What we expect of a package | The core table | label is the join key | region is the key people type | hemi is a closed vocabulary | display is for people | Everything else is yours | Adding your package to r-universe | 1. Fork the r-universe repository | 2. Add yourself to packages.json | 3. Open a pull request | 4. Review | Once you are listed

What we expect of a package | The core table | label is the join key | region is the key people type | hemi is a closed vocabulary | display is for people | Everything else is yours | Adding your package to r-universe | 1. Fork the r-universe repository | 2. Add yourself to packages.json | 3. Open a pull request | 4. Review | Once you are listed

Getting started | Mapping data | Subcortical atlases | Camera and background

Basic Shiny integration | Output sizing | Reactive data | Updating camera and background | Complete example | Performance tips

Getting started | Mapping data | Subcortical atlases | Camera and background

Basic Shiny integration | Output sizing | Reactive data | Updating camera and background | Complete example | Performance tips

Cortical atlases | Stacking all views | Subcortical and tract atlases | Horizontal and vertical | Grid layouts | Picking specific views | Grouping by slice type | Adding view labels | Zooming in on regions of interest | Focus on the regions in your data | Name the focus regions explicitly | Control the margin with zoom_pad | Dropping the grey context | The sf workflow

What's in a brain atlas | Your first brain plot | Arranging views | Showing only certain hemispheres or views | Plotting your own data | Faceting | Highlighting specific regions | Scales and themes | Going further | Finding more atlases

The brain shape is drawn by a stat | Repeated regions are combined | Faceting comes for free | Colour, including bins, is just a scale | The three pieces, if you want to build on them

How matching works | A minimal example | Constraining matches with extra columns | Faceting across groups | Troubleshooting | Full control with sf

Cortical atlases | Stacking all views | Subcortical and tract atlases | Horizontal and vertical | Grid layouts | Picking specific views | Grouping by slice type | Adding view labels | Zooming in on regions of interest | Focus on the regions in your data | Name the focus regions explicitly | Control the margin with zoom_pad | Dropping the grey context | The sf workflow

What's in a brain atlas | Your first brain plot | Arranging views | Showing only certain hemispheres or views | Plotting your own data | Faceting | Highlighting specific regions | Scales and themes | Going further | Finding more atlases

The brain shape is drawn by a stat | Repeated regions are combined | Faceting comes for free | Colour, including bins, is just a scale | The three pieces, if you want to build on them

How matching works | A minimal example | Constraining matches with extra columns | Faceting across groups | Troubleshooting | Full control with sf

Available surfaces | Cortical | Cerebellar | Accessing meshes | Integration with ggseg3d | Mesh structure

Available surfaces | Cortical | Cerebellar | Accessing meshes | Integration with ggseg3d | Mesh structure

Migrating code to the 0.1.0 region keys | Do not use display for this | The accessors return rows, not a set | Adding display to your own atlas | label must be unique | 2D coverage is not validated | Migrating an atlas package to sf-optional | The recipe | What migrate_atlas_files() does | Keeping sf instead | Verifying the result

What is a ggseg_atlas? | Anatomy of an atlas | Three atlas types | Core: the region table | Querying an atlas | Extracting render-ready data | Checking and converting

Migrating code to the 0.1.0 region keys | Do not use display for this | The accessors return rows, not a set | Adding display to your own atlas | label must be unique | 2D coverage is not validated | Migrating an atlas package to sf-optional | The recipe | What migrate_atlas_files() does | Keeping sf instead | Verifying the result

What is a ggseg_atlas? | Anatomy of an atlas | Three atlas types | Core: the region table | Querying an atlas | Extracting render-ready data | Checking and converting

The manipulation toolkit | Keeping and removing regions | Context regions | Renaming regions | Managing views | Cleaning up geometry | Reordering and gathering | Adding metadata | A full pipeline

The manipulation toolkit | Keeping and removing regions | Context regions | Renaming regions | Managing views | Cleaning up geometry | Reordering and gathering | Adding metadata | A full pipeline

Parameter hierarchy | Available options | Setting options in R | Verbosity | Cleanup | Skip existing | Output directory | Geometry | Environment variables | Overriding defaults | Recipes | Development and debugging | Production and CI | Iterating on the geometry

Inspecting an atlas | Removing regions | Keeping regions | Context regions | Labels versus regions | Adding metadata columns | View management | Keeping specific views | Removing views | Reordering views | Removing small regions from views | Gathering views | Adjusting geometry after the fact | Start with atlas_polish() | Reducing the vertex count | Rounding off the staircase | Context and core are two different problems | Rebuilding the atlas | Putting it together

