From c8cd56125e5f69bd738fb8f7e3b51cc0e0268a34 Mon Sep 17 00:00:00 2001 From: gabrielodom Date: Thu, 30 Nov 2023 22:33:25 -0500 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- about.html | 83 +++----------------- index.html | 13 ++- lessons/lesson01_greater_data_science.html | 14 ++++ lessons/lesson02_introduction_to_R.html | 14 ++++ lessons/lesson02s_scripts.html | 14 ++++ lessons/lesson03_introduction_to_Quarto.html | 14 ++++ lessons/lesson04_ggplot.html | 14 ++++ lessons/lesson04s_examples.html | 14 ++++ lessons/lesson05_RStudio_projects.html | 14 ++++ lessons/lesson06_atomic_vectors.html | 14 ++++ lessons/lesson07_lists_and_tibbles.html | 14 ++++ lessons/lesson08_Data_Read_Write.html | 14 ++++ lessons/lesson09_dplyr.html | 14 ++++ lessons/lesson09s_dplyr_v_base.html | 14 ++++ lessons/lesson10_stringr.html | 14 ++++ lessons/lesson11_functions.html | 25 +++--- lessons/lesson12_purrr.html | 14 ++++ lessons/lesson13_eda_w_tidyverse.html | 14 ++++ robots.txt | 1 + search.json | 6 +- sitemap.xml | 75 ++++++++++++++++++ 22 files changed, 330 insertions(+), 85 deletions(-) create mode 100644 robots.txt create mode 100644 sitemap.xml diff --git a/.nojekyll b/.nojekyll index ecff415..72dd30b 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -5f6342b8 \ No newline at end of file +6d2bbe37 \ No newline at end of file diff --git a/about.html b/about.html index f6e75ea..186e5bd 100644 --- a/about.html +++ b/about.html @@ -15,69 +15,6 @@ div.column{display: inline-block; vertical-align: top; width: 50%;} div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} ul.task-list{list-style: none;} -pre > code.sourceCode { white-space: pre; position: relative; } -pre > code.sourceCode > span { display: inline-block; line-height: 1.25; } -pre > code.sourceCode > span:empty { height: 1.2em; } -.sourceCode { overflow: visible; } -code.sourceCode > span { color: inherit; text-decoration: inherit; } -div.sourceCode { margin: 1em 0; } -pre.sourceCode { margin: 0; } -@media screen { -div.sourceCode { overflow: auto; } -} -@media print { -pre > code.sourceCode { white-space: pre-wrap; } -pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; } -} -pre.numberSource code - { counter-reset: source-line 0; } -pre.numberSource code > span - { position: relative; left: -4em; counter-increment: source-line; } -pre.numberSource code > span > a:first-child::before - { content: counter(source-line); - position: relative; left: -1em; text-align: right; vertical-align: baseline; - border: none; display: inline-block; - -webkit-touch-callout: none; -webkit-user-select: none; - -khtml-user-select: none; -moz-user-select: none; - -ms-user-select: none; user-select: none; - padding: 0 4px; width: 4em; - color: #aaaaaa; - } -pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; } -div.sourceCode - { } -@media screen { -pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } -} -code span.al { color: #ff0000; font-weight: bold; } /* Alert */ -code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */ -code span.at { color: #7d9029; } /* Attribute */ -code span.bn { color: #40a070; } /* BaseN */ -code span.bu { } /* BuiltIn */ -code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */ -code span.ch { color: #4070a0; } /* Char */ -code span.cn { color: #880000; } /* Constant */ -code span.co { color: #60a0b0; font-style: italic; } /* Comment */ -code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */ -code span.do { color: #ba2121; font-style: italic; } /* Documentation */ -code span.dt { color: #902000; } /* DataType */ -code span.dv { color: #40a070; } /* DecVal */ -code span.er { color: #ff0000; font-weight: bold; } /* Error */ -code span.ex { } /* Extension */ -code span.fl { color: #40a070; } /* Float */ -code span.fu { color: #06287e; } /* Function */ -code span.im { } /* Import */ -code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */ -code span.kw { color: #007020; font-weight: bold; } /* Keyword */ -code span.op { color: #666666; } /* Operator */ -code span.ot { color: #007020; } /* Other */ -code span.pp { color: #bc7a00; } /* Preprocessor */ -code span.sc { color: #4070a0; } /* SpecialChar */ -code span.ss { color: #bb6688; } /* SpecialString */ -code span.st { color: #4070a0; } /* String */ -code span.va { color: #19177c; } /* Variable */ -code span.vs { color: #4070a0; } /* VerbatimString */ -code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */ @@ -88,6 +25,7 @@ + @@ -266,13 +204,9 @@

