Instructions

This checklist confirms that you have completed all the technical setup required for EPI 553. This assignment is graded for completion only and should take 30-45 minutes to complete.

How to Use This Checklist: 1. Work through each section below 2. Mark items as complete as you verify them 3. Answer the reflection questions 4. Save this document with your name (e.g., LastName_FirstName_Setup_Checklist.Rmd) 5. Knit to HTML (Ctrl+Shift+K) 6. Upload the HTML file to Brightspace by January 29, 2026

Section 1: R & RStudio Installation

Objective: Verify that R and RStudio are installed and up-to-date.

# Run this code to check your R installation
cat("R Version:", paste(R.version$major, R.version$minor, sep="."), "\n")

## R Version: 4.5.2

cat("Platform:", R.version$platform, "\n")

## Platform: x86_64-w64-mingw32

Completion checklist:

R is installed (version 4.0 or later)
- If older than 4.0, download from https://www.r-project.org/
RStudio is installed and functional
- Check: Help → About RStudio
- Current version shown: RStudio/2025.05.1+513
You can open and read this document in RStudio
You successfully ran the R code above without errors

Reflection Question 1: What version of R and RStudio are you running? (Screenshot or write the versions below)

Your answer:

R Version: 4.5.2

Section 2: Required Packages

Objective: Verify that all required packages are installed and load without errors.

# This code checks and loads required packages
required_packages <- c(
  "tidyverse", "rmarkdown", "knitr", "ggplot2", "dplyr", 
  "car", "lmtest", "sandwich", "stargazer", "broom"
)

cat("Loading required packages...\n\n")

## Loading required packages...

all_loaded <- TRUE
for (pkg in required_packages) {
  tryCatch({
    library(pkg, character.only = TRUE)
    cat("✓", pkg, "loaded successfully\n")
  }, error = function(e) {
    cat("✗", pkg, "FAILED to load\n")
    all_loaded <<- FALSE
  })
}

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ readr     2.1.6
## ✔ forcats   1.0.1     ✔ stringr   1.6.0
## ✔ ggplot2   4.0.1     ✔ tibble    3.3.1
## ✔ lubridate 1.9.4     ✔ tidyr     1.3.2
## ✔ purrr     1.2.1     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

## ✓ tidyverse loaded successfully
## ✓ rmarkdown loaded successfully
## ✓ knitr loaded successfully
## ✓ ggplot2 loaded successfully
## ✓ dplyr loaded successfully

## Loading required package: carData
## 
## Attaching package: 'car'
## 
## The following object is masked from 'package:dplyr':
## 
##     recode
## 
## The following object is masked from 'package:purrr':
## 
##     some

## ✓ car loaded successfully

## Loading required package: zoo
## 
## Attaching package: 'zoo'
## 
## The following objects are masked from 'package:base':
## 
##     as.Date, as.Date.numeric

## ✓ lmtest loaded successfully
## ✓ sandwich loaded successfully

## 
## Please cite as: 
## 
##  Hlavac, Marek (2022). stargazer: Well-Formatted Regression and Summary Statistics Tables.
##  R package version 5.2.3. https://CRAN.R-project.org/package=stargazer

## ✓ stargazer loaded successfully
## ✓ broom loaded successfully

cat("\n")

if (all_loaded) {
  cat("✓ All packages loaded successfully!\n")
} else {
  cat("⚠ Some packages failed. Run the code in Appendix A to install them.\n")
}

## ✓ All packages loaded successfully!

Completion checklist:

All 10 packages loaded without errors
- If any failed, run the installation code in Appendix A and try again
You restarted R after installing packages (Ctrl+Shift+F10 in RStudio)
All packages loaded successfully on second attempt

Reflection Question 2: Did any packages fail to load initially? If yes, which ones and how did you resolve it?

Your answer:

At the first attempt packages "tidyverse", "ggplot2", "dplyr", "car", "lmtest", "sandwich", "stargazer" and "broom" were failed to load. After copying code from Appendix A and running it in "Console" , all packages were loaded successfully. After restarting R studio (Ctrl+Shift+F10), I re-run chunk in Section 2, and finally got "All packages loaded successfully!"

Section 3: Working Directory & Project Structure

Objective: Set up your project directory with proper folder organization.

