168

book/06-corsi-analysis.Rmd

@@ -3,47 +3,11 @@
 
 ```{r echo = FALSE, message=FALSE, warning=FALSE}
 library(tidyverse)
-
-# Set the seed for reproducibility
-set.seed(123)
-
-# Define the number of participants
-n_participants <- 600
-
-# Define the variables
-Gender <- c(rep('Woman', n_participants * 0.5),
-            rep('Man', n_participants * 0.40),
-            rep('Non-Binary', n_participants * 0.1))
-
-Age <- sample(18:60, n_participants, replace = TRUE)
-
-# Set conditions and mean Corsi scores
-Condition <- c(rep('8 hours sleep', n_participants * 1/3),
-               rep('4 hours sleep', n_participants * 1/3),
-               rep('Sleep deprived', n_participants * 1/3))
-
-Mean_Corsi_Score <- ifelse(Condition == '8 hours sleep', 6, ifelse(Condition == '4 hours sleep', 5, 4))
-
-# Simulate Corsi scores around mean, considering a small correlation with age
-Corsi_Score <- round(rnorm(n_participants, Mean_Corsi_Score + 0.01*(Age - mean(Age)), sd = 1))
-Corsi_Score <- ifelse(Corsi_Score > 9, 9, ifelse(Corsi_Score < 0, 0, Corsi_Score))
-
-# Create a data frame
-data <- data.frame(Participant = 1:n_participants,
-                   Gender = sample(Gender),
-                   Age = Age,
-                   Condition = Condition,
-                   Corsi_Score = Corsi_Score)
-
-# Define Demographic data
-demographic_data <- data %>% 
-  select(Participant, Gender, Age, Condition)
-
-# Define Score data
-score_data <- data %>% 
-  select(Participant, Corsi_Score)
-
-full_dat <- inner_join(x = demographic_data, y = score_data, by = "Participant")
+demographic_data <- read_csv("data/corsi/demographic_data.csv")
+score_data <- read_csv("data/corsi/score_data.csv")
+full_dat <- inner_join(x = demographic_data, 
+                       y = score_data, 
+                       by = "Participant")
 
 ```
 
@@ -215,7 +179,7 @@ age_control <- analysis_data %>%
 `r unhide()`
 
 
-How many participants are left in the sample after filtering for age? `r fitb(163)`
+How many participants are left in the sample after filtering for age? `r fitb(168)`
 
 ## Activity 5: Summarise
 

book/packages.bib

@@ -23,6 +23,14 @@ @Manual{R-dplyr
   url = {https://CRAN.R-project.org/package=dplyr},
 }
 
+@Manual{R-faux,
+  title = {faux: Simulation for Factorial Designs},
+  author = {Lisa DeBruine},
+  year = {2023},
+  note = {R package version 1.2.1},
+  url = {https://github.com/debruine/faux},
+}
+
 @Manual{R-forcats,
   title = {forcats: Tools for Working with Categorical Variables (Factors)},
   author = {Hadley Wickham},
@@ -40,11 +48,26 @@ @Manual{R-ggplot2
 }
 
 @Manual{R-glossary,
-  title = {glossary: Glossaries for Markdown and Quarto Documents},
+  title = {glossary: PsyTeachR Glossary of Statistical and Coding Terms},
   author = {Lisa DeBruine},
+  year = {2022},
+  note = {R package version 0.0.0.9002},
+}
+
+@Manual{R-kableExtra,
+  title = {kableExtra: Construct Complex Table with kable and Pipe Syntax},
+  author = {Hao Zhu},
+  year = {2021},
+  note = {R package version 1.3.4},
+  url = {https://CRAN.R-project.org/package=kableExtra},
+}
+
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
   year = {2023},
-  note = {R package version 1.0.0},
-  url = {https://CRAN.R-project.org/package=glossary},
+  note = {R package version 1.42},
+  url = {https://yihui.org/knitr/},
 }
 
 @Manual{R-lubridate,
@@ -71,6 +94,14 @@ @Manual{R-readr
   url = {https://CRAN.R-project.org/package=readr},
 }
 
+@Manual{R-rvest,
+  title = {rvest: Easily Harvest (Scrape) Web Pages},
+  author = {Hadley Wickham},
+  year = {2022},
+  note = {R package version 1.0.3},
+  url = {https://CRAN.R-project.org/package=rvest},
+}
+
 @Manual{R-stringr,
   title = {stringr: Simple, Consistent Wrappers for Common String Operations},
   author = {Hadley Wickham},
@@ -121,6 +152,14 @@ @Manual{R-webexercises
   url = {https://github.com/psyteachr/webexercises},
 }
 
