🫁Intro to Biostatistics Unit 11 – Statistical Software & Data Management

Key Statistical Concepts

• Understand the difference between descriptive statistics summarizes and describes the basic features of a dataset and inferential statistics uses sample data to make inferences about a larger population
• Recognize the importance of measures of central tendency (mean, median, mode) provides information about the typical or central value in a dataset
• Differentiate between measures of dispersion (range, variance, standard deviation) quantifies the amount of variation or spread in a dataset
• Identify the properties of normal distribution a symmetric, bell-shaped curve with a well-defined mean and standard deviation
  • Approximately 68% of data falls within one standard deviation of the mean, 95% within two standard deviations, and 99.7% within three standard deviations
• Comprehend the concept of hypothesis testing a statistical method used to make decisions or draw conclusions about a population based on sample data
• Distinguish between null hypothesis (assumes no significant difference or effect) and alternative hypothesis (assumes a significant difference or effect)
• Interpret p-values the probability of obtaining the observed results or more extreme results, assuming the null hypothesis is true
  • A small p-value (typically < 0.05) suggests strong evidence against the null hypothesis, while a large p-value (> 0.05) indicates weak evidence against the null hypothesis

Introduction to Statistical Software

• Familiarize yourself with popular statistical software packages (R, Python, SAS, SPSS, Stata) used for data analysis, visualization, and statistical modeling in biostatistics
• Understand the benefits of using statistical software automates complex calculations, handles large datasets, and provides a wide range of built-in statistical functions and tests
• Learn the basic syntax and commands of the chosen statistical software to perform data manipulation, analysis, and visualization tasks
• Explore the integrated development environment (IDE) or graphical user interface (GUI) of the software to navigate through different features and options
• Utilize built-in help documentation, online resources, and community forums to troubleshoot issues and learn advanced techniques in the statistical software
• Practice importing and exporting various data file formats (CSV, Excel, JSON) to and from the statistical software
• Discover the power of libraries or packages in extending the functionality of the statistical software by providing additional tools and methods for specific analysis tasks

Data Types and Structures

• Understand the different data types (numeric, character, logical, factor) used to represent variables in statistical software
  • Numeric data represents quantitative values (integers or floating-point numbers)
  • Character data represents text or string values
  • Logical data represents binary values (TRUE or FALSE)
  • Factor data represents categorical variables with a fixed number of levels or categories
• Recognize the importance of data structures (vectors, matrices, data frames) in organizing and manipulating data in statistical software
  • Vectors are one-dimensional arrays that hold elements of the same data type
  • Matrices are two-dimensional arrays with rows and columns, where all elements are of the same data type
  • Data frames are two-dimensional structures similar to matrices but can hold columns of different data types
• Learn how to create, access, and modify elements within data structures using indexing and subsetting techniques
• Understand the concept of missing values (NA, NaN) and how they are handled in different data structures and statistical analyses
• Explore advanced data structures (lists, arrays, tibbles) that provide additional flexibility and functionality for complex data manipulation tasks
• Practice reshaping data between wide and long formats using functions like

  pivot_longer()

  and

  pivot_wider()

  to facilitate different types of analyses

Data Cleaning and Preprocessing

• Recognize the importance of data cleaning and preprocessing ensures data quality, consistency, and suitability for analysis
• Identify and handle missing values through techniques like deletion, imputation, or interpolation based on the nature of the missing data and the analysis requirements
• Detect and resolve inconsistencies, errors, and outliers in the dataset using summary statistics, visualization, or domain knowledge
• Perform data type conversions (numeric to factor, character to date) to ensure variables are in the appropriate format for analysis
• Apply data normalization or standardization techniques (z-score, min-max scaling) to bring variables to a common scale or distribution
• Conduct data transformations (log, square root, Box-Cox) to improve the normality, linearity, or homoscedasticity of variables
• Merge or join multiple datasets based on common variables or keys to create a unified dataset for analysis
• Subset or filter data based on specific conditions or criteria to focus on relevant observations or variables

