laser-orientation-badge.rmd

---
title: "LASER Badge"
subtitle: "LASER Institute Orientation"
author: "Mark LaVenia"
date: "`r format(Sys.Date(),'%B %e, %Y')`"
output:
  html_document:
    toc: yes
    toc_depth: 4
    toc_float: yes
    code_folding: show
    code_download: TRUE
editor_options:
  markdown:
    wrap: 72
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, error = TRUE)
```

![](img/LASER_Hx.png){width="40%"}

## Introduction

Welcome to your first LASER badge! This LASER Orientation Badge is
really a warm-up activity to introduce you to R Markdown and the coding
case studies that we will be using in the machine learning, network
analysis, and text mining labs. It is a chance to become familiar with
how RStudio and R Markdown works.

You may have used R before-or you may not have! Either is fine as this
task will be designed with the assumption that you have not used R
before. It includes "reaches" for anyone who may want to do a bit more.

In the context of doing so, we'll focus on the following tasks:

1.  Reading data into R (in the **Prepare** section)
2.  Preparing and "wrangling" data in table (think spreadsheet!) format
    (in the **Wrangle** section)
3.  Creating some plots (in the **Explore** section)
4.  Running a model - specifically, a regression model (in the **Model**
    section)
5.  Finally, creating a reproducible report of your work you can share
    with others (in the **Communicate** section)

### The LASER Cycle

You may be wondering what these bolded terms above refer to; what's so
special about preparing, wrangling, exploring, and modeling data - and
communicating results? We're using these terms as a part of a framework,
or model, for what we mean by doing learning in STEM education research.

The particular framework we are using comes from the work of Krumm et
al.'s [*Learning Analytics Goes to
School*](https://github.com/laser-institute/essential-readings/blob/main/laser-orientation/Learning%20Analytics%20Goes%20to%20School.pdf)*.*
You can check that out, but don't feel any need to dive deep for now -
we'll be spending more time on this in first day of the summer
institute. For now, know that this document is organized around three of
the five components of what we're referring to as the **LASER cycle**.

Click the green arrow to the right of the "code chunk" below to view the
image (more on that process of clicking the green arrow and what it
does, too, in a moment)!

```{r}
knitr::include_graphics("img/laser-cycle.png")
```

### How to use this R Markdown document

This is an R Markdown file as indicated by the .rmd extension at the end
of the file name. R Markdown documents are fully reproducible and use a
productive [notebook
interface](https://bookdown.org/yihui/rmarkdown/notebook.html) to
combine narrative text and "chunks" of code to produce a range of
formatted outputs including: formats
including [HTML](https://bookdown.org/yihui/rmarkdown/html-document.html), [PDF](https://bookdown.org/yihui/rmarkdown/pdf-document.html), [MS
Word](https://bookdown.org/yihui/rmarkdown/word-document.html), [Beamer](https://bookdown.org/yihui/rmarkdown/beamer-presentation.html), [HTML5
slides](https://bookdown.org/yihui/rmarkdown/ioslides-presentation.html), [Tufte-style
handouts](https://bookdown.org/yihui/rmarkdown/tufte-handouts.html), [books](https://bookdown.org/), [dashboards](https://rmarkdown.rstudio.com/flexdashboard/), [shiny
applications](https://bookdown.org/yihui/rmarkdown/shiny-documents.html), [scientific
articles](https://github.com/rstudio/rticles), [websites](https://bookdown.org/yihui/rmarkdown/rmarkdown-site.html),
and more.

There are two keys to your use of R Markdown for this activity:

1.  First, be sure that you are viewing the document in the "Visual
    Editor" mode. You can use this mode by clicking the word "Visual" on
    the left side of the toolbar above.
2.  Second, click "Knit" next to the yarn ball at the top of this screen
    to preview the document as you work through it. This will allow you
    to see your code and the input in a rendered - easy-to-read -
    document, just as others will see this document when shared. Try
    knitting the document now and see what happens.

Let's get started! We are glad you are here and to begin this exciting
(and challenging) journey together.

## 1. PREPARE

By preparing, we refer to developing a question or purpose for the
analysis, which you likely know from your research can be difficult!
This part of the process also involves developing an understanding of
the data and what you may need to analyze the data. This often involves
looking at the data and its documentation. For now, we'll focus on just
a few parts of this process, diving in much more deeply over the coming
weeks.

### Packages 📦

R uses "packages," add-ons that enhance its functionality. One package
that we'll be using is the tidyverse. To load the tidyverse, click the
green arrow in the right corner of the block-or "chunk"-of code that
follows.