Parameter hierarchy | Available options | Setting options in R | Verbosity | Cleanup | Skip existing | Output directory | Geometry | Environment variables | Overriding defaults | Recipes | Development and debugging | Production and CI | Iterating on the geometry

Inspecting an atlas | Removing regions | Keeping regions | Context regions | Labels versus regions | Adding metadata columns | View management | Keeping specific views | Removing views | Reordering views | Removing small regions from views | Gathering views | Adjusting geometry after the fact | Start with atlas_polish() | Reducing the vertex count | Rounding off the staircase | Context and core are two different problems | Rebuilding the atlas | Putting it together

The shortest path | Picking a creation function | What's inside a ggseg_atlas | How each pipeline works | Post-processing | System requirements | Tutorials

What each pipeline needs | FreeSurfer | Parallel processing | Progress bars | Checking your setup

The shortest path | Picking a creation function | What's inside a ggseg_atlas | How each pipeline works | Post-processing | System requirements | Tutorials

What each pipeline needs | FreeSurfer | Parallel processing | Progress bars | Checking your setup

The old system | The current system | Converting old atlases | From a ggseg3d_atlas only | From both 2D and 3D objects | From a 2D ggseg_atlas only | Specifying atlas type | Batch conversion | Post-conversion checklist | Lessons learned from batch conversion | 3D data is not always preserved | Palette entries may not match core rows exactly | Labels with special characters lose sf coverage | Skip ggseg3d tests for atlases without 3D data | Troubleshooting | When to recreate instead

The old system | The current system | Converting old atlases | From a ggseg3d_atlas only | From both 2D and 3D objects | From a 2D ggseg_atlas only | Specifying atlas type | Batch conversion | Post-conversion checklist | Lessons learned from batch conversion | 3D data is not always preserved | Palette entries may not match core rows exactly | Labels with special characters lose sf coverage | Skip ggseg3d tests for atlases without 3D data | Troubleshooting | When to recreate instead

Two ways to configure | Precedence | Configuring per call with lychee_options() | Sharing settings with a lychee.toml file | Reference

Setup | Discover what you can reach | Quick overview of a zone | Traffic analytics | Web Analytics (RUM) | DNS records | Page Rules | Cache purging | Zone settings | Email Routing | Turnstile (CAPTCHA replacement) | Workers | Pages, R2, Tunnels | Firewall + Rulesets | Escape hatches | Error handling

Setup | Discovering what you can reach | DNS records | Purging cache | Zone settings | Calling endpoints the package does not wrap | Error handling

Reading a single stats file | Reading stats files across subjects | Reading FreeSurfer stats tables | Cleaning label suffixes | Filtering non-region rows

Reading a single stats file | Reading stats files across subjects | Reading FreeSurfer stats tables | Cleaning label suffixes | Filtering non-region rows

API token (recommended) | Create a token | Store the token | Global API Key (legacy) | Find the key | Store the credentials | Verify the credentials | Per-call credentials | Troubleshooting | Never commit credentials

Web Analytics (RUM) site catalogue | GraphQL Analytics | HTTP requests per day for a zone | Top countries for a Web Analytics (RUM) site | Error handling | Tidy wrappers | HTTP traffic over time | Cache hit ratio | DNS queries | Firewall events | Real-user (RUM) views | Picking the right query

The palette | Colour scales for ggplot2 | Available palettes | Custom tints and shades | The theme | R Markdown templates | Putting it together

Finding the binary | The direct route | Wrappers | Parcellate CIFTI data | Compute a correlation matrix | Reduce across maps | Surface curvature | Map a volume to a surface | Math expressions | Getting help | Using wbcmd with ciftiTools | Controlling verbosity

What a random rotation needs to do | Euler ZYZ rotations | Rodrigues axis-angle rotations | Where Rodrigues has the edge | Geometric transparency | Axis uniformity is explicit | Numerical stability | Idiomatic R | Where Euler has the edge | How much does the difference matter? | Choosing a method | Summary | References

What a random rotation needs to do | Euler ZYZ rotations | Rodrigues axis-angle rotations | Where Rodrigues has the edge | Geometric transparency | Axis uniformity is explicit | Numerical stability | Idiomatic R | Where Euler has the edge | How much does the difference matter? | Choosing a method | Summary | References

