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COD_week8_MGK_BTE3207_midterm .Rmd
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---
title: "COD_Midterm_BTE3207"
author: "Minsik Kim"
date: "2023-10-21"
output:
rmdformats::downcute:
downcute_theme: "chaos"
code_folding: show
fig_width: 6
fig_height: 6
df_print: paged
editor_options:
chunk_output_type: inline
markdown:
wrap: 72
---
```{r warning=FALSE, message=FALSE, echo=FALSE, results='hide', setup}
#===============================================================================
#BTC.LineZero.Header.1.1.0
#===============================================================================
#R Markdown environment setup and reporting utility.
#===============================================================================
#RLB.Dependencies:
# knitr, magrittr, pacman, rio, rmarkdown, rmdformats, tibble, yaml
#===============================================================================
#Input for document parameters, libraries, file paths, and options.
#=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
knitr::opts_chunk$set(message=FALSE, warning = FALSE)
path_working <- "/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/scripts/BTE3207_Advanced_Biostatistics"
path_library <- "/Library/Frameworks/R.framework/Resources/library"
str_libraries <- c("tidyverse", "pacman", "yaml")
YAML_header <-
'---
title: "BTE3207 week 7-1"
author: "Minsik Kim"
date: "2032.10.10"
output:
rmdformats::downcute:
downcute_theme: "chaos"
code_folding: hide
fig_width: 6
fig_height: 6
---'
seed <- "20230920"
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
#Loads libraries, file paths, and other document options.
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
FUN.LineZero.Boot <- function() {
.libPaths(path_library)
require(pacman)
pacman::p_load(c("knitr", "rmarkdown", "rmdformats", "yaml"))
knitr::opts_knit$set(root.dir = path_working)
str_libraries |> unique() |> sort() -> str_libraries
pacman::p_load(char = str_libraries)
set.seed(seed)
}
FUN.LineZero.Boot()
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
#Outputs R environment report.
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
FUN.LineZero.Report <- function() {
cat("Line Zero Environment:\n\n")
paste("R:", pacman::p_version(), "\n") |> cat()
cat("Libraries:\n")
for (str_libraries in str_libraries) {
paste(
" ", str_libraries, ": ", pacman::p_version(package = str_libraries),
"\n", sep = ""
) |> cat()
}
paste("\nOperating System:", pacman::p_detectOS(), "\n") |> cat()
paste(" Library Path:", path_library, "\n") |> cat()
paste(" Working Path:", path_working, "\n") |> cat()
paste("Seed:", seed, "\n\n") |> cat()
cat("YAML Header:\n")
cat(YAML_header)
}
FUN.LineZero.Report()
```
Function to be used.
```{r}
lm_eqn <- function(m){
eq <- substitute(italic(y) == a + b %.% italic(x)*","~~italic(r)^2~"="~r2,
list(a = format(unname(coef(m)[1]), digits = 2),
b = format(unname(coef(m)[2]), digits = 2),
r2 = format(summary(m)$r.squared, digits = 3)))
as.character(as.expression(eq));
}
```
# Example 9
```{r}
p9_data <- data.frame(subejct = 1:8,
before = c(126, 131, 129, 122, 130, 131, 128, 134),
after = c(131, 121, 131, 114, 133, 119, 127, 129)) %>%
mutate(change = before - after)
t.test(p9_data$change)
#or
t.test(p9_data$after, p9_data$before, paired = T)
```
# Example 10
```{r}
p10_data <- data.frame(subejct = 1:20,
group = c(replicate(10, "low_carb"), replicate(10, "low_fat")),
data = c(-10.8, -10.6, 3.5, 10.4, -7.4, -2.6, -6.5, 1.7, -2.9, -7.6,
-1.3, -0.9, -1.2, -0.5, -1.6, -0.9, -2.5, -5, -3.4, -1.9))
t.test(x = subset(p10_data, p10_data$group == "low_carb")$data,
y = subset(p10_data, p10_data$group == "low_fat")$data,
paired = F,
var.equal = F)
```
# Example 11
```{r}
p11_data <- data.frame(group = c("obese", "not_obese"),
low_fat = c(52, 130),
low_carb = c(30, 209),
no_diet = c(90, 130)) %>%
column_to_rownames("group") %>% t %>% data.frame()
library(epitools)
oddsratio(as.matrix(p11_data), rev = "rows")
chisq.test(p11_data)
```
# Example 12
```{r}