# Check current working directory
cat("Your current working directory:\n")

## Your current working directory:

cat(getwd(), "\n\n")

## C:/Users/AA843241/OneDrive - University at Albany - SUNY/Desktop/RStudio

# Check for R Project file
#Code from Yiming
rproj_files <- list.files(pattern = "\\.Rproj$", ignore.case = TRUE)
if (length(rproj_files) > 0) {
  cat("✓ R Project file detected:", rproj_files[1], "\n")
} else {
  cat("⚠ No R Project file found in this folder.\n")
}

## ✓ R Project file detected: 553_coding.Rproj

#Thank you, Yiming!

# Check for suggested folders
cat("\nFolder structure check:\n")

## 
## Folder structure check:

folders <- c("data", "scripts", "outputs", "figures")
for (folder in folders) {
  if (dir.exists(folder)) {
    cat("✓", folder, "/ exists\n")
  } else {
    cat("○", folder, "/ (needs to be created)\n")
  }
}

## ✓ data / exists
## ✓ scripts / exists
## ✓ outputs / exists
## ✓ figures / exists

Completion checklist:

Working directory is set to your course project folder
- Path: ________________________________________________
R Project file (.Rproj) exists in your project directory
Four folders exist: data/, scripts/, outputs/, figures/
- Run this code if folders are missing:
```
dir.create("data")
dir.create("scripts")
dir.create("outputs")
dir.create("figures")
```
You can navigate between these folders in RStudio’s Files pane

Reflection Question 3: Describe your folder structure. What is the full path to your project directory?

Your answer:

Example: /Users/jsmith/Documents/Albany/EPI553

Your path:

C:/Users/AA843241/OneDrive - University at Albany - SUNY/Desktop/RStudio 

Folder has: 
"data", "scripts", "outputs", "figures" folders,
this rmd file, 553_coding Rproj file,  
".RData" file and ".Rhistory" file

Section 4: R Markdown & Rendering

Objective: Confirm you can create, edit, and render R Markdown documents.

# Verify R Markdown package
if (require("rmarkdown", quietly = TRUE)) {
  cat("✓ rmarkdown package is installed and loaded\n")
  cat("✓ You can render to HTML, PDF, and Word formats\n\n")
  cat("To render a document:\n")
  cat("1. Click the 'Knit' button (top of editor) or press Ctrl+Shift+K\n")
  cat("2. Select output format (HTML, PDF, Word)\n")
  cat("3. View the rendered document in RStudio Viewer\n")
} else {
  cat("✗ rmarkdown not found. Run: install.packages('rmarkdown')\n")
}

## ✓ rmarkdown package is installed and loaded
## ✓ You can render to HTML, PDF, and Word formats
## 
## To render a document:
## 1. Click the 'Knit' button (top of editor) or press Ctrl+Shift+K
## 2. Select output format (HTML, PDF, Word)
## 3. View the rendered document in RStudio Viewer

Completion checklist:

You can see the “Knit” button at the top of this document in RStudio
You have successfully rendered an R Markdown file to HTML
- Document rendered: Azamatova_Aigerim_Setup_Checklist.html
- Date/time rendered: 1/26/2026
The rendered HTML file opened automatically in the RStudio Viewer
You can save the rendered HTML file to your outputs/ folder

Reflection Question 4: Describe the process you followed to render this checklist to HTML. What did you click and what happened?

Your answer:

I ran the code from the section 4. As I installed package with install.packages("knitr") last week, it seems like I did not have any problems. 
So after running the code "R Markdown" package was installed and loaded and then I could render file to HTML format. To do so I simply presses "Knit button". After that I could see the proccess in Render section. 
There was an info "Output created: Aigerim_Azamatova_Setup_Checklist.html" and File automatically opened in Google Chrome, as on my computer html files openes automatically there. I had to go to the folder and change property of the file: Opens with - there I chose Rstudio. After the second render my file opened in Rstudio Vewer Automatically. 
But according to the checklist html file should automatically be saved in outputs folder. It does not. There are 3 options in "Knit Directory" - Document Directory, Project Directory, Current working directory. So for now it will be automatically saved to document directory.

Section 5: File Management & Uploads

Objective: Practice saving files and uploading to Brightspace.

Completion checklist:

You know where files are saved on your computer
- Primary save location: Desktop
You can navigate to files using Windows Explorer or Finder
You saved this document with a clear filename: LastName_FirstName_Setup_Checklist.Rmd
You rendered it to HTML: LastName_FirstName_Setup_Checklist.html
You can locate the rendered HTML file on your computer
- Full file path: C:843241- University at Albany - SUNY
You have logged into Brightspace and found the assignment submission area
You know how to upload a file to Brightspace (done or ready to do)

Reflection Question 5: What is the exact filename (including .html extension) of the rendered version of this document?

