Reproducible Research

This is a brief introduction on common practices for reproducible research.
For a more detailed and free course please audit this free course by Harvard.

Reproducible Research is a scientific approach where the data, computational methods, and results of a study are made available in sufficient detail to allow others (or the original researchers at a later time) to independently verify findings, repeat analyses, and build upon previous work.

Store your raw data in a separate folder and never change it

This ensures that everyone has the same beginning of the analysis as you!

Informative naming variables

• Make sure that your variable name is easy to understand and reflect directly its content
  
• Avoid general terms like test, test1, ...
  
• This will improve the readability of your code
  Bad example
  

  # Analyzing patient data
  test <- read.csv("data.csv")
  stuff <- test[test$group == "treatment", ]
  final <- mean(stuff$bloodpressure)
  x <- sd(stuff$bloodpressure)
  result2 <- final/x
  y <- stuff[stuff$age > 40, ]
  z <- mean(y$bloodpressure)
  

  Good example
  

  # Analyzing patient data
  patient_data <- read.csv("data.csv")
  treatment_group <- patient_data[patient_data$group == "treatment", ]
  mean_blood_pressure <- mean(treatment_group$bloodpressure)
  blood_pressure_sd <- sd(treatment_group$bloodpressure)
  standardized_bp <- mean_blood_pressure/blood_pressure_sd
  older_patients <- treatment_group[treatment_group$age > 40, ]
  mean_bp_older_patients <- mean(older_patients$bloodpressure)
  

Overcommenting

Most of the time, your code makes perfect sense for you ... when you write it. But visiting it after a year is another story. I cannot stress how much time I wasted figuring out what was my past self thinking. Therefore, always overcomment things!

A tip: Put yourself in the position of someone who will read your code without knowing too much about the project

These comments should:
1. Provides context about the analysis purpose
2. Explains data content and processing decisions
3. Describes what diagnostics are checking and why

Bad example

# Read the CSV file
df <- read.csv("clinical_trial.csv")  # Reading the CSV file

# Remove rows with missing values
df <- df[complete.cases(df), ]  # This removes rows with NA

# Calculate BMI
df$bmi <- df$weight / (df$height/100)^2  # BMI formula

# Create linear model
model <- lm(response ~ treatment + age + bmi + gender, data = df)  # Building model

Good example

# Clinical trial analysis examining treatment effect on blood pressure
# Dataset contains: patient demographics, treatment assignment, and outcomes
# Date: 2023-03-15, Author: P. Vu

# Remove subjects with missing data (10% of original sample)
# Decision made with PI to use complete case analysis instead of imputation
df <- read.csv("clinical_trial.csv")
df <- df[complete.cases(df), ]

# Calculate BMI - using height in cm converting to meters
# Formula: weight(kg) / height(m)^2
df$bmi <- df$weight / (df$height/100)^2

# Primary analysis: Effect of treatment on blood pressure response
# Adjusting for pre-specified covariates: age, BMI, gender
model <- lm(response ~ treatment + age + bmi + gender, data = df)

# Diagnostics for linear model assumptions
# Checking normality of residuals (required for valid p-values)
residuals <- model$residuals
hist(residuals, main="Histogram of Residuals", xlab="Residual Value")
qqnorm(residuals)
qqline(residuals)
shapiro_result <- shapiro.test(residuals)

# If p > 0.05, normality assumption is reasonable
print(paste("Shapiro-Wilk p-value:", shapiro_result$p.value))

Version control

1. If you use Git, make a habit of commiting often
   • After each logical change:
     • Complete a function/analysis step
     • Fix a bug
     • Add a new feature
   • At the minimum, commit at the end of your work session
   • At any given point that you think you may want to return to
2. Most of your version control can be done via Git but it is always a good idea to add a time stamp to your deliverables like figures, tables.
   A good trick is to use the time function so you do not have to manually change the file name everytime you run.

   # Save the final figure
   ggsave(paste0("../figures/", format(Sys.time(), "%Y_%m_%d"), "_intensify_fig_continuous_power_80.png"))
   

   This code saves the file with the date it was created!

Have a dry lab note

Use softwares like OneNote to document the process of your research. These includes:
- Summary of the papers you read
- Notes for your meetings
You will never know if you have to go back to your old project!

Be patient with yourself!

I must admit, I do not follow these rules 100% of the time.
It is a skill and like every skill, it needs practice.
As long as you are trying to be better! You will be better!
Thank you!