p12_data <- data.frame(group = c("hypertension", "normal"),
low_fat = c(89, 102),
low_carb = c(93, 137)) %>%
column_to_rownames("group")
chisq.test(p12_data)
```
# Statistics on the results
# Score data in baxplot - by each problem set
```{r}
midterm <- readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx") %>%
tidyr::gather(., problemset, score, `1`:`12`, factor_key=TRUE)
midterm %>%
ggplot(aes(x = problemset, y = score, fill = problemset)) +
geom_boxplot() +
scale_fill_brewer(name = "Problem set",
type = "qual",
palette = 3) +
theme_classic(base_family = "serif",
base_size = 13) +
xlab("Problem set") +
ylab("Score")
```
# Score data in histogram - by each problem set
```{r}
midterm %>%
ggplot(aes(x = score, fill = problemset)) +
geom_histogram() +
scale_fill_brewer(name = "Problem set",
type = "qual",
palette = 3) +
facet_wrap(~problemset, scales = "free") +
#guide_legend(title = "Problem set") +
theme_classic(base_family = "serif",
base_size = 13) +
ylab("Number of students")
```
# Score total - summary statistics
```{r}
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx") %>%
.$total %>%
summary
```
# Score total - boxplot and histogram
```{r}
a <- merge(readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx"),
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/BTE3207_2023F_students_list.xlsx") %>% rename(student_id = "학번",
department = "학부(과)",
major = "전공",
year = "학년") %>% select(c("student_id", "department", "major", "year")),
by = "student_id", all = T
) %>%
mutate(year = as.factor(year)) %>%
ggplot(aes(y = total)) +
geom_boxplot() +
theme_classic(base_family = "serif",
base_size = 13) +
theme(legend.position = "top",
axis.text.x = element_blank()) +
xlab("") +
ylab("Total score")
b <- merge(readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx"),
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/BTE3207_2023F_students_list.xlsx") %>% rename(student_id = "학번",
department = "학부(과)",
major = "전공",
year = "학년") %>% select(c("student_id", "department", "major", "year")),
by = "student_id", all = T
) %>%
mutate(year = as.factor(year)) %>%
ggplot(aes(x = total)) +
geom_histogram(binwidth = 7) +
theme_classic(base_family = "serif",
base_size = 13) +
theme(legend.position = "top") +
xlab("Score") +
ylab("Number of students")
ggpubr::ggarrange(a, b, align = "hv", widths = c(1,3))
```
# For fun, a statistical test
Is there a different between junior and senior?
# Total score - boxplot by year
```{r}
merge(readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx"),
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/BTE3207_2023F_students_list.xlsx") %>% rename(student_id = "학번",
department = "학부(과)",
major = "전공",
year = "학년") %>% select(c("student_id", "department", "major", "year")),
by = "student_id", all = T
) %>%
mutate(year = as.factor(year)) %>%
ggplot(aes(y = total, x = year, fill = year)) +
geom_boxplot() +
#facet_wrap(~year, ncol = 1) +
theme_classic(base_family = "serif",
base_size = 13) +
ylab("Score") +
xlab("Year of study at Inha")
```
# Total score - histogram by year
```{r}
merge(readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx"),
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/BTE3207_2023F_students_list.xlsx") %>% rename(student_id = "학번",
department = "학부(과)",
major = "전공",
year = "학년") %>% select(c("student_id", "department", "major", "year")),
by = "student_id", all = T
) %>%
mutate(year = as.factor(year)) %>%
ggplot(aes(x = total, fill = year)) +
geom_histogram(aes(y = ..density..),
binwidth = 2, position = position_identity(), alpha = 0.5) +
scale_fill_brewer(name = "Year of study at Inha",
type = "qual",
palette = 6) +
#facet_wrap(~year, ncol = 1) +
theme_classic(base_family = "serif",
base_size = 13) +
theme(legend.position = "top") +
xlab("Score") +
ylab("Number of students")
```
t-test (unpaired, unequal variance)
H<sub>0</sub> (null hypothesis): true difference in means is 0, i.e., there is no difference between junior and senior
H<sub>a</sub> (alternative hypothesis): true difference in means is not equal to 0.
