R and rstudio basic #15

cathy-y · 2020-10-10T22:50:01Z

Resolving issues for Introduction to R and RStudio basic tutorial

Co-authored-by: Ryan Karimi <[email protected]> Co-authored-by: ymkng <[email protected]> Co-authored-by: Pranav Sampara <[email protected]> Co-authored-by: Cathy <[email protected]> Co-authored-by: Avery Noonan <[email protected]>

r-karimi

Great job Cathy! Just a few notes that might not even be suggestions for you but rather questions for Stephan and the rest of the team. Well done!

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

r-karimi · 2020-10-12T22:43:26Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+
+## Working with data
+
+### Data description


Does this need to be in a "child document?"

I couldn't figure out how to do this on my tutorial though...

Yes, exactly. Look at the Slack#educe, Gil talks about how he set up the child document.

Do I just replace all of the text here with his code? Not super sure what exactly the user is supposed to see here.

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

cathy-y · 2020-10-16T16:23:54Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+
+## Working with data
+
+### Data description


Do I just replace all of the text here with his code? Not super sure what exactly the user is supposed to see here.

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

cathy-y · 2020-10-16T16:55:38Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+## Learning objectives
+
+By the end of this tutorial you should be able to:
+
+- Identify the different components of RStudio.
+- Declare variables in R.
+- Recognize and use functions.
+- Install and load R packages.
+- Load and subset tabular data using tidyverse.
+- Use the `help` function in R console to troubleshoot given a new function.
+The last bullet point can be more descriptive saying, "Use the `help` function in R console to troubleshoot and *identify mandatory parameters* given a new function."
+


Suggested change

## Learning objectives

By the end of this tutorial you should be able to:

- Identify the different components of RStudio.

- Declare variables in R.

- Recognize and use functions.

- Install and load R packages.

- Load and subset tabular data using tidyverse.

- Use the `help` function in R console to troubleshoot given a new function.

The last bullet point can be more descriptive saying, "Use the `help` function in R console to troubleshoot and *identify mandatory parameters* given a new function."

I personally prefer learning objectives with each section

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

Co-authored-by: Ryan Karimi <[email protected]>

r-karimi

Great work this week, Cathy! Your tutorial is taking shape nicely :)

r-karimi · 2020-10-19T06:21:36Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

@@ -7,7 +7,7 @@ output:
    progressive: true
    allow_skip: true
 runtime: shiny_prerendered
-description: This tutorial covers the basics of R and RStudio. You will learn about the different panes and features of RStudio that make coding in R easier, as well as basic skills of the R language itself, such as creating functions and loading packages.
+description: Welcome to R! If you want to analyze and visualize data reproducibly, you've come to the right place. This tutorial covers the basics of R and RStudio. RStudio is a free program used for coding in R. After learning about its features and functionality, we will dive into R language basics, where you will create functions and load packages.


Nice, much better description.

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

r-karimi · 2020-10-19T06:24:23Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

 You can also change the sizes of the panes by dragging the dividers or clicking on the expand and compress icons at the top right corner of each pane. 
-
+```{r quiz: R Tour, echo=FALSE}


Be careful here--users can re-arrange the panes in the Rstudio options. I can imagine someone might not have this configuration...I certainly don't!

r-karimi · 2020-10-19T06:25:51Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+```{r quiz: R Projects, echo=FALSE}
+question("What is not a benefit of using RStudio projects?",
+    answer("All of your files and outputs are linked to the project directory"),
+    answer("R automatically looks for files in the project directory so you don't have to specify a full file path"),
+    answer("When you reopen a project, your code is saved so all you need to do is rerun it", correct=TRUE)
+)


I'm not sure how useful it is having quizzes for this kind of content. What do you think, Cathy and Stephan? Though I can appreciate how it might be useful in getting someone to learn about RStudio projects, I might just give a few use cases, link to the docs, and leave it at that.

r-karimi · 2020-10-19T06:27:15Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

