Add help CS

Author: Adam M. Wilson

07_Reproducibile.Rmd

@@ -1,15 +1,29 @@
 ---
-title: "Reproducible Research"
+title: "Reproducible Research and R Markdown"
+date: 2018-10-10 
+subtitle: 
+reading:
+   - 
+presentation:
+   - day_13_repro.html
+tasks:
+   - Learn how to read R help files effectively
+   - Learn how to search for help
+   - Learn how to create a Minimum Working Example (MWE)
 ---
 
+
 ```{r, echo=FALSE, message=FALSE, results='hide', purl=FALSE}
+source("functions.R")
 source("knitr_header.R")
 ```
 
-<div>
-<iframe src="07_assets/Reproducibile_presentation.html" width=100% height=400px></iframe>
-</div>
-<a target="_blank" href="07_assets/Reproducibile_presentation.html">Click here to open the presentation in a new tab </a>
+`r presframe()`
+
+## Download
+
+`r output_table()`
+
 
 ## R Markdown
 
@@ -20,25 +34,7 @@ Cheatsheet:
 <small><small><small>[https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)</small></small></small>
 
 ## Overview
-Today we will make a copy of a template for your project, edit it, and 'push' it back up to your github account.  You can check out the template code at [https://github.com/AdamWilsonLab/RDataScience_Project](https://github.com/AdamWilsonLab/RDataScience_Project) and the template website at [http://adamwilson.us/RDataScience_Project/](http://adamwilson.us/RDataScience_Project/)
-
-## Install Git on your computer
-
-### Windows and OSX
-http://git-scm.com/downloads
-
-### Linux
-` sudo apt-get install git `
-or similar
-
-
-## Create an account on [GitHub](github.com)
-
-1. Create a GitHub account at [https://github.com/](https://github.com/)
-    * This will be a public account associated with your name
-    * Choose a username wisely for future use
-    * Don't worry about details, you can fill them in later
-2.  To set up a connection that doesn't require you to type in your password every time, [see here](GitSSHNotes.html)    
+Today we will make a copy of a template for your final project, edit it, and 'push' it back up to your github account.  You can check out the template code at [https://github.com/AdamWilsonLab/RDataScience_Project](https://github.com/AdamWilsonLab/RDataScience_Project) and the template website at [http://adamwilson.us/RDataScience_Project/](http://adamwilson.us/RDataScience_Project/)
 
 ## `Fork` the repository to create a linked copy in your GitHub account.
 

07_Reproducibile.md

@@ -1,42 +1,49 @@
 ---
-title: "Reproducible Research"
+title: "Reproducible Research and R Markdown"
+date: 2018-10-10 
+subtitle: 
+reading:
+   - 
+presentation:
+   - day_13_repro.html
+tasks:
+   - Learn how to read R help files effectively
+   - Learn how to search for help
+   - Learn how to create a Minimum Working Example (MWE)
 ---
 
 
 
-<div>
-<iframe src="07_assets/Reproducibile_presentation.html" width=100% height=400px></iframe>
-</div>
-<a target="_blank" href="07_assets/Reproducibile_presentation.html">Click here to open the presentation in a new tab </a>
 
-## R Markdown
 
-Cheatsheet:
+<div class='extraswell'>
+  <button data-toggle='collapse' class='btn btn-link' data-target='#pres'>View Presentation </button>      [Open presentation in a new tab](presentation/day_13_repro.html){target='_blank'}
+<div id='pres' class='collapse'>
+<div class='embed-responsive embed-responsive-16by9'>
+  <iframe class='embed-responsive-item' src='presentation/day_13_repro.html' allowfullscreen></iframe>
+  _Click on presentation and then use the space bar to advance to the next slide
+   or escape key to show an overview._
+</div>
+</div>
+</div>
 
-<a href="https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf"> <img src="07_assets/rmarkdown.png" alt="alt text" width="400"></a>
 
-<small><small><small>[https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)</small></small></small>
+## Download
 
-## Overview
-Today we will make a copy of a template for your project, edit it, and 'push' it back up to your github account.  You can check out the template code at [https://github.com/AdamWilsonLab/RDataScience_Project](https://github.com/AdamWilsonLab/RDataScience_Project) and the template website at [http://adamwilson.us/RDataScience_Project/](http://adamwilson.us/RDataScience_Project/)
+| [<i class='fas fa-code fa-2x' aria-hidden='true'></i><br>  R Script]( scripts/07_Reproducibile_nocomments.R ) | [<i class='fa fa-file-code-o fa-2x'></i> <br> Commented R Script]( scripts/07_Reproducibile.R ) | [<i class='far fa-file-alt fa-2x'></i> <br>  Rmd Script]( scripts/07_Reproducibile.Rmd )|
+|:--:|:-:|:-:|
 
-## Install Git on your computer
 
-### Windows and OSX
-http://git-scm.com/downloads
+## R Markdown
 
-### Linux
-` sudo apt-get install git `
-or similar
+Cheatsheet:
 