About

-

About this site

-
-
1 + 1
-
-
[1] 2
-
-
+

Hi folks! I’m Gabriel Odom, and I hope that this material was helpful to you.

+

History of this material: I started writing the very first versions of these lessons back in spring of 2018 when I was a postdoc at the Sylvester Comprehensive Cancer Center. The Biostats/Bioinformatics group had weekly “research clinics” for the other postdocs and junior faculty to learn about various computational topics that could be helpful in their work. This material started off as four lessons (I can’t remember exactly what the topics were, but I think it was intro to R, ggplot, organizing work into scripts, and dplyr). The lessons were well received. That fall, I ended up teaching 9 weeks on R as part of “Survey of Statistical Computing” for the grad students in the school of medicine, and I also joined The Carpentries group at the University of Miami. After I joined Florida International University, I spent some time building out these lessons semester after semester (and with help and feedback from some awesome graduate students), and I taught this class every year. Now, I’m finally organizing and restructuring most of the lessons and scripts that I’ve worked on and taught from these past few years into a website to help my students have easy access to the material even after they finish class.

+

Motivation: My experiences teaching with The Carpentries, to medical school students, and to public health students gave me a lot of one-on-one time with high-performing people who did not come from math / computer science backgrounds. I want to present the material in a logical way to people with hardly any computing background, but who still want to learn the basics for their research. As my friend Prof. Raymond Balise points out, we should assume students “can both point and click with a mouse”, and that’s about it. In that vein, if you come across parts of these lessons where I assume you know more than you do, please leave an issue ticket on the GitHub repository for this book (if you don’t know how to create a new issue, here’s a guide: https://www.techrepublic.com/article/how-to-create-github-issue/). I hope that this material is accessible to everyone.

@@ -374,6 +308,15 @@

About

} }); + diff --git a/index.html b/index.html index 048f852..3849a3a 100644 --- a/index.html +++ b/index.html @@ -25,6 +25,7 @@ + @@ -212,7 +213,7 @@

PHC 6701: R for Data Science // Advanced R

About

-

These are the written lecture materials for the class PHC 6701 (commonly known as “Advanced R”) at Florida International University’s Stempel College of Public Health.

+

These are the written lecture materials for the class PHC 6701 (commonly known as “Advanced R”) at Florida International University’s Stempel College of Public Health. The source code and data sets for this book are available here: https://github.com/gabrielodom/PHC6701_r4ds.

Getting Started

@@ -229,6 +230,7 @@

Getting Started

  • Setting up R/RStudio: https://derailment.netlify.app/2019-12-22-configuring-rstudio/
  • If you want help, there is a great community of R programmers on Slack: https://rfordatasci.com/.
    • +
  • Sign up for GitHub using your student email address: https://docs.github.com/en/get-started/quickstart/creating-an-account-on-github
    • @@ -332,6 +334,15 @@

    Getting Started

    } }); + diff --git a/lessons/lesson01_greater_data_science.html b/lessons/lesson01_greater_data_science.html index cd30b80..0cada11 100644 --- a/lessons/lesson01_greater_data_science.html +++ b/lessons/lesson01_greater_data_science.html @@ -90,6 +90,8 @@ + + @@ -598,6 +600,18 @@