Your answer:

Example: Smith_John_Setup_Checklist.html

Your filename:
Azamatova_Aigerim_Setup_Checklist.html

Section 6: Data & Code Practice

Objective: Verify you can work with data and run code in R.

Let’s do a quick practice analysis:

# Load data
library(tidyverse)

# Use built-in mtcars dataset
cat("Dataset: mtcars (Motor Trend Car Road Tests)\n")

## Dataset: mtcars (Motor Trend Car Road Tests)

cat("Sample of data:\n")

## Sample of data:

print(head(mtcars, 3))

##                mpg cyl disp  hp drat    wt  qsec vs am gear carb
## Mazda RX4     21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
## Mazda RX4 Wag 21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
## Datsun 710    22.8   4  108  93 3.85 2.320 18.61  1  1    4    1

cat("\n\nBasic Summary Statistics:\n")

## 
## 
## Basic Summary Statistics:

summary(mtcars$mpg)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   10.40   15.43   19.20   20.09   22.80   33.90

Create a simple visualization:

mtcars %>%
  ggplot(aes(x = wt, y = mpg, color = factor(cyl))) +
  geom_point(size = 3, alpha = 0.7) +
  geom_smooth(method = "lm", se = FALSE, alpha = 0.5) +
  labs(
    title = "Fuel Efficiency vs Weight",
    subtitle = "EPI 553 - Setup & Workflow Checklist",
    x = "Weight (1000 lbs)",
    y = "Miles Per Gallon (mpg)",
    color = "Cylinders"
  ) +
  theme_minimal() +
  theme(
    plot.title = element_text(size = 14, face = "bold"),
    legend.position = "bottom"
  )

Fit a regression model:

# Fit a simple linear regression model
model <- lm(mpg ~ wt + factor(cyl), data = mtcars)

cat("Linear Regression Model: mpg ~ weight + cylinders\n\n")

## Linear Regression Model: mpg ~ weight + cylinders

print(summary(model))

## 
## Call:
## lm(formula = mpg ~ wt + factor(cyl), data = mtcars)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.5890 -1.2357 -0.5159  1.3845  5.7915 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   33.9908     1.8878  18.006  < 2e-16 ***
## wt            -3.2056     0.7539  -4.252 0.000213 ***
## factor(cyl)6  -4.2556     1.3861  -3.070 0.004718 ** 
## factor(cyl)8  -6.0709     1.6523  -3.674 0.000999 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.557 on 28 degrees of freedom
## Multiple R-squared:  0.8374, Adjusted R-squared:   0.82 
## F-statistic: 48.08 on 3 and 28 DF,  p-value: 3.594e-11

# Extract key results
cat("\n\nKey Results:\n")

## 
## 
## Key Results:

cat("R-squared:", round(summary(model)$r.squared, 4), "\n")

## R-squared: 0.8374

cat("Residual Std. Error:", round(summary(model)$sigma, 4), "\n")

## Residual Std. Error: 2.5569

Completion checklist:

Data loaded successfully (mtcars)
Summary statistics displayed without errors
Plot rendered correctly showing relationship between weight and mpg
Regression model ran successfully and displayed results

Reflection Question 6: Looking at the plot above, describe the relationship between vehicle weight (x-axis) and fuel efficiency (y-axis). What does the model suggest?

Your answer:

The plot shows negative association between vehicle weight and fuel efficiency. Regression model suggests there is statistically significant negative association between car weight and fuel efficiency miles per gallons, after accounting for the number of cylinders (factor(cyl)6 factor(cyl)8)

---

# Final Completion Checklist

Use this final checklist to confirm you've completed everything:

| Item | Status | Notes |
|------|--------|-------|
| ✓ Completed all 6 sections above | ☐ | |
| ✓ Answered all 6 reflection questions | ☐ | |
| ✓ Successfully rendered this document to HTML | ☐ | |
| ✓ Saved rendered HTML with correct filename | ☐ | |
| ✓ Ready to upload to Brightspace | ☐ | |

---

# Submission Instructions

For this course, you will submit your work in **two ways**:

1. **Upload .Rmd file to Brightspace** (for assignment completion)
2. **Publish to RPubs** (for portfolio & reproducibility)

