|
1 Introduction: Biostatistics and R |
|
|
1.1 Purpose of this Text |
|
|
1.2 Development of Biostatistics |
|
|
1.3 Development of R |
|
|
1.4 How R is Used in this Text |
|
|
1.5 Import Data into R |
|
|
1.6 Addendum1: Efficient Programming with R, Project Workflow, and Good Programming Practices (gpp) |
|
|
1.7 Addendum2: Preview of Descriptive Statistics and Graphics Using R |
|
|
1.8 Addendum3: R and Beautiful Graphics |
|
|
1.9 Addendum4: Research Designs Used in Biostatistics |
|
|
1.10 Prepare to Exit, Save, and Later Retrieve this R Session |
|
|
1.11 External Data and/or Data Resources Used in this Lesson |
|
|
2 Data Exploration, Descriptive Statistics, and Measures of Central Tendency |
|
|
2.1 Background |
|
|
2.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
2.3 Organize the Data and Display the Code Book |
|
|
2.4 Conduct a Visual Data Check Using Graphics (e.g., Figures) |
|
|
2.5 Descriptive Statistics for Initial Analysis of the Data |
|
|
2.6 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
2.7 Statistical Test(s) |
|
|
2.8 Summary |
|
|
2.9 Addendum1: Specialized External Packages and Functions |
|
|
2.10 Addendum2: Parametric v Nonparametric |
|
|
2.11 Addendum3: Additional Practice Datasets for Data with Normal Distribution Patterns and Data That Do Not Exhibit Normal Distribution Patterns |
|
|
2.12 Prepare to Exit, Save, and Later Retrieve this R Session |
|
|
2.13 External Data and/or Data Resources Used in this Lesson |
|
|
3 Student's t-Test for Independent Samples |
|
|
3.1 Background |
|
|
3.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
3.3 Organize the Data and Display the Code Book |
|
|
3.4 Conduct a Visual Data Check Using Graphics (e.g., Figures) |
|
|
3.5 Descriptive Statistics for Initial Analysis of the Data |
|
|
3.6 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
3.7 Statistical Test(s) |
|
|
3.8 Summary of Outcomes |
|
|
3.9 Addendum1: t-Statistic v z-Statistic |
|
|
3.10 Addendum2: Parametric v Nonparametric |
|
|
3.11 Addendum3: Additional Practice Datasets for Data with Normal Distribution Patterns and Data That Do Not Exhibit Normal Distribution Patterns |
|
|
3.12 Prepare to Exit, Save, and Later Retrieve This R Session |
|
|
3.13 External Data and/or Data Resources Used in this Lesson |
|
|
4 Student's t-Test for Matched Pairs |
|
|
4.1 Background |
|
|
4.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
4.3 Organize the Data and Display the Code Book |
|
|
4.4 Conduct a Visual Data Check Using Graphics(e.g., Figures) |
|
|
4.5 Descriptive Statistics for Initial Analysis of the Data |
|
|
4.6 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
4.7 Statistical Test(s) |
|
|
4.8 Summary of Outcomes |
|
|
4.9 Addendum1: R-Based Tools for Unstacked (e.g. Wide) Data |
|
|
4.10 Addendum2: Stacked Data and Student's t-Test for Matched Pairs |
|
|
4.11 Addendum 3: The Impact of N on Student's t-Test |
|
|
4.12 Addendum 4: Parametric v Nonparametric |
|
|
4.13 Addendum5: Additional Practice Datasets for Data with Normal Distribution Patterns and Data That Do Not Exhibit Normal Distribution Patterns |
|
|
4.14 Prepare to Exit, Save, and Later Retrieve This R Session |
|
|
4.15 External Data and/or Data Resources Used in this Lesson |
|
|
5 Oneway Analysis of Variance (ANOVA) |
|
|
5.1 Background |
|
|