    Our Very First R Cod } }); + diff --git a/lessons/lesson02_introduction_to_R.html b/lessons/lesson02_introduction_to_R.html index edf4a3a..6ceb3d6 100644 --- a/lessons/lesson02_introduction_to_R.html +++ b/lessons/lesson02_introduction_to_R.html @@ -90,6 +90,8 @@ + + @@ -844,6 +846,18 @@

    Getting Help

    } }); + diff --git a/lessons/lesson02s_scripts.html b/lessons/lesson02s_scripts.html index 2682eda..66c9727 100644 --- a/lessons/lesson02s_scripts.html +++ b/lessons/lesson02s_scripts.html @@ -27,6 +27,8 @@ + + @@ -358,6 +360,18 @@

    My First R Script

    } }); + diff --git a/lessons/lesson03_introduction_to_Quarto.html b/lessons/lesson03_introduction_to_Quarto.html index 33e39c7..1e23883 100644 --- a/lessons/lesson03_introduction_to_Quarto.html +++ b/lessons/lesson03_introduction_to_Quarto.html @@ -27,6 +27,8 @@ + + @@ -636,6 +638,18 @@

    Annotating your Work< } }); + diff --git a/lessons/lesson04_ggplot.html b/lessons/lesson04_ggplot.html index 5ff6f43..642277e 100644 --- a/lessons/lesson04_ggplot.html +++ b/lessons/lesson04_ggplot.html @@ -90,6 +90,8 @@ + + @@ -1051,6 +1053,18 @@

    Online examples:

    } }); + diff --git a/lessons/lesson04s_examples.html b/lessons/lesson04s_examples.html index 249d95d..36f3973 100644 --- a/lessons/lesson04s_examples.html +++ b/lessons/lesson04s_examples.html @@ -90,6 +90,8 @@ + + @@ -1125,6 +1127,18 @@

    Editing your own th } }); + diff --git a/lessons/lesson05_RStudio_projects.html b/lessons/lesson05_RStudio_projects.html index 2cef95b..c86893d 100644 --- a/lessons/lesson05_RStudio_projects.html +++ b/lessons/lesson05_RStudio_projects.html @@ -90,6 +90,8 @@ + + @@ -852,6 +854,18 @@

    DO: Create a Project + diff --git a/lessons/lesson06_atomic_vectors.html b/lessons/lesson06_atomic_vectors.html index da6a0c7..1bfe904 100644 --- a/lessons/lesson06_atomic_vectors.html +++ b/lessons/lesson06_atomic_vectors.html @@ -90,6 +90,8 @@ + + @@ -1277,6 +1279,18 @@

    } }); + diff --git a/lessons/lesson07_lists_and_tibbles.html b/lessons/lesson07_lists_and_tibbles.html index 6196b97..1a49a02 100644 --- a/lessons/lesson07_lists_and_tibbles.html +++ b/lessons/lesson07_lists_and_tibbles.html @@ -90,6 +90,8 @@ + + @@ -1456,6 +1458,18 @@

    Symbol Subsetting

    } }); + diff --git a/lessons/lesson08_Data_Read_Write.html b/lessons/lesson08_Data_Read_Write.html index a6fc2ab..e4d734e 100644 --- a/lessons/lesson08_Data_Read_Write.html +++ b/lessons/lesson08_Data_Read_Write.html @@ -90,6 +90,8 @@ + + @@ -868,6 +870,18 @@

    Aside: The Pipe Operator

    } }); + diff --git a/lessons/lesson09_dplyr.html b/lessons/lesson09_dplyr.html index 110719f..4f36102 100644 --- a/lessons/lesson09_dplyr.html +++ b/lessons/lesson09_dplyr.html @@ -90,6 +90,8 @@ + + @@ -1776,6 +1778,18 @@

    Airline wit } }); + diff --git a/lessons/lesson09s_dplyr_v_base.html b/lessons/lesson09s_dplyr_v_base.html index 0998600..117d51d 100644 --- a/lessons/lesson09s_dplyr_v_base.html +++ b/lessons/lesson09s_dplyr_v_base.html @@ -90,6 +90,8 @@ + + @@ -1126,6 +1128,18 @@