+@Manual{R-xml2,
+  title = {xml2: Parse XML},
+  author = {Hadley Wickham and Jim Hester and Jeroen Ooms},
+  year = {2023},
+  note = {R package version 1.3.4},
+  url = {https://CRAN.R-project.org/package=xml2},
+}
+
 @Book{bookdown2016,
   title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
   author = {Yihui Xie},
@@ -140,6 +179,38 @@ @Book{ggplot22016
   url = {https://ggplot2.tidyverse.org},
 }
 
+@Manual{glossary2022,
+  title = {PsyTeachR Glossary of Statistical and Coding Terms},
+  author = {{PsyTeachR Team}},
+  year = {2022},
+  url = {https://psyteachr.github.io/glossary/},
+  doi = {10.5281/zenodo.6619215},
+  version = {0.0.0.9002},
+  publisher = {Zenodo},
+  note = {v0.0.0.9002},
+}
+
+@Book{knitr2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {https://yihui.org/knitr/},
+}
+
+@InCollection{knitr2014,
+  booktitle = {Implementing Reproducible Computational Research},
+  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
+  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  year = {2014},
+  note = {ISBN 978-1466561595},
+}
+
 @Article{lubridate2011,
   title = {Dates and Times Made Easy with {lubridate}},
   author = {Garrett Grolemund and Hadley Wickham},

docs/01-intro.md

@@ -19,7 +19,7 @@ There is a walkthrough video of this chapter available via [Echo360.](https://ec
 
 ## R and RStudio {#sec-intro-r}
 
-R is a programming language that you will write code in. RStudio is an Integrated Development Environment (<a class='glossary'>IDE<span class='def'></span></a>). Think of it as knowing English and using a plain text editor like NotePad to write a book versus using a word processor like Microsoft Word. You could do it, but it would be much harder without things like spell-checking and formatting and you wouldn't be able to use some of the advanced features that Word has developed. In a similar way, you can use R without R Studio but we wouldn't recommend it. RStudio serves as a text editor, file manager, spreadsheet viewer, and more.
+R is a programming language that you will write code in. RStudio is an Integrated Development Environment (<a class='glossary' target='_blank' title='Integrated Development Environment: a program that serves as a text editor, file manager, and provides functions to help you read and write code. RStudio is an IDE for R.' href='https://psyteachr.github.io/glossary/i#ide'>IDE</a>). Think of it as knowing English and using a plain text editor like NotePad to write a book versus using a word processor like Microsoft Word. You could do it, but it would be much harder without things like spell-checking and formatting and you wouldn't be able to use some of the advanced features that Word has developed. In a similar way, you can use R without R Studio but we wouldn't recommend it. RStudio serves as a text editor, file manager, spreadsheet viewer, and more.
 
 * There's an [RStudio IDE Cheatsheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/rstudio-ide.pdf){download=""} you will find helpful to download and keep as a reference.
 
@@ -72,7 +72,7 @@ Do the following, in this order:
 
 ## RStudio panes
 
-RStudio is arranged with four window <a class='glossary'>panes<span class='def'></span></a>. By default, the upper left pane is the **source pane**, where you view, write, and edit code from files and view data tables in a spreadsheet format. **When you first open a new project this pane won't display until you open a document or load in some data** -- don't worry, we'll get to that soon.
+RStudio is arranged with four window <a class='glossary' target='_blank' title='RStudio is arranged with four window "panes".' href='https://psyteachr.github.io/glossary/p#panes'>panes</a>. By default, the upper left pane is the **source pane**, where you view, write, and edit code from files and view data tables in a spreadsheet format. **When you first open a new project this pane won't display until you open a document or load in some data** -- don't worry, we'll get to that soon.
 
 <div class="figure" style="text-align: center">
 <img src="images/intro/rstudio.png" alt="The RStudio IDE" width="100%" />
@@ -85,7 +85,7 @@ The lower left pane is the **console pane**, where you can type in commands and
 Try using the console as a calculator - type `1 + 1` and press enter.
 :::
 
-The right panes have several different tabs that show you information about your code. The most used tab in the upper right pane is the **Environment** tab. The Environment tab lists some information about the <a class='glossary'>objects<span class='def'></span></a> that you have defined in your code. 
+The right panes have several different tabs that show you information about your code. The most used tab in the upper right pane is the **Environment** tab. The Environment tab lists some information about the <a class='glossary' target='_blank' title='A word that identifies and stores the value of some data for later use.' href='https://psyteachr.github.io/glossary/o#object'>objects</a> that you have defined in your code. 
 
