In R, how to write function that runs t-test on list of dataframes-CodePudding

Using iris dataset as an example, I want to write a user defined function that

run pairwise t-test on all 4 columns exempting Species columns for each data split
export the results as 3 worksheets of a csv file

See below for my attempt:

library(tidyr)
library(reshape) # for melting /stacking the data
library(multcomp) # for pairwise test 
library(xlsx) # export excel file with worksheet

options(scipen = 100)

# dataset
iris

data_stats <- function(data){
    # melt the dataframe
     df <- melt(data, id.vars=c('Species'),var='group')
    
# split the dataframe into three list of dataframe
    dfsplit<-split(df,df$column)
    
    #  pairwise t-test
    results <- pairwise.t.test(dfsplit$value, dfsplit$group,p.adjust.method = "BH")
    
    # export each result as a worksheet of an excel file
    write.xlsx(results, file="Results.xlsx", sheetName="versicolor_stats", row.names=FALSE)
    write.xlsx(results, file="Results.xlsx", sheetName="virginica_stats", append=TRUE, row.names=FALSE)
    write.xlsx(results, file="Results.xlsx", sheetName="setosa_stats", append=TRUE, row.names=FALSE)
    
}
# testing the code on iris data
data_stats(iris)

Please comment and share your code. Thanks

CodePudding user response：

Here is an option with tidyverse - reshape to 'long' format with pivot_longer, then use group_modify to do the pairwise.t.test , tidy the output and unnest the list output

library(dplyr)
library(tidyr)
library(broom)
ttest_out <- iris %>% 
  pivot_longer(cols = -Species) %>% 
  group_by(Species) %>%
  group_modify(~ .x %>%
     summarise(out = list(pairwise.t.test(value, name) %>% 
       tidy))) %>% 
   ungroup %>% 
   unnest(out)

-output

ttest_out
# A tibble: 18 × 4
   Species    group1       group2         p.value
   <fct>      <chr>        <chr>            <dbl>
 1 setosa     Petal.Width  Petal.Length 1.77e- 54
 2 setosa     Sepal.Length Petal.Length 2.77e-132
 3 setosa     Sepal.Length Petal.Width  1.95e-156
 4 setosa     Sepal.Width  Petal.Length 1.61e- 86
 5 setosa     Sepal.Width  Petal.Width  1.13e-123
 6 setosa     Sepal.Width  Sepal.Length 4.88e- 71
 7 versicolor Petal.Width  Petal.Length 5.35e- 90
 8 versicolor Sepal.Length Petal.Length 3.78e- 52
 9 versicolor Sepal.Length Petal.Width  5.02e-125
10 versicolor Sepal.Width  Petal.Length 1.36e- 45
11 versicolor Sepal.Width  Petal.Width  3.46e- 44
12 versicolor Sepal.Width  Sepal.Length 1.25e- 95
13 virginica  Petal.Width  Petal.Length 1.39e- 90
14 virginica  Sepal.Length Petal.Length 6.67e- 22
15 virginica  Sepal.Length Petal.Width  3.47e-110
16 virginica  Sepal.Width  Petal.Length 2.35e- 68
17 virginica  Sepal.Width  Petal.Width  1.87e- 19
18 virginica  Sepal.Width  Sepal.Length 2.47e- 92