    Concluding Remarks

    } }); + diff --git a/lessons/lesson10_stringr.html b/lessons/lesson10_stringr.html index d00344c..82947d8 100644 --- a/lessons/lesson10_stringr.html +++ b/lessons/lesson10_stringr.html @@ -90,6 +90,8 @@ + + @@ -1001,6 +1003,18 @@

    Examp } }); + diff --git a/lessons/lesson11_functions.html b/lessons/lesson11_functions.html index c953c1b..94e9494 100644 --- a/lessons/lesson11_functions.html +++ b/lessons/lesson11_functions.html @@ -90,6 +90,8 @@ + + @@ -497,16 +499,7 @@

    WHILE and 
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    Now, as I played this example on my computer, I had one time where the WHILE loop repeated 60 times before the success condition was reached. In these cases, it would be nice to have a stopping condition. In our example, we can assume that there are only 30 potential date candidates for Todd to meet at the event, so we break the loop if we reach 30 attempts. This “exit” strategy uses the BREAK controller:

    @@ -922,6 +915,18 @@

    Looking “Up”

    } }); + diff --git a/lessons/lesson12_purrr.html b/lessons/lesson12_purrr.html index 3299624..0020442 100644 --- a/lessons/lesson12_purrr.html +++ b/lessons/lesson12_purrr.html @@ -90,6 +90,8 @@ + + @@ -1299,6 +1301,18 @@

    Example: Back to } }); + diff --git a/lessons/lesson13_eda_w_tidyverse.html b/lessons/lesson13_eda_w_tidyverse.html index 62656ec..4fbdd69 100644 --- a/lessons/lesson13_eda_w_tidyverse.html +++ b/lessons/lesson13_eda_w_tidyverse.html @@ -90,6 +90,8 @@ + + @@ -1189,6 +1191,18 @@

