R Programming

  1. Package Management and Development
    1. Using R Packages
      1. Package Discovery
        1. CRAN Task Views
          1. Package Search Strategies
            1. Package Documentation
            2. Package Installation
              1. `install.packages()` Function
                1. Installation Options
                  1. Dependency Management
                    1. Installing from GitHub
                      1. Installing from Source
                      2. Package Loading
                        1. `library()` vs. `require()`
                          1. Package Namespaces
                            1. Selective Function Import
                            2. Package Management
                              1. Updating Packages
                                1. Removing Packages
                                  1. Package Version Management
                                    1. Dependency Conflicts
                                  2. Package Repositories
                                    1. CRAN Repository
                                      1. Package Submission Process
                                        1. Quality Standards
                                          1. Maintenance Requirements
                                          2. Bioconductor
                                            1. Bioinformatics Focus
                                              1. Installation Process
                                                1. Release Cycles
                                                2. GitHub Packages
                                                  1. Development Versions
                                                    1. Installation Methods
                                                    2. Private Repositories
                                                      1. Corporate Package Management
                                                        1. Custom Repositories
                                                      2. Introduction to Package Development
                                                        1. Package Structure
                                                          1. Directory Organization
                                                            1. Required Files
                                                              1. Optional Components
                                                              2. Package Creation
                                                                1. `usethis` Package
                                                                  1. Package Skeleton Creation
                                                                    1. Initial Setup
                                                                    2. Function Development
                                                                      1. Writing Package Functions
                                                                        1. Function Documentation
                                                                          1. Export Specifications
                                                                          2. Documentation with roxygen2
                                                                            1. Roxygen Comments
                                                                              1. Function Documentation
                                                                                1. Package-level Documentation
                                                                                  1. Vignette Creation
                                                                                  2. Testing
                                                                                    1. `testthat` Package
                                                                                      1. Unit Test Creation
                                                                                        1. Test Organization
                                                                                          1. Continuous Testing
                                                                                          2. Package Building and Checking
                                                                                            1. `R CMD build`
                                                                                              1. `R CMD check`
                                                                                                1. CRAN Checks
                                                                                                  1. Error Resolution
                                                                                                  2. Version Control Integration
                                                                                                    1. Git Integration
                                                                                                      1. GitHub Workflows
                                                                                                        1. Continuous Integration

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                                                                                                    14. Advanced R Programming