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Add in magic R command and fix typo
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8 files changed

+175
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‎individual_modules/improve_your_r_code/data_table.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": null,
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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": "markdown",
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"metadata": {},
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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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},
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"source": [
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"# Fast Data Manipulation Using the `data.table` Package\n",
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"## Overview\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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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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},
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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": "3.9.6"
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"version": "3.9.19"
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}
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},
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"nbformat": 4,

‎individual_modules/improve_your_r_code/microbenchmark.ipynb

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{
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"cells": [
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"execution_count": null,
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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": "markdown",
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"metadata": {},
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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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},
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"source": [
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"## Measuring Speed with Microbenchmark\n",
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"One way of measuring the time taken to run an R function is to invoke the `Sys.time()` function from the `base` R package. Consider the following toy function:"
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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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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},
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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": "3.9.6"
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"version": "3.9.19"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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"nbformat_minor": 4
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}

‎individual_modules/improve_your_r_code/parallelisation.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": null,
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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": "markdown",
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"metadata": {},
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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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},
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"source": [
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"# Parallelisation Using the `parallel` Package\n",
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"The following section is based off of [these notes](https://dept.stat.lsa.umich.edu/~jerrick/courses/stat506_f24/16-parallel-processing.html) written by Josh Errickson at the University of Michigan. Additional information can be found in the [documentation](https://stat.ethz.ch/R-manual/R-devel/library/parallel/doc/parallel.pdf) for the parallel package.\n",
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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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},
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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": "3.9.6"
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"version": "3.9.19"
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}
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"nbformat": 4,

‎individual_modules/improve_your_r_code/rcpp.ipynb

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"cells": [
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"execution_count": null,
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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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"cell_type": "markdown",
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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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},
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"source": [
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"# Acceleration via `Rcpp` (advanced)\n",
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"## Overview\n",
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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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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.6"
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"version": "3.9.19"
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}
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"nbformat": 4,

‎individual_modules/improve_your_r_code/style.ipynb

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{
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"cells": [
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"cell_type": "code",
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"execution_count": null,
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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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"tags": [
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"remove-input"
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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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"cell_type": "markdown",
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"metadata": {},
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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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"tags": []
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"source": [
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"# Style Guides and Linters\n",
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"\n",
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"\n",
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"If you have to import a set of libraries, do so at the beginning of the file using `library()` as opposed to loading them sporadically throughout the file.\n",
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"\n",
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"Often, using comments such as `# ---------- ... ------------` can be useful to increase readability and indicate the purpose of each sub-section in the script. For example, one way of organising a small script could be as follows:\n"
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"Often, using comments such as `# ---------- ... ------------` can be useful to increase readability and indicate the purpose of each sub-section in the script. For example, one way of organising a small script could be as follows:"
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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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"name": "python3"
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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": "3.9.6"
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"version": "3.9.19"
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}
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"nbformat": 4,

‎individual_modules/improve_your_r_code/vectorisation.ipynb

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"cells": [
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"execution_count": null,
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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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"tags": [
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"remove-input"
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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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"cell_type": "markdown",
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"metadata": {},
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"slideshow": {
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"tags": []
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"source": [
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"# Vectorization in R\n",
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"For further information, refer to Section 24.5 of [Improving Performance](https://adv-r.hadley.nz/perf-improve.html) by Hadley Wickham.\n",
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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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},
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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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"nbformat": 4,

‎individual_modules/section_landing_pages/improve_your_r_code.md

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- Make use of packages such as `data.table`, `parallel`, `parallelly`, and `Rcpp` to write faster R programs.
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- Understand and apply reproducible and stylistic practices using tools like `styler`.
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## Pre-requisite Knowlede
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## Pre-requisite Knowledge
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This workshop is designed for learners who:
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‎programme_information/improve_your_r_code.ipynb

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"cell_type": "markdown",
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"id": "d12d0776-b63e-4cdf-8af7-2738a6b2ce37",
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"metadata": {
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"slideshow": {
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"tags": []
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"source": [
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"# Improve Your R Code\n",
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"\n",
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"cell_type": "code",
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"execution_count": 1,
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"id": "30d0103f-b3fb-4e2b-91c2-fc5742eede56",
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"metadata": {
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"editable": true,
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"slideshow": {
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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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{
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"data": {

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