    Generating Hypotheses

    } }); + diff --git a/robots.txt b/robots.txt new file mode 100644 index 0000000..c3007cf --- /dev/null +++ b/robots.txt @@ -0,0 +1 @@ +Sitemap: https://gabrielodom.github.io/PHC6701_r4ds/sitemap.xml diff --git a/search.json b/search.json index c53140e..bcc5674 100644 --- a/search.json +++ b/search.json @@ -4,14 +4,14 @@ "href": "index.html", "title": "PHC 6701: R for Data Science // Advanced R", "section": "", - "text": "Getting Started\n\nSetting up your computer:\n\nWindows: https://derailment.netlify.app/2019-11-01-configure-a-windows-pc-for-data-science/ (ignore the stuff about LaTeX)\nMac: https://derailment.netlify.app/2019-10-29-configure-a-mac-for-data-science/ (ignore the stuff about LaTeX)\n\nInstalling R/Rstudio:\n\nWindows: https://derailment.netlify.app/2019-12-10-installing-r-rstudio-on-windows/\nMac: https://derailment.netlify.app/2019-11-16-installing-r-rstudio-on-a-mac/\n\nSetting up R/RStudio: https://derailment.netlify.app/2019-12-22-configuring-rstudio/\nIf you want help, there is a great community of R programmers on Slack: https://rfordatasci.com/." + "text": "Getting Started\n\nSetting up your computer:\n\nWindows: https://derailment.netlify.app/2019-11-01-configure-a-windows-pc-for-data-science/ (ignore the stuff about LaTeX)\nMac: https://derailment.netlify.app/2019-10-29-configure-a-mac-for-data-science/ (ignore the stuff about LaTeX)\n\nInstalling R/Rstudio:\n\nWindows: https://derailment.netlify.app/2019-12-10-installing-r-rstudio-on-windows/\nMac: https://derailment.netlify.app/2019-11-16-installing-r-rstudio-on-a-mac/\n\nSetting up R/RStudio: https://derailment.netlify.app/2019-12-22-configuring-rstudio/\nIf you want help, there is a great community of R programmers on Slack: https://rfordatasci.com/.\nSign up for GitHub using your student email address: https://docs.github.com/en/get-started/quickstart/creating-an-account-on-github" }, { "objectID": "about.html", "href": "about.html", "title": "About", "section": "", - "text": "1 + 1\n\n[1] 2" + "text": "History of this material: I started writing the very first versions of these lessons back in spring of 2018 when I was a postdoc at the Sylvester Comprehensive Cancer Center. The Biostats/Bioinformatics group had weekly “research clinics” for the other postdocs and junior faculty to learn about various computational topics that could be helpful in their work. This material started off as four lessons (I can’t remember exactly what the topics were, but I think it was intro to R, ggplot, organizing work into scripts, and dplyr). The lessons were well received. That fall, I ended up teaching 9 weeks on R as part of “Survey of Statistical Computing” for the grad students in the school of medicine, and I also joined The Carpentries group at the University of Miami. After I joined Florida International University, I spent some time building out these lessons semester after semester (and with help and feedback from some awesome graduate students), and I taught this class every year. Now, I’m finally organizing and restructuring most of the lessons and scripts that I’ve worked on and taught from these past few years into a website to help my students have easy access to the material even after they finish class.\nMotivation: My experiences teaching with The Carpentries, to medical school students, and to public health students gave me a lot of one-on-one time with high-performing people who did not come from math / computer science backgrounds. I want to present the material in a logical way to people with hardly any computing background, but who still want to learn the basics for their research. As my friend Prof. Raymond Balise points out, we should assume students “can both point and click with a mouse”, and that’s about it. In that vein, if you come across parts of these lessons where I assume you know more than you do, please leave an issue ticket on the GitHub repository for this book (if you don’t know how to create a new issue, here’s a guide: https://www.techrepublic.com/article/how-to-create-github-issue/). I hope that this material is accessible to everyone." }, { "objectID": "lessons/lesson01_greater_data_science.html", @@ -606,7 +606,7 @@ "href": "lessons/lesson11_functions.html#while-and-break", "title": "Lesson 11: Functions and Control Flow in R", "section": "WHILE and BREAK", - "text": "WHILE and BREAK\nThe WHILE controller allows us to repeat a task for an undefined number of times. Unlike the FOR control, the WHILE control can continue to run indefinitely. USE WITH EXTREME CAUTION.\nWHILE loops are the foundation controller for most iterative mathematical algorithms. Because they can continue to compute indefinitely, they are also used to model scenarios where unknown or random forces act on objects. For example, pretend that we have a social game where an individual will continue to play until they reach a condition; e.g. speed dating, where a person (say “Todd, a software developer”) will continue to move from table to table until they find “the one”, upon which they exit the game.