The landscape | Distance-based methods | Variogram matching (burt2020) | Spatial autoregressive model (burt2018) | Moran spectral randomization (moran) | Spin-based methods | Original spin test (alexander_bloch) | Greedy assignment (spin_vasa) | Optimal assignment (spin_hungarian) | Parcel spin methods | Maximum overlap (baum) | Majority vote (cornblath) | Comparing null distributions visually | Using permtest_metric() for custom metrics | Building custom null distributions | Decision guide | References

Vertices to parcels | Parcels back to vertices | The high-level wrappers | Parcel centroids | Average centroid | Surface centroid | Geodesic centroid | Building a parcel-level distance matrix | Parcellation and null models together | Practical considerations | References

The landscape | Distance-based methods | Variogram matching (burt2020) | Spatial autoregressive model (burt2018) | Moran spectral randomization (moran) | Spin-based methods | Original spin test (alexander_bloch) | Greedy assignment (spin_vasa) | Optimal assignment (spin_hungarian) | Parcel spin methods | Maximum overlap (baum) | Majority vote (cornblath) | Comparing null distributions visually | Using permtest_metric() for custom metrics | Building custom null distributions | Decision guide | References

Vertices to parcels | Parcels back to vertices | The high-level wrappers | Parcel centroids | Average centroid | Surface centroid | Geodesic centroid | Building a parcel-level distance matrix | Parcellation and null models together | Practical considerations | References

Comparing two brain maps | Adding a spatial null model | Visualising the null distribution | Pre-computing null distributions | Working with real brain map files | Accessing the neuromaps atlas collection | Custom metrics with permtest_metric() | Choosing a null model | What comes next | References

Surface meshes | Building a surface graph | Geodesic distances | Partial distance matrices | Euclidean vs geodesic | Vertex areas | Checking the geometry | Format conversions | Annotation to GIFTI | Morphometry to GIFTI | Resampling between coordinate spaces | Putting it together | References

Comparing two brain maps | Adding a spatial null model | Visualising the null distribution | Pre-computing null distributions | Working with real brain map files | Accessing the neuromaps atlas collection | Custom metrics with permtest_metric() | Choosing a null model | What comes next | References

Surface meshes | Building a surface graph | Geodesic distances | Partial distance matrices | Euclidean vs geodesic | Vertex areas | Checking the geometry | Format conversions | Annotation to GIFTI | Morphometry to GIFTI | Resampling between coordinate spaces | Putting it together | References

Why Use Custom OAuth Credentials | Registering a Meetup OAuth Application | Step 1: Create the OAuth App | Step 2: Note Your Credentials | Storing Custom Credentials | Storing Credentials in your environment | Verifying Stored Credentials | Authenticating with Custom Credentials | Using a Custom Client Name | Supported Keys | 1. JWT Flow (Meetup Pro accounts) | 2. Encrypted OAuth Token File (for CI/CD) | Setting Up Encrypted Token Authentication | Rotating an Encrypted Token in GitHub Actions | 3. OAuth2 Interactive Flow | How Authentication is Chosen

Overview | When to Use Custom Queries | Using extra_graphql in Wrapper Functions | Working with Nested Data | Handling One-to-Many Relationships | Custom Queries from Scratch | Executing Custom Queries | Understanding Pagination | Automatic Pagination in Wrapper Functions | Understanding the Template System | Creating Custom Extractors | Error Handling | Performance Best Practices | Request Only Needed Fields | Batch Queries Efficiently | Monitor Rate Limits | Use Pagination Wisely | Additional Resources | Official Documentation | Related Vignettes | Getting Help

Introduction to GraphQL Introspection | Why Use Introspection? | How GraphQL Schema Works | Recommended Exploration Workflow | The meetupr_schema_* Function Family | Performance Tip: Cache the Schema | Step-by-Step Exploration Workflow | Step 1: Identify Available Entry Points | Step 2: Search for Relevant Types | Step 3: Examine Type Fields | Step 4: Build Your Custom Query | Step 5: Execute Your Query | Working with Mutations | Discovering Available Mutations | Understanding Mutation Structure | Example: RSVP to an Event | Advanced Introspection Patterns | Exploring Enum Values | Finding Required vs. Optional Fields | Discovering Input Types for Mutations | Understanding Pagination Types | Exporting Schema for External Tools | Practical Tips and Workflow | Use the Meetup API Playground | Use Debug Mode | Next Steps

