20260103 - clean up section headers and cross-references

Author: isaactpetersen

R.qmd

@@ -15,7 +15,7 @@ output:
 
 — [Evelyn Hall and Simon 'Yoda' Blomberg, R-help April 2005](https://www.brodrigues.co/blog/2022-06-02-arcane/) (archived at <https://perma.cc/KY9N-2FTT>)
 
-# Learning `R` {#learn}
+# Learning `R` {#sec-learn}
 
 ## Base R
 
@@ -63,7 +63,7 @@ The following are resources for learning `tidyverse`, which is a collection of `
 
 - <https://www.linkedin.com/learning/learning-the-r-tidyverse/welcome?u=42459020> (archived at <https://perma.cc/TD56-FX8R>)
 
-## Getting Help/Questions {#questions}
+## Getting Help/Questions {#sec-questions}
 
 If you have `R` questions, you can ask them in a number of places:
 
@@ -90,7 +90,7 @@ Here are guidelines on providing a minimal, reproducible example: <https://stack
 Here are a good example and guidelines for providing a minimal, reproducible example in `R`: <https://stackoverflow.com/a/5963610> (archived at <https://perma.cc/PC9L-DQZG>).
 Provide a `reprex` whenever possible: <https://reprex.tidyverse.org>.
 
-# Initial Set Up {#setup}
+# Initial Set Up {#sec-setup}
 
 Note: many of these initial setup steps described below are not necessary for general use; many of these steps are necessary only for using lab-related repositories (e.g., to gain API access to export data from `REDCap`, to use absolute paths rather than relative paths so repos can communicate with each other, etc.).
 
@@ -137,7 +137,7 @@ To do this, perform the following steps:
 If the `Rprofile.site` and `.Rprofile` files are correctly set up, they should pre-populate your `path` location when you open R.
 If the contents of the `Global Environment` in `RStudio` are empty, your `Rprofile.site` and/or `.Rprofile` files are not set up correctly.
     - If you get this error (`Error: could not find function "install.packages"`), run the following line manually and then restart `RStudio` after the package finishes installing: `install.packages("fortunes")`
-1. For [reproducibility purposes](#dontSaveWorkspace), prevent `R`/`RStudio` from saving your workspaces automatically using the following steps:
+1. For [reproducibility purposes](#sec-dontSaveWorkspace), prevent `R`/`RStudio` from saving your workspaces automatically using the following steps:
     - With RStudio running, choose `Tools → Global Options` from the menus.
     - In the Options dialog, change the value for `Save workspace to .RData on exit` to `Never`.
     - Click `OK`.
@@ -176,16 +176,16 @@ In general, RAs should not have an API token.
 1. For antialiased plots in `RStudio`, change the Graphics backend to `Cairo`:
 `Tools → Global Options → Graphics`
 
-# Lab Package {#petersenlab}
+# Lab Package {#sec-petersenlab}
 
 The [`petersenlab` package](https://devpsylab.github.io/petersenlab) is here: <https://devpsylab.github.io/petersenlab>.
-To install the [`petersenlab` package](https://devpsylab.github.io/petersenlab), see instructions [here](dataManagement.qmd#labFunctions).
+To install the [`petersenlab` package](https://devpsylab.github.io/petersenlab), see instructions [here](dataManagement.qmd#sec-labFunctions).
 
-# Install Packages {#installPackages}
+# Install Packages {#sec-installPackages}
 
-To install and load `R` packages, see the instructions [here](dataManagement.qmd#loadInstallPackages).
+To install and load `R` packages, see the instructions [here](dataManagement.qmd#sec-loadInstallPackages).
 
