updated filepath for OpenOnDemand

docs/00-introduction.md

@@ -241,7 +241,7 @@ the Source pane.
 In the console, we expect to see the following output :
 
 !!! solution ""
-    `[1] "/home/<USERID>/R4Genomics"`
+    `[1] "/home/shared/<USERID>"`
 
 * Notice, at the Console, you will also see the instruction you executed above the output in blue.
 
@@ -269,7 +269,7 @@ include a comment on the purpose of commands you are learning, e.g.:
          .challenge}
 
 For the purposes of this exercise we want you to be in the directory
-`"/home/<USERID>/R4Genomics"`. What if you weren't? You can set your home
+`"/home/shared/<USERID>/R4Genomics"`. What if you weren't? You can set your home
 directory using the `setwd()` command. Enter this command in your
 script, but *don't run* this yet.
 
@@ -288,7 +288,7 @@ this:
 
 !!! r-project
 
-    `# This sets the working directory setwd("/home/<USERID>/R4Genomics")`
+    `# This sets the working directory setwd("/home/shared/<USERID>/R4Genomics")`
 
 When you run this command, the console repeats the command, but gives
 you no output. Instead, you see the blank R prompt: `>`.

docs/01-r-basics.md

@@ -4,9 +4,9 @@
 
     === "Keypoints"
 
-        - Effectively using R is a journey of months or years. Still you don't
+        - Effectively using R is a journey of months or years. Still, you don't
           have to be an expert to use R and you can start using and analyzing
-          your data with with about a day's worth of training
+          your data with with about a day's worth of training.
         - It is important to understand how data are organized by R in a given
           object type and how the mode of that type (e.g. numeric, character,
           logical, etc.) will determine how R will operate on that data.

docs/03-basics-factors-dataframes.md

@@ -150,7 +150,7 @@ function called `read.csv()`.
         they can do.
 
 Now, let's read in the file `combined_tidy_vcf.csv` which will be
-located in `/home/$USER/R4Genomics/`. Call this data `variants`. The first
+located in `/home/shared/$USER/R4Genomics/`. Call this data `variants`. The first
 argument to pass to our `read.csv()` function is the file path for our
 data. The file path must be in quotes and now is a good time to remember
 to use tab autocompletion. **If you use tab autocompletion you avoid
@@ -161,7 +161,7 @@ typos and errors in file paths.** Use it!
     ```r
     # Read in a CSV file and save it as 'variants'
 
-    variants <- read.csv("/home/<USERID>/R4Genomics/combined_tidy_vcf.csv")
+    variants <- read.csv("/home/shared/<USERID>/R4Genomics/combined_tidy_vcf.csv")
     ```
 
 One of the first things you should notice is that in the Environment