Quick Setup Check | Authentication | Interactive Authentication | Non-Interactive Authentication (CI/CD) | Verification | Basic Usage Examples | Get Group Information | List Group Events | Get Past Events | Filter Events by Date | Get Event Details | Get Event RSVPs | Get Group Members | Search for Groups | Pagination and Rate Limits | Pro Account Features | List All Pro Groups | Network-Wide Events | Debug Mode | Common Issues | Authentication Errors | Multiple Token Warning | Rate Limiting | Group Not Found | Next Steps | Getting Help

Why Use Custom OAuth Credentials | Registering a Meetup OAuth Application | Step 1: Create the OAuth App | Step 2: Note Your Credentials | Storing Custom Credentials | Storing Credentials in your environment | Verifying Stored Credentials | Authenticating with Custom Credentials | Using a Custom Client Name | Supported Keys | 1. JWT Flow (Meetup Pro accounts) | 2. Encrypted OAuth Token File (for CI/CD) | Setting Up Encrypted Token Authentication | Rotating an Encrypted Token in GitHub Actions | 3. OAuth2 Interactive Flow | How Authentication is Chosen

Overview | When to Use Custom Queries | Using extra_graphql in Wrapper Functions | Working with Nested Data | Handling One-to-Many Relationships | Custom Queries from Scratch | Executing Custom Queries | Understanding Pagination | Automatic Pagination in Wrapper Functions | Understanding the Template System | Creating Custom Extractors | Error Handling | Performance Best Practices | Request Only Needed Fields | Batch Queries Efficiently | Monitor Rate Limits | Use Pagination Wisely | Additional Resources | Official Documentation | Related Vignettes | Getting Help

Introduction to GraphQL Introspection | Why Use Introspection? | How GraphQL Schema Works | Recommended Exploration Workflow | The meetupr_schema_* Function Family | Performance Tip: Cache the Schema | Step-by-Step Exploration Workflow | Step 1: Identify Available Entry Points | Step 2: Search for Relevant Types | Step 3: Examine Type Fields | Step 4: Build Your Custom Query | Step 5: Execute Your Query | Working with Mutations | Discovering Available Mutations | Understanding Mutation Structure | Example: RSVP to an Event | Advanced Introspection Patterns | Exploring Enum Values | Finding Required vs. Optional Fields | Discovering Input Types for Mutations | Understanding Pagination Types | Exporting Schema for External Tools | Practical Tips and Workflow | Use the Meetup API Playground | Use Debug Mode | Next Steps

Quick Setup Check | Authentication | Interactive Authentication | Non-Interactive Authentication (CI/CD) | Verification | Basic Usage Examples | Get Group Information | List Group Events | Get Past Events | Filter Events by Date | Get Event Details | Get Event RSVPs | Get Group Members | Search for Groups | Pagination and Rate Limits | Pro Account Features | List All Pro Groups | Network-Wide Events | Debug Mode | Common Issues | Authentication Errors | Multiple Token Warning | Rate Limiting | Group Not Found | Next Steps | Getting Help

Setting Up Authentication | Setting up a client | Add Credentials to Your .Renviron File | Check your Situation report | Accessing forms | Working with the client | Renewing the client secret | Adding colleagues | Troubleshooting | More information

Understanding the basics of APIs | Setting up a custom GET request | Setting up a custom POST request

Setting Up Authentication | Setting up a client | Add Credentials to Your .Renviron File | Check your Situation report | Accessing forms | Working with the client | Renewing the client secret | Adding colleagues | Troubleshooting | More information

Understanding the basics of APIs | Setting up a custom GET request | Setting up a custom POST request

Overview | Listing Attachments | Listing attachments for a specific submission | Listing all attachments for a form | Downloading Attachments | Saving All Attachments | For a Single Submission | For an Entire Form | Summary

Introduction to using Labelled data | Getting labelled data from nettskjemar | Exploring Labelled Data with | Inspecting Labels | Modifying Labels | Benefits of Using Labelled Data

Overview | Listing Attachments | Listing attachments for a specific submission | Listing all attachments for a form | Downloading Attachments | Saving All Attachments | For a Single Submission | For an Entire Form | Summary

Introduction to using Labelled data | Getting labelled data from nettskjemar | Exploring Labelled Data with | Inspecting Labels | Modifying Labels | Benefits of Using Labelled Data

