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Merge pull request #292 from coding-for-reproducible-research/286_remove_r_magic
Change kernel, remove magic, add new R style quiz html
2 parents d98d6c6 + 51121d9 commit 1e7f40c

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‎_config.yml

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- 'individual_modules/introduction_to_r/plots.ipynb'
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- 'individual_modules/introduction_to_r/stats.ipynb'
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- 'individual_modules/introduction_to_r/good_practise.ipynb'
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- 'individual_modules/introduction_to_r/gettingstarted.ipynb'
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- 'individual_modules/regression_analysis_with_R/introduction_to_regression.ipynb'
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- 'individual_modules/regression_analysis_with_R/hypothesis_testing.ipynb'
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- 'individual_modules/regression_analysis_with_R/multiple_linear_regression.ipynb'

‎_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": "#4682B4", "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": "#4682B4", "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": "#4682B4", "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": "#4682B4", "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": "#4682B4", "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": "#4682B4", "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": "#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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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_r_ds.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 R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Regression analysis with R, Working With Data In R"}, {"color": "#FFD700", "id": "Regression analysis with R", "label": "Regression analysis with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Regression analysis with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Advanced Regression Analysis With R "}, {"color": "#FFD700", "id": "Working With Data In R", "label": "Working With Data In R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Working With Data In R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Advanced Regression Analysis With R ", "label": "Advanced Regression Analysis With R ", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Advanced Regression Analysis With R \nCourse Pre-reqs: Regression analysis with R\nSubsequent Courses: None"}, {"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"}]);
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nodes = new vis.DataSet([{"color": "#4682B4", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Regression analysis with R, Working With Data In R"}, {"color": "#4682B4", "id": "Regression analysis with R", "label": "Regression analysis with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Regression analysis with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Advanced Regression Analysis With R "}, {"color": "#4682B4", "id": "Working With Data In R", "label": "Working With Data In R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Working With Data In R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Advanced Regression Analysis With R ", "label": "Advanced Regression Analysis With R ", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Advanced Regression Analysis With R \nCourse Pre-reqs: Regression analysis with R\nSubsequent Courses: None"}, {"color": "#4682B4", "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": "#4682B4", "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": "#4682B4", "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"}]);
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edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to R", "to": "Regression analysis with R", "width": 1}, {"arrows": "to", "from": "Introduction to R", "to": "Working With Data In R", "width": 1}, {"arrows": "to", "from": "Regression analysis with R", "to": "Advanced Regression Analysis With R ", "width": 1}, {"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}]);
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nodeColors = {};

‎contributing/contributing_guidelines.ipynb

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"\n",
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"These tutorials are distrbuted as an R package [cfrr-r-tutorials](https://github.com/coding-for-reproducible-research/cfrr-r-tutorials) and should be developed in that repo. A homepage, with details on the course and instructions for how to launch the tutorial should be included in this repo. \n",
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"\n",
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"#### Guidelines for R Courses:\n",
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"#### Guidelines for R Courses:xw\n",
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"- Use learnr tutorials (`.Rmd` files) for all course materials.\n",
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"- All courses will have a pre-requisite that the participants have some familiarity with R, however the precise details to what is this includes will depend on the course , and needs to be defined. \n",
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"- Incorporate interactive code exercises and quizzes to reinforce learning.\n",
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"- Ensure that tutorials are self-contained and include all necessary data and instructions.\n",
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"- Use clear and concise explanations in markdown to guide learners through the content.\n",
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"- Test all tutorials to ensure they function correctly and provide accurate feedback.\n",
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"\n",
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"#### Adding an R Kernel to Jupyter Notebooks\n",
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"\n",
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"To run the R code within the Jupyter Notebooks used in this repository you will need an R kernel, which you can acquire by following the steps below.\n",
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"\n",
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"##### Install R\n",
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"\n",
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"Install R from the official CRAN website: [https://cran.r-project.org/](https://cran.r-project.org/)\n",
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"\n",
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"Alternatively, on Linux:\n",
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"\n",
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"```bash\n",
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"sudo apt update\n",
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"sudo apt install r-base\n",
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"```\n",
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"\n",
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"##### Install IRKernel from R\n",
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"\n",
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"Open R (in terminal or RStudio) and run:\n",
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"\n",
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"```r\n",
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"install.packages(\"IRkernel\")\n",
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"IRkernel::installspec(name = \"ir\", displayname = \"R\")\n",
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"```\n",
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"\n",
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"- `name`: Internal name used by Jupyter\n",
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"- `displayname`: Name shown in the Jupyter interface\n",
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"\n",
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"This will register the R kernel with Jupyter.\n",
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"\n",
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"##### Verify Installation\n",
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"\n",
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"Run:\n",
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"\n",
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"```bash\n",
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"jupyter kernelspec list\n",
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"```\n",
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"\n",
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"## Course Delivery\n",
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"\n",

‎individual_modules/advanced_regression_analysis_with_R/advanced_regression_analysis_with_R_extras.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "b9ecb632-1728-4245-be1c-649f2165a3fd",
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"metadata": {
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"editable": true,
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"slideshow": {
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"slide_type": ""
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},
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"tags": [
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"remove-input"
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]
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},
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"outputs": [],
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"source": [
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"%load_ext rpy2.ipython"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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},
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"outputs": [],
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"source": [
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"%%R\n",
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"knitr::opts_chunk$set(echo = TRUE)\n",
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"\n",
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"nInd<-175\n",
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}
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],
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"source": [
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"%%R\n",
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"model.int<-lm(CognitionB ~ VisitNum*Sex, dat = cogDat)\n",
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"summary(model.int)"
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]
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}
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],
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"model.int<-lm(CognitionB ~ VisitNum:Sex, dat = cogDat)\n",
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"summary(model.int)"
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}
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"model.int<-lm(CognitionB ~ Sex + VisitNum:Sex, dat = cogDat)\n",
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"summary(model.int)"
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]
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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"display_name": "R",
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"language": "R",
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"name": "ir"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.19"
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"codemirror_mode": "r",
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"file_extension": ".r",
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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "4.3.3"
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}
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},
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"nbformat": 4,

‎individual_modules/advanced_regression_analysis_with_R/advanced_regression_analysis_with_R_summary.ipynb

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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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"display_name": "R",
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"language": "R",
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"name": "ir"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.19"
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"codemirror_mode": "r",
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"file_extension": ".r",
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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "4.3.3"
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}
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},
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"nbformat": 4,

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