@@ -115,11 +133,33 @@ total <- total - 1

 total
 ```
+Now it's your turn! Declare a variable "product" and set its value to 3 * 5. Next, operating on "product", declare a variable called "difference", whose final value is 8.


Suggested change

Now it's your turn! Declare a variable "product" and set its value to 3 * 5. Next, operating on "product", declare a variable called "difference", whose final value is 8.

Now it's your turn! Declare a variable "product" and set its value to the product of the numbers 3 and 5. Next, using the variable "product", declare a variable called "difference", whose final value is 8.

r-karimi · 2020-10-19T06:29:04Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+

Nice job! I might also give a few use cases for functions. Python has those neat recursive functions (not sure if those exist in R), but you could also talk about taking some raw data doing some long processing all in one shot, if you have the processing function already written. This could open the door to the whole API style of programming, though that might be beyond the scope of this tutorial.

r-karimi · 2020-10-19T06:30:48Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

-### Data exploration
-
-Let's explore the data that we've imported into R.
-
-Using different functions, we can look at the dimensions of our data, number of rows, and number of columns:
-```{r}
-#number of rows followed by number of columns
-dim(OTU_metadata_table)
-
-#number of rows
-nrow(OTU_metadata_table)
-
-#number of columns
-ncol(OTU_metadata_table)
-```
-
-We can list the column names using `colnames()`:
-```{r}
-colnames(OTU_metadata_table)
-```
-
-We can select to work with only specific columns/variables from our table using the `select()` function:
-```{r}
-restricted_columns <- select(OTU_metadata_table, Depth, OTU0001, OTU0002,
-                             OTU0004)
-```
-
-We can filter for specific rows based on a column value using the `filter()` function. Here we restrict for rows where the value for `Depth` is smaller than 135. 
-
-```{r}
-above_135_depth <- filter(OTU_metadata_table, Depth < 135)
-```
-
-We can also only choose to work with specific rows based on their position in our data table using the `slice()` function. 
-
-```{r}
-first_five_rows <- slice(OTU_metadata_table, 1:5)
-```
-


Yup, good to delete this. It's covered in wrangling-basic.

…nning of the tutorial, and changed t() function to paste()

r-karimi

Cool, good job Cathy! Feel free to let me know when you think this workshop is done and I'll go ahead and work through the full thing and give some feedback on the organization and flow. Changes in your commits look good this week--keep it up!

r-karimi · 2020-10-27T17:31:58Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+Working with Data:
+
+- Load data into R
+- Save loaded data in the environment


This section is redundant with wrangling-basic, just FYI.

r-karimi · 2020-10-27T17:32:21Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+RStudio Projects:
+
+- List the benefits of using RStudio Projects
+- Create a new RStudio Project
+- Open or switch to an existing RStudio Project
+
+R Scripts:
+
+- Create an R script file
+- List the benefits of using R scripts
+- Annotate R scripts with comments
+
+Variables in R:
+
+- Declare variables
+- Perform operations to change the value of variables
+
+Functions in R:
+
+- Explain what functions and arguments are
+- Use R to understand how any given function works
+- Identify required and optional arguments for functions
+
+R Packages:
+
+- Understand what R packages are and how they are used
+- Install and load packages
+


Nice, this is a much clearer way of conveying the learning goals.

cathy-y · 2020-11-01T13:59:16Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+
+When you start RStudio, you will see something like the following window appear:
+
+![](/images/rstudio.png){width=100%}


This image shows up

cathy-y · 2020-11-01T13:59:30Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+
+When trying to run a command, you see this error:
+
+![](/images/objecterror.png){width=100%}


This image does not show

So where in the repo did you place your image?

r-karimi

Great job Cathy! Very minor edits and suggestions from me this week.

r-karimi · 2020-11-03T02:06:02Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+  question("Where can you go to try to locate 'object'?",
    answer("The console"),
-    answer("Lower right pane", correct=TRUE),
-    answer("Upper right pane"))
+    answer("Lower right pane"),
+    answer("Upper right pane", correct=TRUE))


Yes, this is a neat idea. I like this style of questioning--introducing students to the types of common errors they might encounter is prudent. Well done.

r-karimi · 2020-11-03T02:07:17Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

-```{r Scripts, echo=FALSE}
-quiz(