5.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
5.3 Organize the Data and Display the Code Book |
|
|
5.4 Conduct a Visual Data Check Using Graphics(e.g., Figures) |
|
|
5.5 Descriptive Statistics for Initial Analysis of the Data |
|
|
5.6 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
5.7 Statistical Test(s) |
|
|
5.8 Summary of Outcomes |
|
|
5.9 Addendum1: Other Packages for Display of Oneway ANOVA |
|
|
5.10 Addendum2: Parametric v Nonparametric |
|
|
5.11 Addendum3: Additional Practice Data Sets |
|
|
5.12 Prepare to Exit, Save, and Later Retrieve This R Session |
|
|
5.13 External Data and/or Data Resources Used in this Lesson |
|
|
6 Twoway Analysis of Variance (ANOVA) |
|
|
6.1 Background |
|
|
6.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
6.3 Organize the Data and Display the Code Book |
|
|
6.4 Conduct a Visual Data Check Using Graphics (e.g., Figures) |
|
|
6.5 Descriptive Statistics for Initial Analysis of the Data |
|
|
6.6 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
6.7 Statistical Test(s) |
|
|
6.8 Summary of Outcomes |
|
|
6.9 Addendum 1: Other Packages for Display of Twoway ANOVA |
|
|
6.10 Addendum 2: Parametric v Nonparametric |
|
|
6.11 Addendum 3: Additional Practice Data Sets |
|
|
6.12 Prepare to Exit, Save, and Later Retrieve This R Session |
|
|
6.13 External Data and/or Data Resources Used in this Lesson |
|
|
7 Correlation, Association, Regression, Likelihood, and Prediction |
|
|
7.1 Background |
|
|
7.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
7.3 Organize the Data and Display the Code Book |
|
|
7.4 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
7.5 Statistical Test(s) |
|
|
7.6 Summary of Outcomes |
|
|
7.7 Addendum 1: Multiple Regression |
|
|
7.8 Addendum 2: Likelihood and Odds Ratio |
|
|
7.9 Addendum 3:Parametric v Nonparametric |
|
|
7.10 Addendum 4: Additional Practice Data Sets |
|
|
7.11 Prepare to Exit, Save, and Later Retrieve This R Session |
|
|
7.12 External Data and/or Data Resources Used in this Lesson |
|
|
8 Working with Large and Complex Datasets |
|
|
8.1 Background |
|
|
8.2 Import Data in Comma-Separated Values (.csv) File Format and/or Self Generate the Data Using R-Based Functions |
|
|
8.3 Organize the Data and Display the Code Book |
|
|
8.4 Conduct a Visual Data Check Using Graphics (e.g., Figures) |
|
|
8.5 Descriptive Statistics for Initial Analysis of the Data |
|
|
8.6 Quality Assurance, Data Distribution, and Tests for Normality |
|
|
8.7 Statistical Test(s) |
|
|
8.8 Summary of Outcomes |
|
|
8.9 Addendum1: Additional Graphics, to Show Relationships Between and Among Data |
|
|
8.10 Addendum2: Graphics Using the lattice Package |
|
|
8.11 Addendum3: Graphics Using the ggplot2 Package |
|
|
8.12 Addendum 4: Beyond an Introduction to R - Use the tidyverse to Create Subsets of Original Datasets |
|
|
8.13 Prepare to Exit, Save, and Later Retrieve This R Session |
|
|
8.14 External Data and/or Data Resources Used in this Lesson |
|
|
9 Future Actions and Next Steps |
|
|
9.1 Use of This Text |
|
|
9.2 R and Beautiful Reporting with R Markdown |
|
|
9.3 Future Use of R for Biostatistics |
|
|
9.4 Big Data and Bio Informatics |
|
|
9.5 External Resources |
|
|
9.6 Contact the Authors |
|
|
1 Introduction: Biostatistics and R |
|
|
1.1 Purpose of this Text |
|
|
1.2 Development of Biostatistics |
|
ＥＢ