## Option A: Upload to Brightspace

**Save, Render, and Submit:**

1. **Save this document** with your name: `LastName_FirstName_Setup_Checklist.Rmd`

2. **Render to HTML** by clicking "Knit" (Ctrl+Shift+K)
   - Output file: `LastName_FirstName_Setup_Checklist.html`

3. **Upload to Brightspace:**
   - Go to: EPI 553 → Assignments → Setup & Workflow Checklist
   - Click "Submit Assignment"
   - Upload the HTML file
   - Add any additional notes if needed
   - Click "Submit"

**Deadline:** January 29, 2026

---

## Option B: Publish to RPubs (Recommended - Builds Your Portfolio!)

Publishing to **RPubs** demonstrates your reproducible research skills and creates a professional portfolio. This is **optional but strongly encouraged**.

### Why Publish to RPubs?

- Build a public portfolio of your work
- Show employers your data analysis skills
- Practice reproducible research practices
- Share your work transparently

### Step-by-Step: Publishing to RPubs

#### Step 1: Create an RPubs Account (One-Time Only)

1. Go to https://rpubs.com/
2. Click **"Register"** in the top right
3. Choose a **professional username** (e.g., `lastname_firstname` or `ualbany_ID`)
   - Avoid spaces and special characters
   - This appears in your public URLs
4. Enter your email and password
5. Click **"Register"**
6. Confirm your email via the link sent to your inbox

#### Step 2: Connect RStudio to Your RPubs Account

1. Open RStudio
2. Go to **Tools → Global Options**
3. Click **"Publishing"** in the left menu
4. Click the **"Connect..."** button
5. Select **"RPubs"**
6. Log in with your RPubs credentials
7. Click **"Authorize"**
8. Return to RStudio when finished

#### Step 3: Render and Publish

1. **Render this document:** Click **"Knit"** button (Ctrl+Shift+K)
   
2. **Publish:** Once rendered, look for the **blue "Publish" button** in the Viewer pane (top right)
   - Alternative: Click **▼** next to "Knit" → "Publish Document"
   
3. **Configure Your Publication:**
   - Platform: Select **"RPubs"**
   - Title: `EPI 553: Week 1 Setup Checklist - LastName`
   - Slug (URL ID): `epi553_week1_setup_lastname`
   
4. **Click "Publish"**
   - RPubs processes your document
   - Your document is now live and public!
   - You'll see your unique RPubs URL

#### Step 4: Share Your RPubs Link

1. **Copy your RPubs URL** (e.g., https://rpubs.com/yourusername/epi553_week1_setup_lastname)

2. **Submit to Brightspace:**
   - Go to the assignment submission area
   - Paste your RPubs link in the comments section
   - Include any additional notes

3. **Optional: Share Publicly**
   - Add to your resume or GitHub profile
   - Share on LinkedIn or Twitter
   - Demonstrates your professional capabilities

### RPubs Best Practices

**Professional Presentation:**
- Include your full name as the author
- Use consistent slug naming: `epi553_weekN_lastname`
- Add course number and date to the title
- Update your publication when making corrections

**Privacy & Professionalism:**
- RPubs documents are **public by default**
- Only publish work you're comfortable sharing
- Never include sensitive or confidential data
- Your username is visible in the URL (keep it professional!)

**Building Your Portfolio:**
- Organize chronologically in your RPubs profile
- Link from your CV, resume, or GitHub
- Shows employers your data analysis skills
- Demonstrates commitment to reproducible research

### Troubleshooting RPubs Publishing

**Problem: "Publish button is greyed out"**
- Make sure output format is `html_document`
- Check YAML header at top of file
- Try rendering again (Ctrl+Shift+K)

**Problem: "Cannot connect to RPubs"**
- Verify internet connection
- Re-authorize in Tools → Global Options → Publishing
- Clear RStudio cache: Tools → Global Options → Clear All

**Problem: "Document failed to publish"**
- Check document size (limit ~25MB)
- Ensure no broken links in your document
- Try again in a few minutes

**Need Help?**
- RPubs documentation: https://rpubs.com/about/getting-started
- RStudio guide: https://posit.co/blog/r-markdown-and-rpubs/
- Contact Dr. Masum or Yiming Wang during office hours

---

## Summary: Both Submissions

| Method | Purpose | Required? |
|--------|---------|-----------|
| Brightspace | Ungrade submission | **Yes** |
| RPubs | Professional portfolio | Strongly encouraged |