-  question("How do R scripts make your work reproducible?",
-    answer("Trick question: they work just like Excel and don't make work reproducible"),
-    answer("They keep a record of all actions done to get from raw data to final results", correct=TRUE),
-    answer("You can use them to test different operations on your data")
-),


Is it worth introducing the set.seed() function for reproducible random simulations? Might be out of the scope of this tutorial but it's also a pretty straightforward function. What do you think @cathy-y and @stephan-koenig?

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

Co-authored-by: Ryan Karimi <[email protected]>

…n greater depth, gave examples of common errors for loading and installing packages

Can only link to sections, not subsections

Resmirad · 2021-02-08T23:24:42Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+
+![](/images/rstudio.png){width=100%}
+
+Notice that the window has three "panes":


There are four panes and an option in, tools > global options > pane layout to customize the panels. Would it be useful to include here?

Resmirad · 2021-02-08T23:49:52Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+example_transposed
+```
+### The most helpful function of all: the 'help' function
+You can get information about a specific function by running the command `?<function>` or `help(<function>)` (replace `<function>` by the name of the function you are interested in). This command opens the help page, where you can find all information about a function's purpose and its arguments. For beginners, it is useful to concentrate on the "Examples" and "Arguments" section to understand the typical usage of the function better.


You can also type the function into the search box of the help window in the files plots packages help pane. That way it is never part of the Rscript.

Resmirad · 2021-02-09T00:30:43Z

inst/tutorials/r_and_rstudio_basic/r_and_rstudio_basic.Rmd

+We can filter for specific rows based on a column value using the `filter()` function. Here we restrict for rows where the value for `Depth` is smaller than 135. 
+
+```{r}
+above_135_depth <- filter(OTU_metadata_table, Depth < 135)


The filter function created conflict, worked only as dplyr : : filter(). This issue has been reviewed before for select(), could use either example to demonstrate the notation

stephan-koenig and others added 3 commits May 30, 2020 16:56

Move file from master to individual branch

1bc8755

Fix text formatting and add donwload link for data

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Apply suggestions from TA code review

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Co-authored-by: Ryan Karimi <[email protected]> Co-authored-by: ymkng <[email protected]> Co-authored-by: Pranav Sampara <[email protected]> Co-authored-by: Cathy <[email protected]> Co-authored-by: Avery Noonan <[email protected]>

cathy-y self-assigned this Oct 10, 2020

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Co-authored-by: Ryan Karimi <[email protected]>

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cathy-y added 2 commits October 23, 2020 15:05

Fixed markups for code chunks

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Restructured order of sections, moved learning objectives to the begi…

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…nning of the tutorial, and changed t() function to paste()

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Update r_and_rstudio_basic.html

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Co-authored-by: Ryan Karimi <[email protected]>

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…n greater depth, gave examples of common errors for loading and installing packages

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R and rstudio basic #15

R and rstudio basic #15

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		You can also change the sizes of the panes by dragging the dividers or clicking on the expand and compress icons at the top right corner of each pane.

		```{r quiz: R Tour, echo=FALSE}

	Now it's your turn! Declare a variable "product" and set its value to 3 * 5. Next, operating on "product", declare a variable called "difference", whose final value is 8.
	Now it's your turn! Declare a variable "product" and set its value to the product of the numbers 3 and 5. Next, using the variable "product", declare a variable called "difference", whose final value is 8.


		When you start RStudio, you will see something like the following window appear:

		![](/images/rstudio.png){width=100%}


		When trying to run a command, you see this error:

		![](/images/objecterror.png){width=100%}


		![](/images/rstudio.png){width=100%}

		Notice that the window has three "panes":

R and rstudio basic #15

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R and rstudio basic #15

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