add scritp folder to general project organization + adding section to…

… create subfolder in training_USERNAME project

materials/sections/rstudio-server-setup.qmd

@@ -64,9 +64,10 @@ Some common directories are:
 
 ::: {.column width="55%"}
 - `data`: where we store our data (often contains subdirectories for raw, processed, and metadata data)
-- `R`: contains scripts for cleaning or wrangling, etc. (some find this name misleading if their work has other scripts beyond the R programming language, in which case they call this directory `scripts`)
+- `R`: contains scripts with your custom R functions, etc. (some find this name misleading if their work has other scripts beyond the R programming language, in which case they call this directory `scripts`)
 - `plots` or `figs`: generated plots, graphs, and figures
 - `docs`: summaries or reports of analysis or other relevant project information
+- `scripts:` has all scripts where you clean and wrangle data and run your analysis.
 
 Directory organization will vary from project to project, but the ultimate goal is to create a well organized project for both reproducibility and collaboration.
 :::
@@ -77,6 +78,16 @@ Directory organization will vary from project to project, but the ultimate goal
 :::
 
 
+::: {.callout-tip icon=false}
+## Project Sub-directories
+For this week we are going to create 3 folder (directories) in our `training_{USERNAME}` Rproject.
+
+- In the files pane in RStudio (bottom right), click on Folder button (with a green circle and plus sign) and create 3 new folders: `data`, `plots`, `scripts`.
+
+The idea here is treat this RProject as an example of how to organize our work.
+:::
+
+
 
 ## Moving in an R Project using Paths & Working Directories
 
@@ -98,53 +109,3 @@ Note that once you start working in projects you should basically never need to
 
 Similarly, think about how you work with absolute paths. Could you leverage the working directory of your R project to replace these with relative paths and make your code more portable? Probably!
 
-<!--
-## Setting up R and RStudio on your Computer {#rstudio-personal-setup}
-
-### Check your R Version
-
-For this course, we used the R Version 4.2.2. To check the R Version of your personal computer run this in the Console: ``` R.version$version.string ```. If you need to download R onto your personal computer or update it, you can do so from [CRAN (The Comprehensive R Archive Network)](https://cran.rstudio.com/).
-
-### Check your RStudio Version
-
-For this course, we used the RStudio Version released in December 2022. To check the RStudio Version of your personal computer run this in the Console: ```  RStudio.Version()$version ```. If you need to download RStudio onto your personal computer or update it, you can do so from [Posit](https://posit.co/download/rstudio-desktop/). Note you may need to update your computer's software to download the newest version of RStudio.
-
-Another way to check for RStudio updates is to click "Help" and then "Check for Updates". Follow the prompts.
-
-### Install Packages
-
-In the code chunk below, we have listed out the packages we used for this course. You're welcome to install each package one-by-one by calling the `install.packages("package_name")` function. Or you can copy and paste this code chunk and run it which includes a `for loop` that will check if a package is installed on your personal computer and if not, it will install it. We have also included a line of code that will update our packages. Running this code chunk may take a few minutes.
-
-```{r}
-#| eval: false
-course_packages <- c("dplyr",
-                     "DT",
-                     "forcats",
-                     "ggplot2",
-                     "ggmap",
-                     "knitr",
-                     "leaflet",
-                     "lubridate",
-                     "readr",
-                     "renv",
-                     "rrtools",
-                     "sf",
-                     "scales",
-                     "tidyr",
-                     "usethis")
-
-for (course_packages in course_packages) {
-    
-    if (!(course_packages %in% installed.packages())) { install.packages(course_packages) }
-    
-    }
-
-rm(course_packages) # remove object from Global Environment
-
-# update any out-of-date packages
-update.packages(ask=FALSE)
-
-```
-
--->
-