Descriptive Statistics and Visualization

• Calculate and interpret measures of central tendency (mean, median, mode) to summarize the typical or central value in a dataset
• Compute and interpret measures of dispersion (range, variance, standard deviation) to assess the variability or spread of the data
• Generate frequency tables and contingency tables to summarize categorical variables and their relationships
• Create informative visualizations (histograms, box plots, scatter plots, bar charts) to explore the distribution, relationships, and patterns in the data
  • Histograms display the distribution of a continuous variable using bins and frequencies
  • Box plots provide a summary of the five-number summary (minimum, first quartile, median, third quartile, maximum) and identify outliers
  • Scatter plots show the relationship between two continuous variables
  • Bar charts compare the frequencies or proportions of categorical variables
• Customize visualizations by modifying plot elements (titles, labels, colors, scales) to enhance clarity and aesthetics
• Apply data transformations or faceting techniques to create more informative and targeted visualizations
• Interpret and communicate insights from descriptive statistics and visualizations to stakeholders or decision-makers

Basic Statistical Analyses

• Perform hypothesis tests (t-tests, ANOVA, chi-square) to make inferences about population parameters based on sample data
  • T-tests compare means between two groups or against a known value
  • ANOVA (Analysis of Variance) compares means across multiple groups
  • Chi-square tests assess the association between categorical variables
• Conduct correlation analysis to measure the strength and direction of the linear relationship between two continuous variables
• Apply regression analysis (linear, logistic, Poisson) to model the relationship between a dependent variable and one or more independent variables
  • Linear regression models the relationship between a continuous dependent variable and one or more independent variables
  • Logistic regression models the probability of a binary outcome based on one or more independent variables
  • Poisson regression models the count of events based on one or more independent variables
• Interpret the results of statistical analyses, including coefficients, p-values, confidence intervals, and goodness-of-fit measures
• Assess the assumptions and diagnostics of statistical models to ensure the validity and reliability of the results
• Apply appropriate post-hoc tests or corrections (Bonferroni, Tukey) to control for multiple comparisons or Type I error

Data Management Best Practices

• Develop a clear and consistent naming convention for variables, files, and folders to ensure easy identification and organization
• Use version control systems (Git, SVN) to track changes, collaborate with others, and maintain a history of the data and analysis files
• Implement a structured and hierarchical folder organization system to store raw data, processed data, scripts, and output files separately
• Document data sources, transformations, and analysis steps using README files, codebooks, or data dictionaries to ensure reproducibility and transparency
• Regularly backup and store data in secure and reliable storage systems (cloud storage, external hard drives) to prevent data loss or corruption
• Anonymize or de-identify sensitive or confidential data to protect privacy and comply with ethical and legal requirements
• Validate and verify data integrity through checks for completeness, consistency, and accuracy
• Establish data access and sharing protocols to control who can access, modify, or distribute the data based on roles and permissions

Practical Applications in Biostatistics

• Epidemiological studies: Apply statistical methods to investigate the distribution, determinants, and control of health-related states or events in specified populations
  • Calculate measures of disease frequency (prevalence, incidence) and association (relative risk, odds ratio)
  • Conduct cohort studies or case-control studies to identify risk factors or protective factors for diseases
• Clinical trials: Design and analyze experiments to evaluate the safety and efficacy of new medical interventions (drugs, devices, therapies)
  • Determine sample size and power calculations to ensure adequate statistical power
  • Perform randomization and blinding techniques to minimize bias and confounding
  • Analyze treatment effects using appropriate statistical tests and models
• Survival analysis: Investigate the time until the occurrence of an event of interest (death, relapse, recovery) and factors influencing survival probabilities
  • Estimate survival functions using Kaplan-Meier curves or Cox proportional hazards models
  • Compare survival distributions between groups using log-rank tests or Cox regression
• Diagnostic tests: Evaluate the performance and accuracy of diagnostic tests in detecting or ruling out a disease or condition
  • Calculate sensitivity, specificity, positive predictive value, and negative predictive value
  • Construct and interpret receiver operating characteristic (ROC) curves to assess the trade-off between sensitivity and specificity
• Genomic data analysis: Apply statistical methods to analyze and interpret high-dimensional genomic data (gene expression, DNA methylation, single nucleotide polymorphisms)
  • Perform differential expression analysis to identify genes associated with a particular condition or treatment
  • Conduct pathway analysis or gene set enrichment analysis to identify biological processes or functions overrepresented in a gene list
• Meta-analysis: Combine and synthesize results from multiple independent studies to obtain a more precise and comprehensive estimate of an effect or association
  • Assess heterogeneity between studies using statistical tests (Cochran's Q, I-squared)
  • Estimate pooled effect sizes using fixed-effect or random-effects models based on the assumption of heterogeneity