 In the lower right pane, the most used tabs are the **Files** tab for directory structure, the **Plots** tab for plots, the **Packages** tab for managing add-on packages (we'll explain what these are in the next chapter), and the **Viewer** tab to display reports created by your scripts. You can change the location of panes and what tabs are shown under `Tools > Global Options... > Pane Layout`. When you open a new project, the Files tab will be set to your project working directory and will show a file with the file extension `.Rproj` which is the file that has all the information about your project. Don't delete this file!
 
@@ -141,8 +141,8 @@ birthday <- as.Date("2024-07-11")
 
 You'll see that four objects now appear in the environment pane:
 
-* `name` is <a class='glossary'>character<span class='def'></span></a> (text) data. In order for R to recognise it as text, it **must** be enclosed in double quotation marks `" "`.
-* `age` is <a class='glossary'>numeric<span class='def'></span></a> data. In order for R to recognise this as a number, it **must not** be enclosed in quotation marks. Every year I have to update my age in this book and I am confronted with my own mortality drawing ever closer. 
+* `name` is <a class='glossary' target='_blank' title='A data type representing strings of text.' href='https://psyteachr.github.io/glossary/c#character'>character</a> (text) data. In order for R to recognise it as text, it **must** be enclosed in double quotation marks `" "`.
+* `age` is <a class='glossary' target='_blank' title='A data type representing a real decimal number or integer.' href='https://psyteachr.github.io/glossary/n#numeric'>numeric</a> data. In order for R to recognise this as a number, it **must not** be enclosed in quotation marks. Every year I have to update my age in this book and I am confronted with my own mortality drawing ever closer. 
 * `today` stores the result of the function `Sys.Date()`. This function returns your computer system's date. Unlike `name` and `age`, which are hard-coded (i.e., they will always return the values you enter), the contents of the object `today` will change dynamically with the date. That is, if you run that function tomorrow, it will update the date to tomorrow's date.
 * `birthday` is also a date but it's hard-coded as a specific date. It's wrapped within the `as.Date()` function that tells R to interpret the character string you provide as a date rather than text.
 
@@ -258,7 +258,7 @@ My name is `r name` and I am `r age` years old. It is `r birthday - today` days
 
 As if by magic, that slightly odd bit of text you copied and pasted now appears as a normal sentence with the values pulled in from the objects you created. 
 
-**My name is Emily and I am 38 years old. It is 271 days until my birthday.**
+**My name is Emily and I am 38 years old. It is 268 days until my birthday.**
 
 We're not going to use this function very often in the rest of the course but hopefully you can see just how useful this would be when writing up a report with lots of numbers. R Markdown is an incredibly powerful and flexible format - this book was written using it! 
 
@@ -311,24 +311,24 @@ The glossary at the end of each chapter defines common jargon you might encounte
  </thead>
 <tbody>
   <tr>
-   <td style="text-align:left;"> character </td>
-   <td style="text-align:left;">  </td>
+   <td style="text-align:left;"> [character](https://psyteachr.github.io/glossary/c.html#character){class="glossary" target="_blank"} </td>
+   <td style="text-align:left;"> A data type representing strings of text. </td>
   </tr>
   <tr>
-   <td style="text-align:left;"> IDE </td>
-   <td style="text-align:left;">  </td>
+   <td style="text-align:left;"> [ide](https://psyteachr.github.io/glossary/i.html#ide){class="glossary" target="_blank"} </td>
+   <td style="text-align:left;"> Integrated Development Environment: a program that serves as a text editor, file manager, and provides functions to help you read and write code. RStudio is an IDE for R. </td>
   </tr>
   <tr>
-   <td style="text-align:left;"> numeric </td>
-   <td style="text-align:left;">  </td>
+   <td style="text-align:left;"> [numeric](https://psyteachr.github.io/glossary/n.html#numeric){class="glossary" target="_blank"} </td>
+   <td style="text-align:left;"> A data type representing a real decimal number or integer. </td>
   </tr>
   <tr>
-   <td style="text-align:left;"> object </td>
-   <td style="text-align:left;">  </td>
+   <td style="text-align:left;"> [object](https://psyteachr.github.io/glossary/o.html#object){class="glossary" target="_blank"} </td>
+   <td style="text-align:left;"> A word that identifies and stores the value of some data for later use. </td>
   </tr>
   <tr>
-   <td style="text-align:left;"> panes </td>
-   <td style="text-align:left;">  </td>
+   <td style="text-align:left;"> [panes](https://psyteachr.github.io/glossary/p.html#panes){class="glossary" target="_blank"} </td>
+   <td style="text-align:left;"> RStudio is arranged with four window "panes". </td>
   </tr>
 </tbody>
 </table>