Merge pull request #295 from coding-for-reproducible-research/87_resources

add resources to all courses

Author: liamjberrisford

_static/multiple_regression_hyperplane.html

@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  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"}]);
+                  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"}]);
                   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}]);
 
                   nodeColors = {};

_static/multiple_regression_hyperplane_2.html

@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  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"}]);
+                  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"}]);
                   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}]);
 
                   nodeColors = {};

_static/workshops_network_hpc.html

@@ -120,6 +120,7 @@ parts:
                   - file: individual_modules/introduction_to_julia/implemented_game_of_life
                   - file: individual_modules/introduction_to_julia/visualisation
                   - file: individual_modules/introduction_to_julia/multi_file_project
+                  - file: individual_modules/introduction_to_julia/resources
           - file: course_homepages/python
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_python
@@ -138,6 +139,7 @@ parts:
                   - file: individual_modules/introduction_to_python/analysis_task_1
                   - file: individual_modules/introduction_to_python/analysis_task_2
                   - file: individual_modules/introduction_to_python/analysis_task_3
+                  - file: individual_modules/introduction_to_python/resources
               - file: individual_modules/section_landing_pages/python_for_data_analysis
                 sections:
                   - file: individual_modules/python_for_data_analysis/Python_NumPy
@@ -146,12 +148,14 @@ parts:
                   - file: individual_modules/python_for_data_analysis/Python_ScikitLearn
                   - file: individual_modules/python_for_data_analysis/data-analysis-plotly
                   - file: individual_modules/python_for_data_analysis/data-analysis-task
+                  - file: individual_modules/python_for_data_analysis/resources
               - file: individual_modules/section_landing_pages/introduction_to_machine_learning
                 sections:
                   - file: individual_modules/introduction_to_machine_learning/1_linear_regression
                   - file: individual_modules/introduction_to_machine_learning/2_model_selection
                   - file: individual_modules/introduction_to_machine_learning/3_pipeline_task
                   - file: individual_modules/introduction_to_machine_learning/4_unsupervised_learning
+                  - file: individual_modules/introduction_to_machine_learning/resources
               - file: individual_modules/section_landing_pages/markdown_with_python
                 sections:
                   - file: individual_modules/markdown_with_python/2-Motivation-and-Background
@@ -161,6 +165,7 @@ parts:
                   - file: individual_modules/markdown_with_python/6-Export-the-Document
                   - file: individual_modules/markdown_with_python/7-Markdown-Task-2
                   - file: individual_modules/markdown_with_python/8-Further-Knowledge
+                  - file: individual_modules/markdown_with_python/resources
           - file: course_homepages/R
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_r
@@ -174,6 +179,7 @@ parts:
                   - file: individual_modules/introduction_to_r/plots
                   - file: individual_modules/introduction_to_r/stats
                   - file: individual_modules/introduction_to_r/good_practise
+                  - file: individual_modules/introduction_to_r/resources
               - file: individual_modules/section_landing_pages/regression_analysis_with_R
                 sections:
                   - file: individual_modules/regression_analysis_with_R/introduction_to_regression
@@ -182,13 +188,15 @@ parts:
                   - file: individual_modules/regression_analysis_with_R/logistic_regression
                   - file: individual_modules/regression_analysis_with_R/regression_analysis_with_r_summary.ipynb
                   - file: individual_modules/regression_analysis_with_R/regression_analysis_with_r_extras
+                  - file: individual_modules/regression_analysis_with_R/resources
               - file: individual_modules/section_landing_pages/advanced_regression_analysis_with_R
                 sections:
                   - file: individual_modules/advanced_regression_analysis_with_R/mixed_effects_models
                   - file: individual_modules/advanced_regression_analysis_with_R/expanding_the_mixed_effects_model_framework
                   - file: individual_modules/advanced_regression_analysis_with_R/regression_models_with_interaction_terms
                   - file: individual_modules/advanced_regression_analysis_with_R/advanced_regression_analysis_with_R_summary
                   - file: individual_modules/advanced_regression_analysis_with_R/advanced_regression_analysis_with_R_extras
+                  - file: individual_modules/advanced_regression_analysis_with_R/resources
               - file: individual_modules/section_landing_pages/working_with_data_in_R
                 sections:
                   - file: individual_modules/working_with_data_in_R/introducing_tidyverse
@@ -199,6 +207,7 @@ parts:
                   - file: individual_modules/working_with_data_in_R/reshaping_datasets
                   - file: individual_modules/working_with_data_in_R/strings_and_dates
                   - file: individual_modules/working_with_data_in_R/summary
+                  - file: individual_modules/working_with_data_in_R/resources
               - file: individual_modules/section_landing_pages/improve_your_r_code
                 sections:
                   - file: individual_modules/improve_your_r_code/style
@@ -207,6 +216,7 @@ parts:
                   - file: individual_modules/improve_your_r_code/data_table
                   - file: individual_modules/improve_your_r_code/parallelisation
                   - file: individual_modules/improve_your_r_code/rcpp
+                  - file: individual_modules/improve_your_r_code/resources
               - file: individual_modules/section_landing_pages/Introduction_to_Markdown_in_R
                 sections:
                   - file: individual_modules/Introduction_to_Markdown_in_R/Background_to_Markdown
@@ -217,6 +227,7 @@ parts:
                   - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code
                   - file: individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files
                   - file: individual_modules/Introduction_to_Markdown_in_R/Course_Outro
+                  - file: individual_modules/Introduction_to_Markdown_in_R/resources
           - file: course_homepages/unix
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_unix
@@ -229,6 +240,7 @@ parts:
                   - file: individual_modules/introduction_to_unix/script
                   - file: individual_modules/introduction_to_unix/find
                   - file: individual_modules/introduction_to_unix/additional
+                  - file: individual_modules/introduction_to_unix/resources
       - file: cfrr_program_details/coding_practices_self_study
         sections:
           - file: course_homepages/computational_thinking
@@ -242,6 +254,7 @@ parts:
                   - file: individual_modules/computational_thinking/abstraction
                   - file: individual_modules/computational_thinking/alignment
                   - file: individual_modules/computational_thinking/final_exercise
+                  - file: individual_modules/computational_thinking/resources
           - file: course_homepages/high_performance_computing
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_hpc
@@ -254,6 +267,7 @@ parts:
                   - file: individual_modules/introduction_to_hpc/modules
                   - file: individual_modules/introduction_to_hpc/example_jobs
                   - file: individual_modules/introduction_to_hpc/exploiting_slurm
+                  - file: individual_modules/introduction_to_hpc/resources
               - file: individual_modules/section_landing_pages/parallel_computing
                 sections:
                   - file: individual_modules/parallel_computing/architecture_and_concurrency
@@ -263,6 +277,7 @@ parts:
                   - file: individual_modules/parallel_computing/mpi_simple_communication
                   - file: individual_modules/parallel_computing/mpi_collective_comms
                   - file: individual_modules/parallel_computing/mpi_parallel_fractal
+                  - file: individual_modules/parallel_computing/resources
           - file: course_homepages/software_development
             sections:
               - file: individual_modules/section_landing_pages/software_development_best_practice
@@ -276,6 +291,7 @@ parts:
                   - file: individual_modules/software_development_best_practices/testing
                   - file: individual_modules/software_development_best_practices/collaboration
                   - file: individual_modules/software_development_best_practices/reproducibility
+                  - file: individual_modules/software_development_best_practices/resources
           - file: course_homepages/version_control
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_version_control
@@ -295,6 +311,7 @@ parts:
                   - file: individual_modules/introduction_to_version_control/remote_branches_with_github
                   - file: individual_modules/introduction_to_version_control/collaborating_with_branches
                   - file: individual_modules/introduction_to_version_control/merge_conflicts
+                  - file: individual_modules/introduction_to_version_control/resources
               - file: individual_modules/section_landing_pages/intermediate_version_control
                 sections:
                   - file: individual_modules/intermediate_version_control/introduction
@@ -306,6 +323,7 @@ parts:
                   - file: individual_modules/intermediate_version_control/github_workflows
                   - file: individual_modules/intermediate_version_control/rewriting_history
                   - file: individual_modules/intermediate_version_control/further_topics
+                  - file: individual_modules/intermediate_version_control/resources
       - file: individual_modules/bibliography
 
