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add resources to all courses
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‎_static/multiple_regression_hyperplane.html

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‎_static/multiple_regression_hyperplane_2.html

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‎_static/workshops_network_hpc.html

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// parsing and collecting nodes and edges from the python
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nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#FFD700", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC, Introduction to Version Control with Git and GitHub"}, {"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: None"}]);
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nodes = new vis.DataSet([{"color": "#FF6347", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#FF6347", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC, Introduction to Version Control with Git and GitHub"}, {"color": "#FF6347", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FF6347", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: None"}]);
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edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to HPC", "to": "Parallel Computing", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to HPC", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}]);
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nodeColors = {};

‎_static/workshops_network_python_ds.html

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// parsing and collecting nodes and edges from the python
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nodes = new vis.DataSet([{"color": "#FF6347", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FF6347", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#FF6347", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}, {"color": "#FF6347", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#FF6347", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
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nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#FFD700", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}, {"color": "#FFD700", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#FFD700", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
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edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis", "width": 1}, {"arrows": "to", "from": "Python for Data Analysis", "to": "Introduction to Machine Learning", "width": 1}]);
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nodeColors = {};

‎_toc.yml

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- file: individual_modules/introduction_to_julia/implemented_game_of_life
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- file: individual_modules/introduction_to_julia/visualisation
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- file: individual_modules/introduction_to_julia/multi_file_project
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- file: individual_modules/introduction_to_julia/resources
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- file: course_homepages/python
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- file: individual_modules/section_landing_pages/introduction_to_python
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- file: individual_modules/introduction_to_python/analysis_task_1
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- file: individual_modules/introduction_to_python/analysis_task_2
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- file: individual_modules/introduction_to_python/analysis_task_3
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- file: individual_modules/introduction_to_python/resources
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- file: individual_modules/section_landing_pages/python_for_data_analysis
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- file: individual_modules/python_for_data_analysis/Python_ScikitLearn
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- file: individual_modules/python_for_data_analysis/data-analysis-plotly
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- file: individual_modules/python_for_data_analysis/data-analysis-task
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- file: individual_modules/python_for_data_analysis/resources
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- file: individual_modules/section_landing_pages/introduction_to_machine_learning
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- file: individual_modules/introduction_to_machine_learning/1_linear_regression
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- file: individual_modules/introduction_to_machine_learning/2_model_selection
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- file: individual_modules/introduction_to_machine_learning/3_pipeline_task
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- file: individual_modules/introduction_to_machine_learning/4_unsupervised_learning
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- file: individual_modules/introduction_to_machine_learning/resources
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- file: individual_modules/section_landing_pages/markdown_with_python
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- file: individual_modules/markdown_with_python/6-Export-the-Document
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- file: individual_modules/markdown_with_python/8-Further-Knowledge
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- file: individual_modules/markdown_with_python/resources
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- file: course_homepages/R
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- file: individual_modules/introduction_to_r/good_practise
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- file: individual_modules/regression_analysis_with_R/logistic_regression
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- file: individual_modules/regression_analysis_with_R/regression_analysis_with_r_summary.ipynb
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- file: individual_modules/regression_analysis_with_R/resources
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- file: individual_modules/advanced_regression_analysis_with_R/mixed_effects_models
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- file: individual_modules/advanced_regression_analysis_with_R/resources
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- file: individual_modules/section_landing_pages/working_with_data_in_R
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- file: individual_modules/working_with_data_in_R/summary
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- file: individual_modules/working_with_data_in_R/resources
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- file: individual_modules/section_landing_pages/improve_your_r_code
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- file: individual_modules/improve_your_r_code/parallelisation
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- file: individual_modules/improve_your_r_code/rcpp
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- file: individual_modules/improve_your_r_code/resources
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- file: individual_modules/section_landing_pages/Introduction_to_Markdown_in_R
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- file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code
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- file: individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files
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- file: individual_modules/Introduction_to_Markdown_in_R/Course_Outro
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- file: individual_modules/Introduction_to_Markdown_in_R/resources
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- file: course_homepages/unix
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- caption: Short Courses

‎individual_modules/Introduction_to_Markdown_in_R/resources.md

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# Resources
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Below are useful resources, further reading, and links referenced throughout this course.
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---
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## Official Documentation & Books
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- [R Markdown Cookbook (bookdown)](https://bookdown.org/yihui/rmarkdown-cookbook/)
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- [R Markdown: The Definitive Guide (PDF)](https://posit.co/wp-content/uploads/2022/10/rmarkdown-1.pdf)
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## R & Bioconductor Tutorials
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- [Microbiome Analysis: Alpha Diversity](https://microbiome.github.io/tutorials/Alphadiversity.html)
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- [Microbiome Analysis: Beta Diversity](https://microbiome.github.io/tutorials/Betadiversity.html)
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- [Microbiome Analysis: Composition](https://microbiome.github.io/tutorials/Composition.html)
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- [microbiome (Bioconductor package)](https://www.bioconductor.org/packages/release/bioc/html/microbiome.html)
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## Data Fluency & Reproducibility
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- [Monash Data Fluency: Reproducible Research in R](https://monashdatafluency.github.io/r-rep-res/index.html)
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## Software, AI, and Platforms
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- [Posit (formerly RStudio)](https://posit.co/)
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- [OpenAI ChatGPT](https://openai.com/index/chatgpt/)
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## Example Figures
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- [Sample Figure: Elsevier](https://ars.els-cdn.com/content/image/1-s2.0-S1279770723023655-gr1.jpg)
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## Licensing
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- [Creative Commons BY 4.0](https://creativecommons.org/licenses/by/4.0/)
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- [MIT License](https://opensource.org/licenses/MIT)
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---
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> *If you have suggestions for additional resources, or spot a broken link, please let the course authors know!*

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