-# Update Packages {#updatePackages}
+# Update Packages {#sec-updatePackages}
 
 To update packages, use the following code:
 
@@ -196,20 +196,20 @@ update.packages(checkBuilt = TRUE)
 ```
 
 One indication that the packages might not be updating to the latest version is seeing the same packages showing as needing an update after having run the `update.packages()` function.
-If this does not update the package(s) to the latest version, you may need to install the latest version of the package(s) from source (see the section on "[Initial Set Up](#setup)" of `R` for the software needed to install R packages from source):
+If this does not update the package(s) to the latest version, you may need to install the latest version of the package(s) from source (see the section on "[Initial Set Up](#sec-setup)" of `R` for the software needed to install R packages from source):
 
 ```{r}
 #| eval: false
 
 update.packages(checkBuilt = TRUE, type = "source")
 ```
 
-# Update `R` {#updateR}
+# Update `R` {#sec-updateR}
 
 Instructions adapted from: <https://mirror.las.iastate.edu/CRAN/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f> (archived at <https://perma.cc/W5QW-MA6Q>)
 
 1. Uninstall `R`
-1. Install the new `R` version into a directory that contains no spaces (see Step 2 in the [Initial Set Up](#setup) section above)
+1. Install the new `R` version into a directory that contains no spaces (see Step 2 in the [Initial Set Up](#sec-setup) section above)
 1. [You only need to do this step if you installed packages in the R-version-specific "Library" folder rather than the common/shared "Packages" folder—that is, you don't need to do this step if you used the lab's `Rprofile.site` file, as described above, which installs packages to the common/shared "Packages" folder]:
     - Copy installed packages in the "Library" folder to the "Library" folder in the new installation
 1. In new `R` version folder, copy the current `Rprofile.site` file as a backup (`Rprofile_BACKUP.site`) and overwrite the original file with the lab's version of `Rprofile.site` from here: <https://research-git.uiowa.edu/PetersenLab/R-InitialSetup/-/blob/master/R%20Setup%20Files/Rprofile.site>
@@ -220,22 +220,22 @@ Instructions adapted from: <https://mirror.las.iastate.edu/CRAN/bin/windows/base
     Then, click or tap on "Properties".
     In the Properties window, go to the Compatibility tab.
     At the bottom of the window, check the box next to the "Run this program as an administrator" option, and then click or tap on Apply or OK.
-1. Make sure you have the latest version of the tools necessary to compile packages from source (i.e., Rtools for Windows or `R` Compiler Tools for Rcpp on MacOS; see the instructions in the section on [initial set up](#setup))
+1. Make sure you have the latest version of the tools necessary to compile packages from source (i.e., Rtools for Windows or `R` Compiler Tools for Rcpp on MacOS; see the instructions in the section on [initial set up](#sec-setup))
 1. Open the new `R` version and run `update.packages(checkBuilt = TRUE, ask = FALSE)`, and install any necessary packages
 1. Close R
 1. Delete anything left of the old installation
 
-# Style Guide and Best Practices {#bestPractices}
+# Style Guide and Best Practices {#sec-bestPractices}
 
 ## Create `Rstudio Project`
 
-For each data analysis project (i.e., each [`GitLab`/`GitHub`](#git) repo), create an RStudio Project.
+For each data analysis project (i.e., each [`GitLab`/`GitHub`](#sec-git) repo), create an RStudio Project.
 This helps keep your project files organized.
 
 ## Use `R` Notebooks for "Computational Notebooks"
 
 Using `R` Notebooks for "Computational Notebooks" is helpful for reproducible code that can be shared with others.
-To create computational notebooks see the `Markdown` section on [computational notebooks](markdown.qmd#computationalNotebook) in the Data Analysis guides.
+To create computational notebooks see the `Markdown` section on [computational notebooks](markdown.qmd#sec-computationalNotebook) in the Data Analysis guides.
 
