# install.packages("effsize")
# install.packages("rstatix")

library(readxl)
library(ggpubr)

## Loading required package: ggplot2

library(effsize)
library(rstatix)

## 
## Attaching package: 'rstatix'

## The following object is masked from 'package:stats':
## 
##     filter

A6Q2 <- read_excel("C:/Users/SHRUTI/Downloads/A6Q2.xlsx")
names(A6Q2)

## [1] "ID"     "Before" "After"

head(A6Q2)

## # A tibble: 6 × 3
##      ID Before After
##   <dbl>  <dbl> <dbl>
## 1     1   70.5  47.6
## 2     2   73.2  52.9
## 3     3   87.5  47.2
## 4     4   75.6  58.0
## 5     5   76.0  51.9
## 6     6   88.7  66.3

Before <- A6Q2$Before
After <- A6Q2$After

Differences <- After - Before

mean(Before, na.rm = TRUE)

## [1] 76.13299

median(Before, na.rm = TRUE)

## [1] 75.95988

sd(Before, na.rm = TRUE)

## [1] 7.781323

mean(After, na.rm = TRUE)

## [1] 57.17874

median(After, na.rm = TRUE)

## [1] 58.36459

sd(After, na.rm = TRUE)

## [1] 14.39364

hist(Differences,
     breaks = 15,
     col = "blue",
     border = "white")

boxplot(Differences,
        main = "Distribution of Score Differences (After - Before)",
        ylab = "Difference in Scores",
        col = "blue",
        border = "darkblue")

shapiro.test(Differences)

## 
##  Shapiro-Wilk normality test
## 
## data:  Differences
## W = 0.89142, p-value = 0.02856

# Data for the difference scores appears abnormally distributed (negatively skewed, with a long left tail).
# The difference scores boxplot has one outlier.

# Shapiro-Wilk Difference Scores
# The data is abnormally distributed, (p = .029).
# Shapiro-Wilk was abnormal, so a Wilcoxon Signed-Rank Test is appropriate.

wilcox.test(Before, After, paired = TRUE, na.action = na.omit)

## 
##  Wilcoxon signed rank exact test
## 
## data:  Before and After
## V = 210, p-value = 1.907e-06
## alternative hypothesis: true location shift is not equal to 0

Long <- data.frame(
  Score = c(Before, After),
  Time = factor(rep(c("Before", "After"), each = length(Before)),
                levels = c("Before", "After"))
)

wilcox_effsize(Long, Score ~ Time, paired = TRUE)

## # A tibble: 1 × 7
##   .y.   group1 group2 effsize    n1    n2 magnitude
## * <chr> <chr>  <chr>    <dbl> <int> <int> <ord>    
## 1 Score Before After    0.877    20    20 large

# A Wilcoxon Signed-Rank Test was conducted to determine if there was a difference in weight between Before and After the keto diet.
# Before scores (Mdn = 75.96) were significantly different from After scores (Mdn = 58.36), V = 210, p < .001.
# The effect size was large, r = 0.88.