Overview | Prerequisites | Retrieving All Available Forms | Example: Getting Forms | Retrieving Raw Form Data | Downloading Form Reports | Example: Download a CSV Report | Example: Download an Excel Report | Example: Save SPSS Report to a Custom Path | Custom Output Paths

Overview | Getting an Individual Submission Answer: ns_get_submission | Example: Fetch an Individual Submission

General recommendations | Tidyverse compatible | Download submissions | Fetching Raw Data | Controlling checkbox output

Overview | Prerequisites | Retrieving Metadata for a Form: ns_get_meta | Example: Retrieve Metadata | Exploring the Metadata Object | Example: Access Specific Metadata Fields | Saving Metadata to a File: ns_write_meta | Example: Save Metadata as a JSON File | Example: Save Metadata to a Custom Path | Example: Use Custom JSON Formatting Options

Overview | Prerequisites | Retrieving All Available Forms | Example: Getting Forms | Retrieving Raw Form Data | Downloading Form Reports | Example: Download a CSV Report | Example: Download an Excel Report | Example: Save SPSS Report to a Custom Path | Custom Output Paths

Overview | Getting an Individual Submission Answer: ns_get_submission | Example: Fetch an Individual Submission

General recommendations | Tidyverse compatible | Download submissions | Fetching Raw Data | Controlling checkbox output

Overview | Prerequisites | Retrieving Metadata for a Form: ns_get_meta | Example: Retrieve Metadata | Exploring the Metadata Object | Example: Access Specific Metadata Fields | Saving Metadata to a File: ns_write_meta | Example: Save Metadata as a JSON File | Example: Save Metadata to a Custom Path | Example: Use Custom JSON Formatting Options

The model formula | Keeping original data | Plotting the qdec

Background | Scoring | Equation | Data requirements | Use the zygo functions | References

Background | Scoring | Data requirements | Using the bfi functions | Computing all domains and facets. | Domains | Facets | References

Background | Scoring | Questionnaire Items | Data requirements | Using the ehi functions | Nominal value | Laterality quotient | Combine EHI results into a data.frame | References

Background | Scoring | Data requirements | Using the gds functions | Calculating the GDS sum | Turning the sum into a factor | Computing score and factor in one function | References

Background | Scoring | Data requirements | Use the psqi functions | Component-wise calculations | Global calculation | Calculating all components and global in one go | References

Accessing and working with the data | Turning groups of questions to long format | Using the custom plotting functions | Inspecting meta-data

Pipeline in short | Data location | Data decryption | Data combining | Data editing

Norwegian school history | M-74 | Reforms in 1987 og 1997 | Sources | NOAS data | Assessing factor levels | Recoding vector into factor | Alter factor to year | Converting between schemas | Compute education years from all available schemas | Compile education from several sources

Background | Rationale | Scoring | Using the ipaq functions | Altering times | MET category scores | References

Background | Scoring | Questionnaire items | Suicidality | Data requirements | Using the bdi functions | Nettskjema special case | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Administration & Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Background | Domains & facets | Scoring | Reliability | References

Applying the LCBC themes to ggplot | Colour scales | LCBC scales | Adding logo to plots

Applying the LCBC themes to ggplot | Colour scales | LCBC scales | Adding logo to plots

Introduction | How to use the package | Basic usage | Function documentation | The filter_site() function | Pipe ( %>% ) compatibility | Utility functions | The na_col_rm() function

Background | WASI vs. WPPSI | Subtests | Verbal subtests | Vocabulary | Similarities | Performance subtests | Matrices | Block | Intelligence scores | T-scores vs. Scaled scores | Verbal and Performance scores | Full scale IQ | Conversion tables | Using the iq functions | References

Pre-installed bundles | Prepare the tidyverse packages for install | Prepare your TSD environment for tidyverse | Linux OS libs | Install

Installation | Examples | Limitations

Pre-installed bundles | Prepare the tidyverse packages for install | Prepare your TSD environment for tidyverse | Linux OS libs | Install

Installation | Examples | Limitations

Switching to RHEL7 | Get the latest RStudio | create alias to open rstudio.

Switching to RHEL7 | Get the latest RStudio | create alias to open rstudio.

Recommendation for the R-script | Recommendation for the SLURM script | Submit your job

Recommendation for the R-script | Recommendation for the SLURM script | Submit your job

When installs from mini-CRAN fail | Solving problem 1 | system libs missing | Clang missing | Solving problem 2

When installs from mini-CRAN fail | Solving problem 1 | system libs missing | Clang missing | Solving problem 2