+<a href="https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf"> <img src="07_assets/rmarkdown.png" alt="alt text" width="400"></a>
 
-## Create an account on [GitHub](github.com)
+<small><small><small>[https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)</small></small></small>
 
-1. Create a GitHub account at [https://github.com/](https://github.com/)
-    * This will be a public account associated with your name
-    * Choose a username wisely for future use
-    * Don't worry about details, you can fill them in later
-2.  To set up a connection that doesn't require you to type in your password every time, [see here](GitSSHNotes.html)    
+## Overview
+Today we will make a copy of a template for your final project, edit it, and 'push' it back up to your github account.  You can check out the template code at [https://github.com/AdamWilsonLab/RDataScience_Project](https://github.com/AdamWilsonLab/RDataScience_Project) and the template website at [http://adamwilson.us/RDataScience_Project/](http://adamwilson.us/RDataScience_Project/)
 
 ## `Fork` the repository to create a linked copy in your GitHub account.
 

07_assets/Reproducibile_presentation.html

@@ -0,0 +1,76 @@
+---
+title: "Getting Help!"
+date: 2018-10-10 
+subtitle: Learning more about finding help
+reading:
+   - How to [write a reproducible example](http://adv-r.had.co.nz/Reproducibility.html)
+presentation:
+   - day_12_help.html
+tasks:
+   - Learn how to read R help files effectively
+   - Learn how to search for help
+   - Learn how to create a Minimum Working Example (MWE)
+   - Debug existing code
+   - Save your reprex to your course repository as an html file using Export -> "Save As Webpage" in the RStudio "Viewer" Tab.
+---
+
+```{r, echo=FALSE, message=FALSE, results='hide', purl=FALSE}
+source("functions.R")
+source("knitr_header.R")
+```
+
+`r presframe()`
+
+# Reading
+
+```{r reading,results='asis',echo=F,purl=F}
+md_bullet(rmarkdown::metadata$reading)
+```
+
+# Tasks
+
+```{r tasks,results='asis',echo=F,purl=F}
+md_bullet(rmarkdown::metadata$tasks)
+```
+
+## Download
+
+`r output_table()`
+
+## Libraries
+
+```{r message=F,warning=FALSE}
+library(tidyverse)
+library(reprex)
+library(sf)
+
+library(spData)
+data(world)
+```
+
+## Your problem
+
+You want to make a figure illustrating the distribution of GDP per capita for all countries within each continent using the `world` data in the `spData` package.  Your desired figure looks something like the following:
+
+```{r, echo=F, purl=F, warning=F}
+library(spData)
+library(ggplot2)
+data(world)
+
+ggplot(world,aes(x=gdpPercap, fill=continent))+
+   geom_density(alpha=0.5,color=F)+
+   labs(x="GDP Per Capita",y="Density")+
+   theme(legend.position = "bottom")
+```
+
+You have started working on the figure but can't seem to make it work like you want.  Here is your current version of the code (and the resulting figure):
+
+```{r, warning=F}
+ggplot(world,aes(x=gdpPercap, y=continent, color=continent))+
+   geom_density(alpha=0.5,color=F)
+```
+
+You want to ask for help and so you know that you need to make a reproducible example.  Starting with the code above, make the required edits so you can use `reprex()` to generate a nicely formatted example that you could email or post to a forum to ask for help.  See the [reading](https://reprex.tidyverse.org/) for more help. Note: you do _not_ need to recreate the figure above, only to use `reprex()` to illustrate your question.
+
+If you have extra time, try to fix the code above to make the first figure.
+