```{r}
library(tidyverse)
```

Please do not worry if you saw a number of messages: those probably mean
that the tidyverse loaded just fine. If you see an error, though, try to
interpret or search via your search engine the contents of the error, or
reach out to us for assistance.

### Loading (or reading in) data

Next, we'll load data-specifically, a CSV file, the kind that you can
export from Microsoft Excel or Google Sheets - into R, using the
`read_csv()` function in the next chunk.

Clicking the green arrow runs the code; do that next to read the
`sci-online-classes.csv` file stored in your data folder into your R
environment:

```{r}
d <- read_csv("data/sci-online-classes.csv")
```

Nice work! You should now see a new data "object" named `d` saved in
your Environment pane. Try clicking on it and see what happens.

#### Viewing or inspecting data

Now let's learn another way to inspect our data. Run the next chunk and
look at the results, tabbing left or right with the arrows, or scanning
through the rows by clicking the numbers at the bottom of the pane with
the print-out of the data you loaded:

```{r}
d
```

#### [**Your Turn**]{style="color: green;"} **⤵**

What do you notice about this data set? What do you wonder? Add one-two
thoughts following the dashes next (you can add additional dashes if you
like!):

-   603 obs. of 30 variables

-   Student-level data, including student id, academic performance  at the item level and summary info, context info, and student characteristics

There are other ways to inspect your data; the `glimpse()` function
provides one such way. Run the code below to take a glimpse at your
data.

```{r}
glimpse(d)
```

We have one more question to pose to you: What do rows and columns
typically represent in your area of work and/or research?

Generally, rows typically represent "cases," the units that we measure,
or the units on which we collect data. This is not a trick question!
What counts as a "case" (and therefore what is represented as a row)
varies by (and within) fields. There may be multiple types or levels of
units studied in your field; listing more than one is fine! Also, please
consider what columns - which usually represent variables - represent in
your area of work and/or research.

#### [**Your Turn**]{style="color: green;"} **⤵**

What rows typically (or you think may) represent:

-   rows typically represent individual people, though it can be structured long, with information on an individual person (such as items on a test or points in time) represented as individual rows.

What columns typically (or you think may) represent:

-   Columns typically represent information on an individual person, including context info, such as organization and geographic area to which they are associated.

Next, we'll use a few functions that are handy for preparing data in
table form.

## 2. WRANGLE

By wrangle, we refer to the process of cleaning and processing data,
and, in cases, merging (or joining) data from multiple sources. Often,
this part of the process is very (surprisingly) time-intensive.
Wrangling your data into shape can itself be an important
accomplishment! There are great tools in R to do this, especially
through the use of the {dplyr} R package.

### Selecting variables

Let's select only a few variables.

```{r}
d |> 
  select(student_id, total_points_possible, total_points_earned)
```

Notice how the number of columns (variables) is now different.

Let's *include one additional variable* in your select function.

First, we need to figure out what variables exist in our dataset (or be
reminded of this - it's very common in R to be continually checking and
inspecting your data)!

You can use a function named glimpse() to do this.

```{r}
glimpse(d)
```

#### [**Your Turn**]{style="color: green;"} **⤵**

In the code chunk below, add a new variable to the code below, being
careful to type the new variable name as it appears in the data. We've
added some code to get you started. Consider how the names of the other
variables are separated as you think about how to add an additional
variable to this code.

```{r}
d |> 
  select(student_id, course_id, total_points_possible, total_points_earned)

```

Once added, the output should be different than in the code above -
there should now be an additional variable included in the print-out.

### Filtering variables

Next, let's explore filtering variables. Check out and run the next
chunk of code, imagining that we wish to filter our data to view only
the rows associated with students who earned a final grade (as a
percentage) of 70 - 70% - or higher.

```{r}
d |> 
  filter(FinalGradeCEMS > 70)
```

##### [**Your Turn**]{style="color: green;"} **⤵**

In the next code chunk, change the cut-off from 70% to some other
value - larger or smaller (maybe much larger or smaller - feel free to
play around with the code a bit!).

```{r}
d |> 
  filter(FinalGradeCEMS > 99)
```

What happens when you change the cut-off from 70 to something else? Add
a thought (or more):

-   I changed the cutoff to > 99, which drastically reduced the number of cases, to now only 5 obs.

### Arrange

The last function we'll use for preparing tables is arrange.

We'll combine this arrange() function with a function we used already -
select(). We do this so we can view only the student ID and their final
grade.

```{r}
d |> 
  select(student_id, FinalGradeCEMS) |> 
  arrange(FinalGradeCEMS)
```

Note that arrange works by sorting values in ascending order (from
lowest to highest); you can change this by using the desc() function
with arrange, like the following:

```{r}
d |> 
  select(student_id, FinalGradeCEMS) |> 
  arrange(desc(FinalGradeCEMS))
```

#### [**Your Turn**]{style="color: green;"} **⤵**

In the code chunk below, replace FinalGradeCEMS that is used with both
the select() and arrange() functions with a different variable in the
data set. Consider returning to the code chunk above in which you
glimpsed at the names of all of the variables.

