Fix RStudio terminology and improve lesson flow

episodes/00-before-we-start.Rmd

@@ -234,7 +234,7 @@ The Default Layout is:
   enters into the computer's working memory. The History tab displays all commands 
   that have been executed in the console.
 
-- **Navigation Pane**
+- **Files, Plots, Packages, and Help pane**
   This pane has multiple functions:
 
   - **Files:** Navigate to files saved on your computer and in your working directory
@@ -402,10 +402,9 @@ bioinformatics).
 
 ### **Installing packages using the Packages tab**
 
-Installing CRAN packages can be done from the <kbd>Packages</kbd> tab in the Navigation 
-Pane. Click `Install` and type in the name of the package you're looking for.
+Installing CRAN packages can be done from the <kbd>Packages</kbd> tab in the Files, Plots, Packages, and Help pane. Click `Install` and type in the name of the package you're looking for.
 
-```{r install-packages, echo=FALSE, fig.cap="Click on the Packages tab in the Navigation Pane to download packages from CRAN.", fig.alt="install packages pane showing an entry for installing the 'tidyverse' package"}
+```{r install-packages, echo=FALSE, fig.cap="Click on the Packages tab in the Files, Plots, Packages, and Help pane to download packages from CRAN.", fig.alt="install packages pane showing an entry for installing the 'tidyverse' package"}
 knitr::include_graphics("fig/R_00_Rstudio_03.png")
 ```
 

episodes/01-intro-to-r.Rmd

@@ -101,7 +101,7 @@
 - **Do not use names of functions that already exist in R:** There are some
   names that cannot be used because they are the names of fundamental functions in
   R (e.g., `if`, `else`, `for`, see
   [here](https://stat.ethz.ch/R-manual/R-devel/library/base/html/Reserved.html)
   for a complete list. In general, even if it's allowed, it's best to not use
   other function names (e.g., `c`, `T`, `mean`, `data`, `df`, `weights`). If in
   doubt, check the help to see if the name is already in use.
@@ -308,7 +308,7 @@
 `sum(sqrt(9), 4)` to take the sum of the square root of 9 and add it to 4.
 
 Typing a question mark before a function will pull the help page up in the
-Navigation Pane in the lower right. Type `?sum` to view the help page for the
+Files, Plots, Packages, and Help pane in the lower right. Type `?sum` to view the help page for the
 `sum` function. You can also call `help(sum)`. This will provide the description
 of the function, how it is to be used, and the arguments.
 

episodes/02-starting-with-data.Rmd

@@ -52,35 +52,6 @@ to this episode and follow the instructions on creating an R project folder.
 Once you have created the project, open the project in RStudio.
 
 
-## Getting data into R
-
-We will be using a demo dataset from the University of Houston--Clear Lake 
-Integrated Library System in 2018. It contains a relatively random sample of books 
-from the catalog.
-
-In order to use your data in R, you must import it and turn it into an R *object*. There are many ways to get data into R.
-
-- **Manually**: You can manually create it using the `data.frame()` function in Base R, or the `tibble()` function in the tidyverse.
-
-- **Import it from a file** Below is a very incomplete list
-  - Text: TXT (`readLines()` function)
-  - Tabular data: CSV, TSV (`read.table()` function or `readr` package)
-  - Excel: XLSX (`xlsx` package)
-  - Google sheets: (`googlesheets` package)
-  - Statistics program: SPSS, SAS (`haven` package)
-  - Databases: MySQL (`RMySQL` package)
-
-- **Gather it from the web**: You can connect to webpages, servers, or APIs
-  directly from within R, or you can create a data scraped from HTML webpages
-  using the `rvest` package. For example
-  - the Twitter API with
-    [`twitteR`](https://sites.google.com/site/miningtwitter/questions/talking-about/wordclouds/wordcloud1)
-  - Crossref data with
-    [`rcrossref`](https://cran.r-project.org/web/packages/rcrossref/rcrossref.pdf)
-  - World Bank's World Development Indicators with
-    [`WDI`](https://cran.r-project.org/web/packages/WDI/WDI.pdf).
-
-
 ### Set up your working directory
 
 The working directory is an important concept to understand. It is the place
@@ -159,6 +130,9 @@ read.csv("./data") to represent that sub-directory.
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 
+## Getting data into R
+
+
 ## Downloading the data
 
 Once you have set your working directory, we will create our folder

episodes/04-data-viz-ggplot.Rmd

@@ -60,7 +60,7 @@
 The`lubridate` package is installed with the tidyverse, but is not one of the core tidyverse packages loaded with `library(tidyverse)`, so it needs to be explicitly called. `lubridate` makes working with dates and times easier in R.
 
 We also load the `books_reformatted` data we saved in the previous
 lesson. Here, we'll assign it to `books2`. You can create the reformatted data by running the codes from [here](https://librarycarpentry.github.io/lc-r/03-data-cleaning-and-transformation.html#exporting-data) or by loading the saved CSV file from previous episode.
 
 ```{r, purl=FALSE, eval=FALSE}
 books2 <- read_csv("data_output/books_reformatted.csv")  # load the data and assign it to books
@@ -109,7 +109,7 @@
 - The `mapping` argument defines the variables mapped to various aesthetics of the plot, e.g. the x and y axis.
 - The `geom_function` argument defines the type of plot, e.g. barplot, scatter plot, boxplot.
 
 ::::::::::::::::::::::::::::::::::::::::::::; callout
 
 ## `ggplot2` versus `ggplot`
 
@@ -119,8 +119,8 @@
 
 
 When you run the `ggplot()` function, it plots directly to the Plots tab in the
-Navigation Pane (lower right). Alternatively, you can assign a plot to an R
-object, then call `print()`to view the plot in the Navigation Pane.
+Files, Plots, Packages, and Help pane (lower right). Alternatively, you can assign a plot to an R
+object, then call `print()`to view the plot in the Files, Plots, Packages, and Help pane.
 
 
 ## Creating your first plot