\nBecause WHILE loops can execute until the heat death of the universe, we recommend that you add a print statement that counts how many loops have been made. For example, let’s find out how many dates Todd goes on during the speed dating event:\n\n# Initialize\nhasDate <- 0\nattempts <- 1\n\nwhile (hasDate != 1) {\n \n # Make a condition that only happens with 2.5% chance\n hasDate <- rnorm(1) < -1.96\n attempts <- attempts + 1\n print(attempts)\n \n}\n\n[1] 2\n[1] 3\n[1] 4\n[1] 5\n[1] 6\n[1] 7\n[1] 8\n[1] 9\n[1] 10\n[1] 11\n[1] 12\n[1] 13\n\n\nNow, as I played this example on my computer, I had one time where the WHILE loop repeated 60 times before the success condition was reached. In these cases, it would be nice to have a stopping condition. In our example, we can assume that there are only 30 potential date candidates for Todd to meet at the event, so we break the loop if we reach 30 attempts. This “exit” strategy uses the BREAK controller:\n\n# Initialize\nhasDate <- 0\nattempts <- 1\n\nwhile (hasDate != 1) {\n \n # Make a condition that only happens with 2.5% chance\n hasDate <- rnorm(1) < -1.96\n attempts <- attempts + 1\n \n if(attempts > 30L){\n \n print(\"No date found.\")\n break\n \n }\n \n print(attempts)\n \n}\n\n[1] 2\n[1] 3\n[1] 4\n[1] 5\n[1] 6\n[1] 7\n[1] 8\n[1] 9\n[1] 10\n[1] 11\n[1] 12\n[1] 13\n[1] 14\n[1] 15\n[1] 16\n[1] 17\n[1] 18\n[1] 19\n[1] 20\n[1] 21\n[1] 22\n[1] 23\n[1] 24\n[1] 25\n[1] 26\n[1] 27\n[1] 28\n[1] 29\n[1] 30\n[1] \"No date found.\"\n\n\n\n\n\n\n\n\nExercises\n\n\n\n\nIf you have accidentally written a WHILE loop that runs for eternity, how do you stop it without closing RStudio entirely?\nRead the lessons under the “Decision and Loop” section of DataMentor’s R Programming page: https://www.datamentor.io/r-programming/#tutorial\n\n\n\nDid you notice that if, else, for, while, and break all changed colour when you typed them? That is R telling you that these objects—remember that everything in R is an object—are reserved. That means that we cannot assign values to them or use them for any reason other than their designed purpose." + "text": "WHILE and BREAK\nThe WHILE controller allows us to repeat a task for an undefined number of times. Unlike the FOR control, the WHILE control can continue to run indefinitely. USE WITH EXTREME CAUTION.\nWHILE loops are the foundation controller for most iterative mathematical algorithms. Because they can continue to compute indefinitely, they are also used to model scenarios where unknown or random forces act on objects. For example, pretend that we have a social game where an individual will continue to play until they reach a condition; e.g. speed dating, where a person (say “Todd, a software developer”) will continue to move from table to table until they find “the one”, upon which they exit the game.\nBecause WHILE loops can execute until the heat death of the universe, we recommend that you add a print statement that counts how many loops have been made. For example, let’s find out how many dates Todd goes on during the speed dating event:\n\n# Initialize\nhasDate <- 0\nattempts <- 1\n\nwhile (hasDate != 1) {\n \n # Make a condition that only happens with 2.5% chance\n hasDate <- rnorm(1) < -1.96\n attempts <- attempts + 1\n print(attempts)\n \n}\n\n[1] 2\n[1] 3\n[1] 4\n\n\nNow, as I played this example on my computer, I had one time where the WHILE loop repeated 60 times before the success condition was reached. In these cases, it would be nice to have a stopping condition. In our example, we can assume that there are only 30 potential date candidates for Todd to meet at the event, so we break the loop if we reach 30 attempts. This “exit” strategy uses the BREAK controller:\n\n# Initialize\nhasDate <- 0\nattempts <- 1\n\nwhile (hasDate != 1) {\n \n # Make a condition that only happens with 2.5% chance\n hasDate <- rnorm(1) < -1.96\n attempts <- attempts + 1\n \n if(attempts > 30L){\n \n print(\"No date found.\")\n break\n \n }\n \n print(attempts)\n \n}\n\n[1] 2\n[1] 3\n[1] 4\n[1] 5\n[1] 6\n[1] 7\n[1] 8\n[1] 9\n[1] 10\n[1] 11\n[1] 12\n[1] 13\n[1] 14\n[1] 15\n[1] 16\n[1] 17\n[1] 18\n[1] 19\n[1] 20\n[1] 21\n[1] 22\n[1] 23\n[1] 24\n[1] 25\n[1] 26\n[1] 27\n[1] 28\n[1] 29\n[1] 30\n[1] \"No date found.\"\n\n\n\n\n\n\n\n\nExercises\n\n\n\n\nIf you have accidentally written a WHILE loop that runs for eternity, how do you stop it without closing RStudio entirely?\nRead the lessons under the “Decision and Loop” section of DataMentor’s R Programming page: https://www.datamentor.io/r-programming/#tutorial\n\n\n\nDid you notice that if, else, for, while, and break all changed colour when you typed them? That is R telling you that these objects—remember that everything in R is an object—are reserved. 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