```{r}
d |> 
  select(student_id, FinalGradeCEMS, Points_Earned) |> 
  arrange(desc(Points_Earned))
```

### Reach 1 🎉

Can you compose a series of functions that include the select(),
filter(), and arrange functions? Recall that you can "pipe" the output
from one function to the next as when we used select() and arrange()
together in the code chunk above.

*This reach is not required/necessary to complete; it's just for those
who wish to do a bit more with these functions at this time (we'll do
more in class, too!)*

```{r}
glimpse(d)

d |> 
  select(student_id, TimeSpent, Points_Earned) |> 
  arrange(desc(Points_Earned), desc(TimeSpent))

```

## 3. EXPLORE

Exploratory data analysis, or exploring your data, involves processes of
*describing* your data (such as by calculating the means and standard
deviations of numeric variables, or counting the frequency of
categorical variables) and, often, visualizing your data prior. In this
section, we'll create a few plots to explore our data.

### Histogram

The code below creates a histogram, or a distribution of the values, in
this case for students' final grades.

```{r}
ggplot(d, aes(x = FinalGradeCEMS)) +
  geom_histogram()
```

You can change the color of the histogram bars by specifying a color as
follows:

```{r}
ggplot(d, aes(x = FinalGradeCEMS)) +
  geom_histogram(fill = "blue")
```

### Changing colors

#### [**Your Turn**]{style="color: green;"} **⤵**

In the code chunk below, change the color to one of your choosing;
consider this list of valid color names here:
<http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf>

```{r}
ggplot(d, aes(x = FinalGradeCEMS)) +
  geom_histogram(fill = "darkviolet")
```

Finally, we'll make one more change; visualize the distribution of
another variable in the data - one other than FinalGradeCEMS. You can do
so by swapping out the name for another variable with FinalGradeCEMS.
Also, change the color to one other than blue.

```{r}
glimpse(d)

ggplot(d, aes(x = Points_Earned)) +
  geom_histogram(fill = "darkviolet")
```

### Reach 2 🎉

Completed the above? Nice job! Try for a "reach" by creating a scatter
plot for the relationship between two variables. You will need to pass
the names of two variables to the code below for what is now simply XXX
(a placeholder).

```{r}
ggplot(d, aes(x = TimeSpent, y = Points_Earned)) +
  geom_point()
```

## 4. MODEL

"Model" is one of those terms that has many different meanings. For our
purpose, we refer to the process of simplifying and summarizing our
data. Thus, models can take many forms; calculating means represents a
legitimate form of modeling data, as does estimating more complex
models, including linear regressions, and models and algorithms
associated with machine learning tasks. For now, we'll run a linear
regression to predict students' final grades.

Below, we predict students' final grades (`FinaGradeCEMS`, which is on a
0-100 point scale) on the basis of the time they spent on the course
(measured through their learning management system in minutes,
`TimeSpent`, and the subject (one of five) of their specific course.

```{r}
m1 <- lm(FinalGradeCEMS ~ TimeSpent + subject, data = d)
summary(m1)
```

#### [**Your Turn**]{style="color: green;"} **⤵**

Notice how above the variables are separated by a + symbol. Below, add
*another* - a third - variable to the regression model. Specifically,
add a variable students' initial, self-reported interest in science,
`int` - and any other variable(s) you like! What do you notice about the
results? 

-   I added semester to the model. With S116 as the reference category, there was statistically signficiant ( p < .05) difference in final grades for students in Semester S216, at an estimated -4 points.

We're going to dive into this *much* more: if you have many
questions now, you're in the right spot!

```{r}
table(d$semester, useNA = "ifany")

m2 <- lm(FinalGradeCEMS ~ TimeSpent + subject + semester, data = d)
summary(m2)
```

## 5. COMMUNICATE

Great job! Once you've finished your work, Upon doing so, you should see
a new `laser-orientation-badge.html`.

Congratulations, you've completed your Models & Inference Badge!
Complete the following steps to submit your work for review by

1.  Change the name of the `author:` in the [YAML
    header](https://monashdatafluency.github.io/r-rep-res/yaml-header.html)
    at the very top of this document to your name. As noted in
    [Reproducible Research in
    R](https://monashdatafluency.github.io/r-rep-res/index.html), The
    YAML header controls the style and feel for knitted document but
    doesn't actually display in the final output.

2.  Click the yarn icon above to "knit" your data product to a
    [HTML](https://bookdown.org/yihui/rmarkdown/html-document.html) file
    that will be saved in your R Project folder.

3.  Commit your changes in GitHub Desktop and push them to your online
    GitHub repository.

4.  Publish your HTML page the web using one of the following
    [publishing methods](https://rpubs.com/cathydatascience/518692):

    -   Publish on [RPubs](https://rpubs.com) by clicking the "Publish"
        button located in the Viewer Pane when you knit your document.
        Note, you will need to quickly create a RPubs account.

    -   Publishing on GitHub using either [GitHub
        Pages](https://pages.github.com) or the [HTML
        previewer](http://htmlpreview.github.io).

5.  Post a new discussion on GitHub to our [Foundations Badges
    forum](https://github.com/orgs/laser-institute/teams/foundations/discussions/2).
    In your post, include a link to your published web page and a short
    reflection highlighting one thing you learned from this lab and one
    thing you'd like to explore further.