 ## Separate sections in code
 
@@ -259,7 +259,7 @@ To create computational notebooks see the `Markdown` section on [computational n
 It is important to comment code frequently and clearly.
 You want you (and others) to easily be able to understand your code if you come back to it several years later!
 
-## Don't save your workspace image {#dontSaveWorkspace}
+## Don't save your workspace image {#sec-dontSaveWorkspace}
 
 For reproducibility purposes, it is important [**not** to save your workspace image](https://www.r-bloggers.com/2017/04/using-r-dont-save-your-workspace/) (archived at <https://perma.cc/9SCZ-L4DE>).
 It is best practices to begin `R` each session with a clean workspace.
@@ -311,10 +311,10 @@ However, do make sure to save your `R` scripts before exiting Rstudio.
 - [Hierarchical Linear Modeling](hlm.qmd)
 - [Item Response Theory](irt.qmd)
 - [Longitudinal Data Analysis](lda.qmd)
-- [Mediation](sem.qmd#mediation)
-- [Moderation/Interaction](regression.qmd#moderation)
+- [Mediation](sem.qmd#sec-mediation)
+- [Moderation/Interaction](regression.qmd#sec-moderation)
 - [Multiple Imputation](multipleImputation.qmd)
-- [Principal Component Analysis](pca.hqmdtml)
+- [Principal Component Analysis](pca.qmd)
 - [Regression](regression.qmd)
 - [Structural Equation Modeling](sem.qmd)
 
@@ -359,11 +359,11 @@ pandoc version 1.12.3 or higher is required and was not found.
 
 The solution to this problem [can be found at this link](https://stackoverflow.com/questions/28432607/pandoc-version-1-12-3-or-higher-is-required-and-was-not-found-r-shiny) (archived at <https://perma.cc/YX57-BPRS>)
 
-# Using R Script to Commit and Push Changes {#gitPush}
+# Using R Script to Commit and Push Changes {#sec-gitPush}
 
 When using R to perform such actions as rendering sites and processing data, it can be useful to include code that commits and pushes relevant changes into the appropriate `git` repository. 
 The steps below assume that you have `Git` and the `GitHub` desktop app installed.
-The instructions to download and configure `git` software can be found [here](git.Rmd#toBegin)
+The instructions to download and configure `git` software can be found [here](git.Rmd#sec-toBegin)
 
 1. Install and/or load `git2r` package
    ```r
@@ -437,7 +437,7 @@ The instructions to download and configure `git` software can be found [here](gi
       - Using a [Personal Access Token](https://docs.gitlab.com/user/profile/personal_access_tokens/)
       - Using an [SSH key](https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key)
       - Encrypting credential information and storing the encrypted credential file somewhere accessible for use
-         - See [here](https://research-git.uiowa.edu/PetersenLab/R-InitialSetup/-/blob/master/REDCap%20Credentials/Encrypt%20REDCap%20Token.R) for an exmaple of encryption and key creation
+         - See [here](https://research-git.uiowa.edu/PetersenLab/R-InitialSetup/-/blob/master/REDCap%20Credentials/Encrypt%20REDCap%20Token.R) for an example of encryption and key creation
          - Using the encrypted credential and encryption key:
 
             ```r
@@ -457,7 +457,7 @@ The instructions to download and configure `git` software can be found [here](gi
             push(repo, credentials = cred_user_pass("insertUsername", myPassword))
             ```
 
-# Using `try()` Statements {#try}
+# Using `try()` Statements {#sec-try}
 
 [`try()` statements](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/try) can be very useful in cases where you would like code to continue running even if a certain line errors out. 
 If the code inside of the statement results in an error, the `try()` statement will allow R to simply jump to the next line of code, rather than halting the entire process.
@@ -606,7 +606,7 @@ usethis::use_version()
 
 1. Then, check the package: Ctrl-Shift-E
 
-1. Then, run [`R CMD check`](#rCmdCheck)
+1. Then, run [`R CMD check`](#sec-rCmdCheck)
 
 1. Then, install the package:
 
@@ -633,7 +633,7 @@ or:
 install.packages("NAME_OF_PACKAGE")
 ```
 