   - caption: Short Courses

_static/workshops_network_python_ds.html

@@ -0,0 +1,39 @@
+# Resources
+
+Below are useful resources, further reading, and links referenced throughout this course.
+
+---
+
+## Official Documentation & Books
+
+- [R Markdown Cookbook (bookdown)](https://bookdown.org/yihui/rmarkdown-cookbook/)
+- [R Markdown: The Definitive Guide (PDF)](https://posit.co/wp-content/uploads/2022/10/rmarkdown-1.pdf)
+
+## R & Bioconductor Tutorials
+
+- [Microbiome Analysis: Alpha Diversity](https://microbiome.github.io/tutorials/Alphadiversity.html)
+- [Microbiome Analysis: Beta Diversity](https://microbiome.github.io/tutorials/Betadiversity.html)
+- [Microbiome Analysis: Composition](https://microbiome.github.io/tutorials/Composition.html)
+- [microbiome (Bioconductor package)](https://www.bioconductor.org/packages/release/bioc/html/microbiome.html)
+
+## Data Fluency & Reproducibility
+
+- [Monash Data Fluency: Reproducible Research in R](https://monashdatafluency.github.io/r-rep-res/index.html)
+
+## Software, AI, and Platforms
+
+- [Posit (formerly RStudio)](https://posit.co/)
+- [OpenAI ChatGPT](https://openai.com/index/chatgpt/)
+
+## Example Figures
+
+- [Sample Figure: Elsevier](https://ars.els-cdn.com/content/image/1-s2.0-S1279770723023655-gr1.jpg)
+
+## Licensing
+
+- [Creative Commons BY 4.0](https://creativecommons.org/licenses/by/4.0/)
+- [MIT License](https://opensource.org/licenses/MIT)
+
+---
+
+> *If you have suggestions for additional resources, or spot a broken link, please let the course authors know!*