```{r}
data <- merge(readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx"),
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/BTE3207_2023F_students_list.xlsx") %>% rename(student_id = "학번",
department = "학부(과)",
major = "전공",
year = "학년") %>% select(c("student_id", "department", "major", "year")),
by = "student_id", all = T
)
t.test(subset(data, data$year == "4") %>% .$total,
subset(data, data$year == "3") %>% .$total,
paired = F, var.equal = F)
```
**p**-value is 0.48. Therefore, we accect the null hypothesis (there is no significant difference between mean of junior and senior).
Alternatively,
```{r}
merge(readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/Midterm_result/BTE3207_2023F_midterm_results.xlsx"),
readxl::read_excel("/Users/minsikkim/Dropbox (Personal)/Inha/5_Lectures/Advanced biostatistics/2023F/BTE3207_2023F_students_list.xlsx") %>% rename(student_id = "학번",
department = "학부(과)",
major = "전공",
year = "학년") %>% select(c("student_id", "department", "major", "year")),
by = "student_id", all = T
) %>%
mutate(year = as.factor(year)) %>%
lm(total ~ year, data = .) %>%
summary
```
Correlation - % score by their orders
```{r}
midterm <- midterm %>%
mutate(problem_full_score = case_when(problemset == 1 ~ 6,
problemset == 2 ~ 5,
problemset == 3 ~ 5,
problemset == 4 ~ 5,
problemset == 5 ~ 5,
problemset == 6 ~ 5,
problemset == 7 ~ 9,
problemset == 8 ~ 5,
problemset == 9 ~ 6,
problemset == 10 ~ 6,
problemset == 11 ~ 9,
problemset == 12 ~ 8,
.default = 0),
perc_score = score/problem_full_score * 100)
midterm %>%
ggplot(aes(x = as.numeric(problemset), y = perc_score, color = as.numeric(problemset))) +
geom_jitter() +
theme_classic(base_family = "serif", base_size = 20) +
viridis::scale_color_viridis() +
xlab("Problem set order") +
ylab("% right answer") #+
#geom_smooth(method = "lm")
midterm %>%
ggplot(aes(x = as.numeric(problemset), y = perc_score, color = as.numeric(problemset))) +
geom_jitter() +
theme_classic(base_family = "serif", base_size = 20) +
viridis::scale_color_viridis() +
xlab("Problem set order") +
ylab("% right answer") +
geom_smooth(method = "lm") +
geom_label(x = 7.5, y = 100,
label = lm_eqn(lm(data = midterm,perc_score ~ as.numeric(problemset))),
parse = TRUE,
family='serif',
size = 8, label.size = 0, color = "blue")
```
```{r}
lm(data = midterm, perc_score ~ as.numeric(problemset)) %>% summary
```
We are going to learn more about the linear model, at the later half of the semester!
# Bibliography
```{r warning=FALSE, message=FALSE, echo=FALSE}
#===============================================================================
#BTC.LineZero.Footer.1.1.0
#===============================================================================
#R markdown citation generator.
#===============================================================================
#RLB.Dependencies:
# magrittr, pacman, stringr
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
#BTC.Dependencies:
# LineZero.Header
#===============================================================================
#Generates citations for each explicitly loaded library.
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
str_libraries <- c("r", str_libraries)
for (str_libraries in str_libraries) {
str_libraries |>
pacman::p_citation() |>
print(bibtex = FALSE) |>
capture.output() %>%
.[-1:-3] %>% .[. != ""] |>
stringr::str_squish() |>
stringr::str_replace("_", "") |>
cat()
cat("\n")
}
#===============================================================================
```