-## `R CMD check` {#rCmdCheck}
+## `R CMD check` {#sec-rCmdCheck}
 
 1. Build the source package (`.tar.gz` file)
     - Click on the "Build" tab in the top-right pane of RStudio, and then click "Build Source Package", or run the following code in the `R` console:
@@ -672,7 +672,7 @@ devtools::build(pkg = "D:/Documents/GitHub/petersenlab")
 
 1. Then, delete the created folder whose name begins with ".Rd2pdf..."
 
-1. In the R Console, build the source package in `R` (or using the instructions described [above](#rCmdCheck)):
+1. In the R Console, build the source package in `R` (or using the instructions described [above](#sec-rCmdCheck)):
 
 ```{r}
 #| eval: false
@@ -812,11 +812,11 @@ Unofficial documentation:
 
 - <https://usethis.r-lib.org/reference/licenses.html>
 
-# Troubleshooting {#troubleshootingR}
+# Troubleshooting {#sec-troubleshootingR}
 
 To troubleshoot `R` issues, be resourceful.
 Try googling the error message or issue you are experiencing.
-See [here](#questions) for a list of places you can pose `R`-related questions for help.
+See [here](#sec-questions) for a list of places you can pose `R`-related questions for help.
 In addition, particular errors/warnings/issues are included below:
 
 ## General Troubleshooting Tips
@@ -860,7 +860,7 @@ Code can be wrapped in `try()` statements so that if an error occurs, the script
 These `try()` statements are particularly useful when rendering a site; if they are not used, a single error will halt the entire process. `try()` statements allow the code to continue running in spite of a line or two erroring out.
 
 If you have already incorporated `try()` statements and are still experiencing fatal errors in code, check to make sure that the smallest possible "unit" of code is wrapped in `try()` statements, rather than large sections of code. 
-See [here](#try) for more information.
+See [here](#sec-try) for more information.
 
 ## Warning: `PACKAGENAME` package in `FILEPATH` library will not be updated
 

SPSS.qmd

@@ -2,13 +2,13 @@
 title: "SPSS"
 ---
 
-# When to use `SPSS` {#whenSPSS}
+# When to use `SPSS` {#sec-whenSPSS}
 
  We use [R](R.qmd) for almost all data analysis.
  However, [R](R.qmd) is code-based and has a steep learning curve.
  As a result, undergraduate students in the lab most often use `SPSS` or [`jamovi`](jamovi.qmd) for their research projects (e.g., [Honors projects](https://devpsylab.github.io/LabWiki/honors.html) and [SROP projects](https://devpsylab.github.io/LabWiki/expectations-SROP.html)), because `SPSS` and [`jamovi`](jamovi.qmd) have a point-and-click interface.
 
-# Creating a `SPSS` Syntax File to Import a `.csv` Data File {#import}
+# Creating a `SPSS` Syntax File to Import a `.csv` Data File {#sec-import}
 
 A `.csv` file is a "comma-separated values" file—a file whose values are separated by commas.
 The lab will provide you with a `.csv` in your member user folder.
@@ -34,7 +34,7 @@ Next, save the data in `SPSS` format (`.sav`) with the below steps:
    - On the open data file, select `save as` and `paste`
    - This will copy and paste the syntax at the **end of the syntax file** in the import script.
    The completed import script will now read the `.csv` file and convert it to an `SPSS` data file (`.sav`).
-   - At this point, you can proceed [here](#analysis) to start your analysis script! 
+   - At this point, you can proceed [here](#sec-analysis) to start your analysis script! 
 
 Example (you will need to update the filepath to your particular filepath):
 
@@ -61,53 +61,53 @@ SAVE OUTFILE='\\lc-rs-store24.hpc.uiowa.edu\lss_itpetersen\Lab\Members\HAWKID\Th
   /COMPRESSED.
 ```
 
-# Data Management {#dataManagement}
+# Data Management {#sec-dataManagement}
 
 Add any data management/transformations at the end of your `import.sps` file (after importing your data), so you re-run the transformations each time you update the data file.
 
-# Recode Variables {#recode}
+# Recode Variables {#sec-recode}
 
 <https://stats.oarc.ucla.edu/spss/modules/creating-and-recoding-variables/> (archived at <https://perma.cc/YJ2H-SRZM>)
 
 <https://wlm.userweb.mwn.de/SPSS/wlmsreco.htm> (archived at <https://perma.cc/G4FN-PYPV>)
 
-## Average Across Variables {#averageVars}
+## Average Across Variables {#sec-averageVars}
 
 ```
 COMPUTE cbcl_externalizingPOM_Average = MEAN(cbcl_externalizingPOM_Father,cbcl_externalizingPOM_Mother,cbcl_externalizingPOM_Secondary).
 COMPUTE cbq_inhibitoryControl_Average = MEAN(cbq_inhibitoryControl_Father,cbq_inhibitoryControl_Mother,cbq_inhibitoryControl_Secondary).
 EXECUTE.
 ```
 
