如何使用嵌套数据框创建整齐的相关性？

Question

这个问题之前已经部分回答（例如，），但是——据我所知——没有使用可重现示例的完整答案。我想从嵌套数据框中按名称 select 变量，计算成对相关性，然后将相关系数和 p 值添加到具有适当名称列的未嵌套数据框中。以下示例产生了预期的结果：

library(tidyverse)
library(broom)

df <- mtcars %>% 
  nest(data = everything()) %>% 
  mutate(cor_test = map(data, ~ cor.test(.x$mpg, .x$disp)),
         tidied = map(cor_test, tidy)) %>% 
  unnest(tidied) %>% 
  select(-c(cor_test, statistic, parameter, conf.low, conf.high, method, alternative)) %>% 
  rename(c(mpg_disp_estimate = estimate, mpg_disp_p.value = p.value)) %>% 
  mutate(cor_test = map(data, ~ cor.test(.x$mpg, .x$cyl)),
         tidied = map(cor_test, tidy)) %>% 
  unnest(tidied) %>% 
  select(-c(cor_test, statistic, parameter, conf.low, conf.high, method, alternative)) %>% 
  rename(c(mpg_cyl_estimate = estimate, mpg_cyl_p.value = p.value)) %>% 
  mutate(cor_test = map(data, ~ cor.test(.x$disp, .x$cyl)),
         tidied = map(cor_test, tidy)) %>% 
  unnest(tidied) %>% 
  select(-c(cor_test, statistic, parameter, conf.low, conf.high, method, alternative)) %>% 
  rename(c(disp_cyl_estimate = estimate, disp_cyl_p.value = p.value))

显然，这不是一个好的解决方案，因为它涉及一遍又一遍地重复相同的代码。有没有办法用 purrr 和 broom 更优雅地实现这个目标？

Answer 1

我们可以用 combn 做到这一点。获取数据列名称与 combn 的成对组合，从数据中提取列值，应用 cor.test、return tidyied 输出，创建 'categ' 列来标识测试中使用的列，并将 tibble 输出的 list 绑定到单个 data.frame

library(dplyr)
library(broom)
library(stringr)
out <- combn(names(mtcars), 2, FUN = function(x)  
           tidy(cor.test(mtcars[[x[1]]], mtcars[[x[2]]])) %>% 
       mutate(categ = str_c(x, collapse="_"), .before = 1), 
          simplify = FALSE) %>%
    bind_rows

-输出

out
# A tibble: 55 x 9
#   categ    estimate statistic  p.value parameter conf.low conf.high method                               alternative
#   <chr>       <dbl>     <dbl>    <dbl>     <int>    <dbl>     <dbl> <chr>                                <chr>      
# 1 mpg_cyl    -0.852     -8.92 6.11e-10        30  -0.926     -0.716 Pearson's product-moment correlation two.sided  
# 2 mpg_disp   -0.848     -8.75 9.38e-10        30  -0.923     -0.708 Pearson's product-moment correlation two.sided  
# 3 mpg_hp     -0.776     -6.74 1.79e- 7        30  -0.885     -0.586 Pearson's product-moment correlation two.sided  
# 4 mpg_drat    0.681      5.10 1.78e- 5        30   0.436      0.832 Pearson's product-moment correlation two.sided  
# 5 mpg_wt     -0.868     -9.56 1.29e-10        30  -0.934     -0.744 Pearson's product-moment correlation two.sided  
# 6 mpg_qsec    0.419      2.53 1.71e- 2        30   0.0820     0.670 Pearson's product-moment correlation two.sided  
# 7 mpg_vs      0.664      4.86 3.42e- 5        30   0.410      0.822 Pearson's product-moment correlation two.sided  
# 8 mpg_am      0.600      4.11 2.85e- 4        30   0.318      0.784 Pearson's product-moment correlation two.sided  
# 9 mpg_gear    0.480      3.00 5.40e- 3        30   0.158      0.710 Pearson's product-moment correlation two.sided  
#10 mpg_carb   -0.551     -3.62 1.08e- 3        30  -0.755     -0.250 Pearson's product-moment correlation two.sided  
# … with 45 more rows

如果我们想创建一个宽幅面，使用pivot_wider

library(tidyr)
out1 <- combn(names(mtcars), 2, FUN = function(x)  
       tidy(cor.test(mtcars[[x[1]]], mtcars[[x[2]]])) %>% 
   mutate(categ = str_c(x, collapse="_"), .before = 1), 
      simplify = FALSE) %>%
  bind_rows %>% 
  select(categ, estimate, p.value) %>%
  pivot_wider(names_from = categ, values_from = c(estimate, p.value))

如果我们想在嵌套数据中使用，将上面的代码包装在一个函数中，然后 map 覆盖 list 'data' 列

library(purrr)
f1 <- function(dat) {
     combn(names(dat), 2, FUN = function(x)  
      tidy(cor.test(dat[[x[1]]], dat[[x[2]]])) %>% 
       mutate(categ = str_c(x, collapse="_"), .before = 1), 
     simplify = FALSE) %>%
     bind_rows %>% 
     select(categ, estimate, p.value) %>%
     pivot_wider(names_from = categ, values_from = c(estimate, p.value))
   }

mtcars %>%
    nest(data = everything()) %>%
    mutate(out = map(data, f1))
# A tibble: 1 x 2
#  data               out               
#  <list>             <list>            
#1 <tibble [32 × 11]> <tibble [1 × 110]>

如何使用嵌套数据框创建整齐的相关性？

How to create tidy correlations using nested dataframes?

r

dplyr

broom

purrr