median(Sepal.Length),
Q3=quantile(Sepal.Length, probs = 0.75),
max=max(Sepal.Length))
# A tibble: 3 x 6
Species min Q1 median Q3 max
<fct> <dbl> <dbl> <dbl> <dbl> <dbl>
1 setosa 4.3 4.8 5 5.2 5.8
2 versicolor 4.9 5.6 5.9 6.3 7
3 virginica 4.9 6.22 6.5 6.9 7.9
This last piece of code produces exactly what I am looking for, but I am wondering why there isn't a shorter syntax that doesn't force me to repeat the variable.
You're missing the ~ in front of the quantile function in the summarise_at call that failed. Try the following:
five_number_summary <- iris %>%
group_by(Species) %>%
summarise_at(vars(Sepal.Length),
list(min=min, Q1=~quantile(., probs = 0.25),
median=median, Q3=~quantile(., probs = 0.75),
max=max))
five_number_summary
# A tibble: 3 x 6
Species min Q1 median Q3 max
<fct> <dbl> <dbl> <dbl> <dbl> <dbl>
1 setosa 4.3 4.8 5 5.2 5.8
2 versicolor 4.9 5.6 5.9 6.3 7
3 virginica 4.9 6.22 6.5 6.9 7.9