-## Rename Variables {#renameVars}
+## Rename Variables {#sec-renameVars}
 
 ```
 RENAME VARIABLES (ses_hollingsheadSES = SES).
 ```
 
-## Mean-Center Variables {#meanCenter}
+## Mean-Center Variables {#sec-meanCenter}
 
 ```
 COMPUTE ses_hollingsheadSES_mc = ses_hollingsheadSES - mean_ses.
 COMPUTE adi_nationalRank_mc = adi_nationalRank - mean_adiN.
 EXECUTE.
 ```
 
-## Compute Interaction Terms {#interaction}
+## Compute Interaction Terms {#sec-interaction}
 
 ```
 COMPUTE ses_adi_interaction = ses_hollingsheadSES_mc * adi_nationalRank_mc.
 EXECUTE.
 ```
 
-## Save Data File {#saveData}
+## Save Data File {#sec-saveData}
 
 ```
 SAVE OUTFILE='\\lc-rs-store24.hpc.uiowa.edu\lss_itpetersen\Lab\Members\HAWKID\Thesis\Data\srs_idWave.sav'
   /COMPRESSED.
 ```
 
-# Creating a `SPSS` Syntax File for Analysis {#analysis}
+# Creating a `SPSS` Syntax File for Analysis {#sec-analysis}
 
 1. To create a new syntax file, select file then new then syntax
    - Save file as: `descriptives.sps`
@@ -118,28 +118,28 @@ In your despriptives syntax file, the analysis should now be added. For each sub
 1. Create a new `SPSS` syntax file for your analysis. In this syntax file, add your analysis
    - e.g., regressions
 
-## Frequencies {#frequencies}
+## Frequencies {#sec-frequencies}
 
 ```
 FREQUENCIES VARIABLES=tc_sex tc_hispanic tc_race tc_ethnicity 
   /ORDER=ANALYSIS.
 ```
 
-## Descriptives {#descriptives}
+## Descriptives {#sec-descriptives}
 
 ```
 DESCRIPTIVES VARIABLES=ICsim IClim IChg ICcbq ses_hollingsheadSES ADINat EXTBx 
   /STATISTICS=MEAN STDDEV MIN MAX KURTOSIS SKEWNESS.
 ```
 
-## Histograms {#histograms}
+## Histograms {#sec-histograms}
 
 ```
 GRAPH
   /HISTOGRAM=ses_hollingsheadSES.
 ```
 
-## Correlations {#correlations}
+## Correlations {#sec-correlations}
 
 ```
 CORRELATIONS
@@ -149,7 +149,7 @@ CORRELATIONS
   /MISSING=PAIRWISE.
 ```
 
-## Multiple Regression {#multipleRegression}
+## Multiple Regression {#sec-multipleRegression}
 
 ```
 REGRESSION
@@ -161,7 +161,7 @@ REGRESSION
 /METHOD=ENTER predictor1 predictor2 predictor3.
 ```
 
-## Mediation {#mediation}
+## Mediation {#sec-mediation}
 
 First, download and run the [`PROCESS` macro](https://www.processmacro.org/download.html).
 
@@ -196,7 +196,7 @@ PROCESS
   .
 ```
 
-## Moderation {#moderation}
+## Moderation {#sec-moderation}
 
 1. Calculate means of the predictor and moderator
    ```
@@ -237,9 +237,9 @@ PROCESS
       - <https://github.com/connorjmccabe/InterActive>
       - <https://connorjmccabe.shinyapps.io/interactive/> (archived at <https://perma.cc/93G6-ALDP>)
 
-# Best Practices {#bestPractices}
+# Best Practices {#sec-bestPractices}
 
- - Use `SPSS` syntax files (`.sps`) for performing all commands, including [importing data](#import), computing variables, recoding variables, running analyses, etc.
+ - Use `SPSS` syntax files (`.sps`) for performing all commands, including [importing data](#sec-import), computing variables, recoding variables, running analyses, etc.
  The benefit of using `SPSS` syntax files (and code-based files, more generally) is that they allow you to reproduce your findings again with the same data file.
  This is important so you do not have to remember all of the steps you followed to generate the analysis.
  This also allows you to quickly re-run the analysis if the data file is updated due to the collection of more data.