CS_07.Rmd

@@ -0,0 +1,80 @@
+---
+title: "Getting Help!"
+date: 2018-10-10 
+subtitle: Learning more about finding help
+reading:
+   - How to [write a reproducible example](http://adv-r.had.co.nz/Reproducibility.html)
+presentation:
+   - day_12_help.html
+tasks:
+   - Learn how to read R help files effectively
+   - Learn how to search for help
+   - Learn how to create a Minimum Working Example (MWE)
+   - Debug existing code
+   - Save your reprex to your course repository as an html file using Export -> "Save As Webpage" in the RStudio "Viewer" Tab.
+---
+
+
+
+
+<div class='extraswell'>
+  <button data-toggle='collapse' class='btn btn-link' data-target='#pres'>View Presentation </button>      [Open presentation in a new tab](presentation/day_12_help.html){target='_blank'}
+<div id='pres' class='collapse'>
+<div class='embed-responsive embed-responsive-16by9'>
+  <iframe class='embed-responsive-item' src='presentation/day_12_help.html' allowfullscreen></iframe>
+  _Click on presentation and then use the space bar to advance to the next slide
+   or escape key to show an overview._
+</div>
+</div>
+</div>
+
+
+# Reading
+
+- How to [write a reproducible example](http://adv-r.had.co.nz/Reproducibility.html)
+
+# Tasks
+
+- Learn how to read R help files effectively
+- Learn how to search for help
+- Learn how to create a Minimum Working Example (MWE)
+- Debug existing code
+- Save your reprex to your course repository as an html file using Export -> "Save As Webpage" in the RStudio "Viewer" Tab.
+
+## Download
+
+| [<i class='fas fa-code fa-2x' aria-hidden='true'></i><br>  R Script]( scripts/CS_07_nocomments.R ) | [<i class='fa fa-file-code-o fa-2x'></i> <br> Commented R Script]( scripts/CS_07.R ) | [<i class='far fa-file-alt fa-2x'></i> <br>  Rmd Script]( scripts/CS_07.Rmd )|
+|:--:|:-:|:-:|
+
+## Libraries
+
+
+```r
+library(tidyverse)
+library(reprex)
+library(sf)
+
+library(spData)
+data(world)
+```
+
+## Your problem
+
+You want to make a figure illustrating the distribution of GDP per capita for all countries within each continent using the `world` data in the `spData` package.  Your desired figure looks something like the following:
+
+![](CS_07_files/figure-html/unnamed-chunk-3-1.png)<!-- -->
+
+You have started working on the figure but can't seem to make it work like you want.  Here is your current version of the code (and the resulting figure):
+
+
+```r
+ggplot(world,aes(x=gdpPercap, y=continent, color=continent))+
+   geom_density(alpha=0.5,color=F)
+```
+
+![](CS_07_files/figure-html/unnamed-chunk-4-1.png)<!-- -->
+
+You want to ask for help and so you know that you need to make a reproducible example.  Starting with the code above, make the required edits so you can use `reprex()` to generate a nicely formatted example that you could email or post to a forum to ask for help.  See the [reading](https://reprex.tidyverse.org/) for more help. Note: you do _not_ need to recreate the figure above, only to use `reprex()` to illustrate your question.
+
+If you have extra time, try to fix the code above to make the first figure.
+

CS_07.md

@@ -9,7 +9,7 @@ Course content is designed to be flexible to accommodate student interest and ab
 In the table below, R4DS refers to [_R for Data Science_ by Garrett Grolemund and Hadley Wickham](http://r4ds.had.co.nz) and, while GCR refers to [_Geocomputation with R_ by Robin Lovelace, Jakub Nowosad, and Jannes Muenchow (CRC Press, 2018)](https://geocompr.robinlovelace.net/).
 
 
-```{r, echo=FALSE, message=FALSE, purl=FALSE}
+```{r, echo=FALSE, message=FALSE, purl=FALSE, eval=F}
 source("functions.R")
 library(fullcalendar)
 library(lubridate)

CS_07_files/figure-html/unnamed-chunk-3-1.png

@@ -9,5 +9,4 @@ Course content is designed to be flexible to accommodate student interest and ab
 In the table below, R4DS refers to [_R for Data Science_ by Garrett Grolemund and Hadley Wickham](http://r4ds.had.co.nz) and, while GCR refers to [_Geocomputation with R_ by Robin Lovelace, Jakub Nowosad, and Jannes Muenchow (CRC Press, 2018)](https://geocompr.robinlovelace.net/).
 
 
-<!--html_preserve--><div id="htmlwidget-686092dc917a388ea16d" style="width:672px;height:480px;" class="fullcalendar html-widget"></div>
-<script type="application/json" data-for="htmlwidget-686092dc917a388ea16d">{"x":{"firstDay":1,"height":500,"aspectRatio":1.75,"header":{"right":"week,month,listMonth"},"footer":{"right":"today prev,next, title"},"titleFormat":" MM-YYYY","events":[{"date":"2018-08-30","title":"CS_01","type":"CS","url":"./CS_01.html","color":"red"},{"date":"2018-09-06","title":"CS_02","type":"CS","url":"./CS_02.html","color":"red"},{"date":"2018-09-13","title":"CS_03","type":"CS","url":"./CS_03.html","color":"red"},{"date":"2018-09-20","title":"CS_04","type":"CS","url":"./CS_04.html","color":"red"},{"date":"2018-09-25","title":"CS_05","type":"CS","url":"./CS_05.html","color":"red"},{"date":"2018-10-04","title":"CS_06","type":"CS","url":"./CS_06.html","color":"red"},{"date":"2018-09-06","title":"TK_01","type":"TK","url":"./TK_01.html","color":"green"},{"date":"2018-09-11","title":"TK_02","type":"TK","url":"./TK_02.html","color":"green"}]},"evals":[],"jsHooks":[]}</script><!--/html_preserve-->
+

CS_07_files/figure-html/unnamed-chunk-4-1.png

@@ -46,6 +46,11 @@ Weekly courses due before topic in class
 * [Exploratory Data Analysis in R: Case Study](https://www.datacamp.com/courses/exploratory-data-analysis-in-r-case-study)
 * [Spatial Analysis in R with sf and raster](https://www.datacamp.com/courses/spatial-analysis-in-r-with-sf-and-raster)
 
+## New Module: troubleshooting code
+* reading helpfiles
+* break down your code
+* reading error messages
+
 ## Git Classroom
 * setup git account
 * use github classroom