# Workshop

###### tags: `R` `Statistics` `workshop`

## Dataset
**Data Set Information:**
** This dataset contains the medical records of **66 patients who had Hepatic portal venousgas(HPVG)**. Each patient profile has **13 clinical variables**.
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**Attribute Information:**
* Patient No: id
* Sex (0:Female; 1:Male): sex
* Age (years): age
* Symptom onset to ED presentation (hours): p_time
* Body temperature (℃): bt
* Pulse rate (bpm): pr
* Respiratory rate (breaths/min):rr
* Mean arterial pressure (mmHg): bp
* Rapid Acute Physiology Score: RAPS
* Rapid Emergency Medicine Score: REMS
* Modified Early Warning Score: MEWS
* Management (0:Conservative; 1:Surgery): management
* ED presentation to operation (hours): op_time
* End outcome (0:Survival; 1:Death): outcome

[PLoS ONE12(9):e0184813.](https://doi.org/10.1371/journal.pone.0184813)

## Some Useful R Code and Package

# loading library
library(pwr) # for power analysis
library(openxlsx) # for open and save excel file
library(dplyr) # for data transformation
library(ggplot2) # for graph

# import xxxx.txt file and name it data
data <- read.table("data/xxxx.txt", header = T, sep = "\t")
# import xxxx.xlsx file and name it data1
data1 <- readWorkbook("data/xxxx.xlsx")

# check the structures of datasets
str(data)

# write to xlsx file
write.xlsx(my.table, file = "table.xlsx", colNames = T, rowNames = T)

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### Basic R function

# calculate mean, SD, quantile
mean(data$x)
sd(data$x)
quantile(data$x)
summary(data$x)

# The Shapiro-Wilk Test For Normality
shapiro.test(data$x)

# perform t-test
t.test(data$a, data$b)

# perform Mann Whitney U Test
wilcox.test(data$a, data$b)

# make a table
my_table <- table(data$a, data$b)

# make a table with define lable
my_table2 <- table(Sex = data$a, Angina_type = data$b)

# change row name
rownames(my_table) <- c("female","male")

# change column name
colnames(my_table) <- c("Typical","Atypical","Non-anginal pain", "Asymptomatic")

# perform Chi-square test of independence
chisq.test(my_table)

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### dplyr

* Use a data frame and create a data frame
* Comparisons: >, >=, <, <=, !=, and ==
* Logical operator: & (and), | (or), and ! (not)
<br/>

**filter():** Pick observations by their values

# find male with heart failure
m_hf <- filter(data, sex == 1, target == 1)
str(m_hf)

# find patient with thalassemia
thal_p1 <- filter(data, thal == 2 | thal == 3)
str(thal_p1)

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**arrange():** Reorder the rows

# arrange in ascending order
data_arr <- arrange(data, thal)

# in descending order
data_arr <- arrange(data1, desc(thal))

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**select():** Pick variables by their names

# pick age, sex and ca columns
age_sex_ca <- select(data, age, sex, ca)

# pick the columns from cp to fbs
cp_to_fbs <- select(data, cp:fbs)

# remove the columns from cp to fbs
no_cp_to_fbs <- select(data, -(cp:fbs))

# remane the restecg column
new_data <- rename(data1, ekg = restecg)

<br/>

**mutate():** Create new variable
**transmute():** keep the new variables only

# add new columns age_sex and cp_fbs
new_columns <- mutate(data, age_sex = age - 10 * sex, cp_fbs = cp + fbs)

# save only the new columns
new_data <- transmute(data, age_sex = age - 10 * sex, cp_fbs = cp + fbs)

<br/>

**summarize():** summary
**group_by():** operate group by group

# summarize the mean of age, SD and total pt number
summarize(data, age_mean = mean(age), sd = sd(age), n= n())

# group by sex and cp 
group <- group_by(data, sex, cp)
summarize(group1, age_mean = mean(age), sd = sd(age), n= n())

# use count
data %>% count(sex, cp)
data %>% count(sex, target)

# seperate the data by sex
# %>% is pipe
female <- heights %>% filter(sex =="Female" )
male <- heights %>% filter(sex =="Male" )

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### ggplot2

# Histogram
ggplot(data=df, aes(x= x)) + geom_histogram(binwidth= 1)

# Dotplot
ggplot(data = df, aes(x = x, y = y)) +  geom_dotplot(binaxis ='y', stackdir = 'center', stackratio = 0.5, dotsize = 0.3)

# Box Plot   
ggplot(data = df, aes(x = x, y = y)) +  geom_boxplot()  +
  scale_x_discrete(labels=c("0" = "Female", "1" = "male"))
  
# Bar Plot
ggplot(data = data, aes(x = x, fill = a )) + geom_bar()

ggplot(data = data, aes(x = x, fill = a )) + 
  geom_bar(position = "dodge")  +
  scale_x_discrete(
            labels = c("a1", "a2", "a3", "a4")
                  )
                               

</br>

## Today's Workshop
:::info
PLOS journals require authors to make all data necessary to replicate their study’s findings publicly available without restriction at the time of publication. As a result, we can easily download the raw data of the published article. Today, we will use the dataset from plos one website to perform the analysis. Our goal is to **re-create the table 1 from the dataset** and to **identify any statistical misusage**.

:::
</br>

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### Rapid Emergency Medicine Score: A novel prognostic tool for predicting the outcomes of adult patients with hepatic portal venous gas in the emergency department

### Table 1

### Methods
::: success
**Statistical Analysis:**
Numerical and categorical variables are shown as mean ± SD, and frequencies are displayed as percentages (%). Univariate analyses were applied to study the association between predictors and mortality, while categorical and numerical variables were analyzed with a chi-square test and two-sample t-test respectively.
:::

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