From 3ca7a1965e048d66bd12ea63169cb91489651a03 Mon Sep 17 00:00:00 2001 From: Adam Claridge-Chang Date: Sat, 9 Sep 2023 21:44:37 +0800 Subject: [PATCH] New Additional Resource page Moved Additional Resources into its own page. --- nbs/05_Additional_resources.ipynb | 161 ++++++++++++++++++++++++++++++ nbs/index.ipynb | 17 +--- 2 files changed, 164 insertions(+), 14 deletions(-) create mode 100644 nbs/05_Additional_resources.ipynb diff --git a/nbs/05_Additional_resources.ipynb b/nbs/05_Additional_resources.ipynb new file mode 100644 index 0000000..e88f0f0 --- /dev/null +++ b/nbs/05_Additional_resources.ipynb @@ -0,0 +1,161 @@ +{ + "cells": [ + { + "cell_type": "raw", + "id": "32b64810", + "metadata": {}, + "source": [ + "---\n", + "output-file: Additional.html\n", + "title: 05. Additional resources\n", + "\n", + "---" + ] + }, + { + "cell_type": "markdown", + "id": "4dc195ef", + "metadata": {}, + "source": [ + "## Additional resources and building your skills\n", + "\n", + "Try using the [estimationstats.com](https://www.estimationstats.com/#/) web app to analyze your own grouped data.\n", + "\n", + "Open and have a look at the sample multivariate\n", + "[data](https://docs.google.com/spreadsheets/d/1F0c5I_S9_NnLKPMQxJkEfzGfhzQeR26SgkiHSTFwKDE/edit?usp=sharing).\n", + "Go through the [introductory\n", + "notebook](https://drive.google.com/file/d/1m_l4k5ZaUc03hpvcfBd_Riy2nXYDpFXg/view?usp=sharing)\n", + "that demonstrates data analysis.\n", + "\n", + "We recommend the following texts to strengthen your data-analysis and\n", + "presentation skills. They can be dipped into over the coming months or\n", + "years, and used as references. Being familiar with some or all of this\n", + "material will help you write your first-author paper/s and doctoral\n", + "thesis.\n", + "\n", + "### *Key resources*\n", + "\n", + "- Estimation: Our\n", + " [estimationstats.com](https://www.estimationstats.com/#/background)\n", + " site has introductory information on estimation and specific types\n", + " of\n", + " [analyses](https://www.estimationstats.com/#/user-guide/two-independent-groups)\n", + " and [effect\n", + " sizes](https://www.estimationstats.com/#/about-effect-sizes).\n", + "\n", + "- Datavis: Claus Wilke’s free online\n", + " [book](https://clauswilke.com/dataviz/index.html) is a great\n", + " introduction to data visualization, and a style guide. It is written\n", + " in R, which is the best language for statistics.\n", + "\n", + "- Coding: There are many online resources to learn coding. Published\n", + " in 2021, [A Data-Centric Introduction to\n", + " Computing](https://dcic-world.org/) uses a Python-like teaching\n", + " language ([Pyret](https://www.pyret.org/)) to introduce key concepts\n", + " in computer science.\n", + "\n", + "### *Additional resources*\n", + "\n", + "#### *Some are free, some you will need to buy or borrow from the library.*\n", + "\n", + "- Estimation: If you want to learn about estimation statistics in\n", + " greater depth, there is Calin-Jageman and Cumming’s\n", + " [textbook](http://thenewstatistics.com/itns/) that is well-written,\n", + " funny, and clear. The authors also run a\n", + " [blog](https://thenewstatistics.com/itns/).\n", + "\n", + "- Estimation: Christoph Bernard’s account of the pioneering experience\n", + " of a major journal (*eNeuro*) recommending estimation as standard:\n", + " the [initial\n", + " announcement](https://www.eneuro.org/content/6/4/ENEURO.0259-19.2019),\n", + " [author\n", + " feedback](https://blog.eneuro.org/2021/02/discussion-est-stats-author-feedback),\n", + " and [after one\n", + " year](https://www.eneuro.org/content/8/2/ENEURO.0091-21.2021).\n", + "\n", + "- Coding: The paid coding tutorial [Learn Python The Hard\n", + " Way](https://learncodethehardway.org/python/) has a good reputation,\n", + " but there are also many free options (see\n", + " [DCIC](https://dcic-world.org/) above) with great reviews.\n", + "\n", + "- Coding: It will help to learn to use your computer’s\n", + " [Unix-style](https://youtu.be/tc4ROCJYbm0) command-line\n", + " [shell](https://en.wikipedia.org/wiki/Unix_shell). This interface\n", + " will allow you to use package managers like\n", + " [conda](https://docs.conda.io/en/latest/) and\n", + " [homebrew](https://brew.sh/), version-control tools like\n", + " [git](https://git-scm.com/), and other important tools. There are\n", + " many [books](https://www.linuxcommand.org/index.php) about the\n", + " shell, with only minor differences between MacOS,\n", + " [Windows](https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/),\n", + " and Linux.\n", + "\n", + "- Datavis: A brief guide to oral–visual data presentations\n", + " ([talks](http://www.howtogiveatalk.com/)).\n", + "\n", + "- Datavis: A reader-funded textbook on\n", + " [typography](http://practicaltypography.com/presentations.html),\n", + " including for slides. Since so much communication relies on text,\n", + " typography is an important part of the data interface.\n", + "\n", + "- Datavis: For historical perspectives, Edward Tufte’s\n", + " [books](https://www.edwardtufte.com/tufte/) are classic texts to\n", + " develop your design skills, and there is Friendly and Wainer’s\n", + " [History of Data\n", + " Visualization](https://friendly.github.io/HistDataVis/).\n", + "\n", + "- As you progress, you will want to develop your skills in areas like\n", + " bioinformatics, image processing, and/or machine learning. The iris\n", + " dataset is widely used for training in multivariate data analysis,\n", + " with many online tutorials.\n", + " \n", + "- The social reasons to learn programming also apply to programming for research." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "acd30338-0dd6-4949-87cf-57d0844c239f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%%HTML\n", + "" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cef28733", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/nbs/index.ipynb b/nbs/index.ipynb index 747d7a5..26a4bdd 100644 --- a/nbs/index.ipynb +++ b/nbs/index.ipynb @@ -26,13 +26,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "**Part of GMS6812 2022: Foundations of Precision Medicine hands-on workshops (PhD programme in Clinical and Translational Sciences)**\n", - "\n", - "__________________________\n", - "\n", - "9 am - 1 pm, Febuary 14, 2023\n", - "\n", - "Duke-NUS Medical School" + "**This material is used in Duke-NUS Medical School classes:**\n", + "* GMS6812 2022: Foundations of Precision Medicine hands-on workshops for the PhD programme in Clinical and Translational Sciences.\n", + "* IBM Ethics and Personal and Professional Development Session" ] }, { @@ -47,13 +43,6 @@ "\n", "If we have more time in class, you will also be introduced to our estimation statistics package [DABEST Introduction](dabest_introduction.html).\n" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {