Summary Statistics Tables in R With gtsummary

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1. library(tidyverse)
   
2. library(gtsummary)
   
3. library(gapminder)
   
4. 
   
5. gap <- gapminder %>%
   
6.   dplyr::mutate_all(~ ifelse(
   
7.     sample(c(TRUE, FALSE), size = length(.), replace = TRUE, prob = c(0.8, 0.2)),
   
8.     as.character(.),
   
9.     NA
   
10.   )) %>%
    
11.   dplyr::mutate_at(vars(year:gdpPercap), ~ as.numeric(.)) %>%
    
12.   dplyr::mutate(gdpPercap = ifelse(gdpPercap > median(gdpPercap, na.rm = TRUE), "high", "low"))

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1. gap %>%
   
2.   gtsummary::tbl_summary(
   
3.     label = list(
   
4.       continent ~ "Continent", year ~ "Year",
   
5.       lifeExp ~ "Life Expectancy", pop ~ "Population",
   
6.       gdpPercap ~ "GDP per Capita"
   
7.     ),
   
8.     type = all_continuous() ~ "continuous2",
   
9.     statistic = all_continuous() ~ c(
   
10.       "{median} ({p25}, {p75})",
    
11.       "{min}, {max}"
    
12.     )
    
13.   ) %>%
    
14.   add_n() %>%
    
15.   bold_labels() %>%
    
16.   modify_header(label ~ "**Variable**")

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关键词：Statistics statistic Summary Statist tables

1. my_theme <-
   
2.   list(
   
3.     "tbl_summary-str:default_con_type" = "continuous2",
   
4.     "tbl_summary-str:continuous_stat" = c(
   
5.       "{median} ({p25} - {p75})",
   
6.       "{mean} ({sd})",
   
7.       "{min} - {max}"
   
8.     ),
   
9.     "tbl_summary-str:categorical_stat" = "{n} / {N} ({p}%)",
   
10.     "style_number-arg:big.mark" = "",
    
11.     "tbl_summary-fn:percent_fun" = function(x) style_percent(x, digits = 3)
    
12.   )
    
13. 
    
14. gtsummary::set_gtsummary_theme(my_theme)
    
15. 
    
16. gap %>%
    
17.   gtsummary::tbl_summary(
    
18.     by = continent,
    
19.     missing = "always",
    
20.     missing_text = "Missing",
    
21.     list(
    
22.       year ~ "Year",
    
23.       lifeExp ~ "Life Expectancy", pop ~ "Population",
    
24.       gdpPercap ~ "GDP per Capita"
    
25.     )
    
26.   ) %>%
    
27.   add_n() %>%
    
28.   bold_labels() %>%
    
29.   modify_header(label ~ "**Variable**") %>%
    
30.   add_p()

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1. my_modified_gtsummary_tbl <- function(...) {
   
2.   gtsummary::tbl_summary(
   
3.     ...
   
4.   ) %>%
   
5.     add_n() %>%
   
6.     bold_labels() %>%
   
7.     modify_header(label ~ "**Variable**") %>%
   
8.     add_p()
   
9. }
   
10. 
    
11. gap %>%
    
12.   my_modified_gtsummary_tbl(
    
13.     by = continent,
    
14.     missing = "always",
    
15.     missing_text = "Missing",
    
16.     list(
    
17.       year ~ "Year",
    
18.       lifeExp ~ "Life Expectancy", pop ~ "Population",
    
19.       gdpPercap ~ "GDP per Capita"
    
20.     )
    
21.   )

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1. my_modified_gtsummary_tbl <- function(...) {
   
2.   gtsummary::tbl_summary(
   
3.     ...
   
4.   ) %>%
   
5.     add_n() %>%
   
6.     bold_labels() %>%
   
7.     modify_header(label ~ "**Variable**") %>%
   
8.     add_p()
   
9. }
   
10. 
    
11. gap %>%
    
12.   my_modified_gtsummary_tbl(
    
13.     by = continent,
    
14.     missing = "always",
    
15.     missing_text = "Missing",
    
16.     list(
    
17.       year ~ "Year",
    
18.       lifeExp ~ "Life Expectancy", pop ~ "Population",
    
19.       gdpPercap ~ "GDP per Capita"
    
20.     )
    
21.   )

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