**You will submit:**
1. **Required:** .Rmd file to Brightspace
2. **Optional but recommended:** RPubs link to Brightspace comments

---

# Troubleshooting

## R & RStudio Issues

**Quick Issues:**

- **"Cannot find package X"** 
  - Run: `install.packages("package_name")`
  - Make sure you're connected to the internet
  
- **"Object not found"** 
  - Make sure you ran all code chunks above in order
  - Try running code manually in the console
  
- **Plot doesn't show** 
  - Check that ggplot2 loaded correctly
  - Verify all required packages are installed
  
- **Knit button missing** 
  - Make sure this is a .Rmd file, not .R
  - Click in the document first, then look for Knit button
  
- **Firewall blocking package downloads**
  - Connect to UAlbany WiFi or use VPN
  - Try installing with: `install.packages(pkg, type = "source")`

## RPubs Publishing Issues

**Common Problems:**

- **"Publish button is greyed out"**
  - Make sure output format is `html_document`
  - Check YAML header has correct formatting
  - Try rendering again (Ctrl+Shift+K)

- **"Cannot connect to RPubs"**
  - Check your internet connection
  - Re-authorize: Tools → Global Options → Publishing → Connect
  - Clear RStudio cache if persistent

- **"Publishing failed" error**
  - Check document size (should be under 25MB)
  - Ensure no broken links in your code or text
  - Try publishing again in a few minutes
  - Check that your username contains no spaces

- **"Already published to this slug"**
  - Use a different slug/URL name
  - Or republish to update existing document

## Still Having Trouble?

**For R/RStudio Help:**
- UAlbany IT Help Desk: 518-442-3700 or helpdesk@albany.edu
- Office hours with Dr. Masum or Yiming Wang

**For RPubs Help:**
- RPubs documentation: https://rpubs.com/about/getting-started
- RStudio publishing guide: https://posit.co/blog/r-markdown-and-rpubs/

**For Course Content Questions:**

**Instructor (Dr. Muntasir Masum):**
- Email: mmasum@albany.edu
- Office: Pine Bush 255
- Office Hours: Tuesdays & Thursdays, 10:20 am - 11:30 am

**Teaching Assistant (Yiming Wang):**
- Email: ywang98@albany.edu
- Office Hours: **Mondays & Wednesdays, 11:30 am - 4:30 pm**

**Please reach out by January 27 if you have persistent issues!**

---

# Appendix A: Installing Packages (If Needed)

If packages failed to load in Section 2, run this code:


``` r
# Install all required packages
required_packages <- c(
  "tidyverse", "rmarkdown", "knitr", "ggplot2", "dplyr", 
  "car", "lmtest", "sandwich", "stargazer", "broom"
)

# Install each package
for (pkg in required_packages) {
  if (!require(pkg, character.only = TRUE)) {
    cat("Installing", pkg, "...\n")
    install.packages(pkg, dependencies = TRUE)
  }
}

cat("\n✓ Installation complete!\n")
cat("Now restart R: Ctrl+Shift+F10\n")
cat("Then reload this document and try Section 2 again.\n")

Appendix B: Creating Folders (If Needed)

If you need to create the folder structure, run this code in the R Console:

# Create folders if they don't exist
if (!dir.exists("data")) {
  dir.create("data")
  cat("✓ Created data/ folder\n")
}

if (!dir.exists("scripts")) {
  dir.create("scripts")
  cat("✓ Created scripts/ folder\n")
}

if (!dir.exists("outputs")) {
  dir.create("outputs")
  cat("✓ Created outputs/ folder\n")
}

if (!dir.exists("figures")) {
  dir.create("figures")
  cat("✓ Created figures/ folder\n")
}

cat("\nAll folders created successfully!\n")

Successfully completing this checklist means you are ready for Week 1 of EPI 553!

For questions or concerns, reach out to Dr. Masum or Yiming Wang.

Good luck! 🎓

EPI 553: Setup & Workflow Checklist

Principles of Statistical Inference II (Spring 2026)

Muntasir Masum

Due by: End of Week 1 (January 26, 2026)

Instructions

Section 1: R & RStudio Installation

Section 2: Required Packages

Section 3: Working Directory & Project Structure

Section 4: R Markdown & Rendering

Section 5: File Management & Uploads

Section 6: Data & Code Practice

Appendix B: Creating Folders (If Needed)