section headings & link to chapters

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OuhscBbmc · Oct 17, 2018 · 58fcd2e · 58fcd2e
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diff --git a/ch-architecture.Rmd b/ch-architecture.Rmd
@@ -1,14 +1,21 @@
-Architecture Principles
+Architecture Principles {#architecture}
 ====================================
 
-1. Encapsulation
-1. Leverage team member's strenghts & avoid weaknesses
-    1. Focused code files
-    1. Metadata for content experts
-1. Scales
-    1. Single source & single analysis
-    1. Multiple sources & multiple analyses
-1. Consistency
-    1. Across Files
-    1. Across Languages
-    1. Across Projects
+Encapsulation
+------------------------------------
+
+Leverage team member's strenghts & avoid weaknesses
+------------------------------------
+1. Focused code files
+1. Metadata for content experts
+
+Scales
+------------------------------------
+1. Single source & single analysis
+1. Multiple sources & multiple analyses
+
+Consistency
+------------------------------------
+1. Across Files
+1. Across Languages
+1. Across Projects
diff --git a/ch-automation.Rmd b/ch-automation.Rmd
@@ -1,7 +1,17 @@
-# Automation
+Automation {#automation}
+====================================
 
-1. Flow File in R
-1. Makefile
-1. SSIS
-1. cron Jobs & Task Scheduler
-1. sink log files
+Flow File in R
+------------------------------------
+
+Makefile
+------------------------------------
+
+SSIS
+------------------------------------
+
+cron Jobs & Task Scheduler
+------------------------------------
+
+Sink Log Files
+------------------------------------
diff --git a/ch-collaboration.Rmd b/ch-collaboration.Rmd
@@ -1,11 +1,17 @@
-# Parallel Collaboration
+Parallel Collaboration {#collaboration}
+====================================
 
-1. Social Contract
-    1. Issues
-    1. Organized Commits & Coherent Diffs
-    1. Branch & Merge Strategy
-1. Code Reviews
-    1. Daily Reviews of PRs
-    1. Periodic Reviews of Files
-1. Remote
-    1. Headset & sharing screens
+Social Contract
+------------------------------------
+1. Issues
+1. Organized Commits & Coherent Diffs
+1. Branch & Merge Strategy
+
+Code Reviews
+------------------------------------
+1. Daily Reviews of PRs
+1. Periodic Reviews of Files
+
+Remote
+------------------------------------
+1. Headset & sharing screens
diff --git a/ch-data-persisted.Rmd b/ch-data-persisted.Rmd
@@ -1,18 +1,22 @@
-# Data at Rest
+Data at Rest {#data-at-rest}
+====================================
 
-1. Data States
-    1. Raw
-    1. Derived
-        1. Project-wide File on Repo
-        1. Project-wide File on Protected File Server
-        1. User-specific File on Protected File Server
-        1. Project-wide Database
-    1. Original
-1. Data containers
-    1. csv
-    1. rds
-    1. SQLite
-    1. Central Enterprise database
-    1. Central REDCap database
-    1. Containers to avoid for raw/input
-        1. Proprietary like xlsx, sas7bdat
+Data States
+------------------------------------
+1. Raw
+1. Derived
+    1. Project-wide File on Repo
+    1. Project-wide File on Protected File Server
+    1. User-specific File on Protected File Server
+    1. Project-wide Database
+1. Original
+
+Data Containers
+------------------------------------
+1. csv
+1. rds
+1. SQLite
+1. Central Enterprise database
+1. Central REDCap database
+1. Containers to avoid for raw/input
+    1. Proprietary like xlsx, sas7bdat
diff --git a/ch-documentation.Rmd b/ch-documentation.Rmd
@@ -1,8 +1,21 @@
-# Documentation
-
-1. Team-wide
-1. Project-specific
-1. Dataset origin & structure
-1. Issues & Tasks
-1. Flow Diagrams
-1. Setting up new machine ([example](https://github.com/OuhscBbmc/RedcapExamplesAndPatterns/blob/master/DocumentationGlobal/ResourcesInstallation.md))
+Documentation {#documentation}
+====================================
+
+Team-wide
+------------------------------------
+
+Project-specific
+------------------------------------
+
+Dataset Origin & Structure
+------------------------------------
+
+Issues & Tasks
+------------------------------------
+
+Flow Diagrams
+------------------------------------
+
+Setting up new machine
+------------------------------------
+([example](https://github.com/OuhscBbmc/RedcapExamplesAndPatterns/blob/master/DocumentationGlobal/ResourcesInstallation.md))
diff --git a/ch-file-prototype.Rmd b/ch-file-prototype.Rmd
@@ -1,12 +1,32 @@
-# Prototypical File
-
-1. Clear Memory
-1. Load Sources
-1. Load Packages
-1. Declare Globals
-1. Load Data
-1. Tweak Data
-1. (Unique Content)
-1. Verify Values
-1. Specify Output Columns
-1. Save to Disk or Database
+Prototypical File {#file-prototype}
+====================================
+
+Clear Memory
+------------------------------------
+
+Load Sources
+------------------------------------
+
+Load Packages
+------------------------------------
+
+Declare Globals
+------------------------------------
+
+Load Data
+------------------------------------
+
+Tweak Data
+------------------------------------
+
+(Unique Content)
+------------------------------------
+
+Verify Values
+------------------------------------
+
+Specify Output Columns
+------------------------------------
+
+Save to Disk or Database
+------------------------------------
diff --git a/ch-patterns.Rmd b/ch-patterns.Rmd
@@ -1,10 +1,26 @@
-# Patterns
-
-1. Ellis
-1. Arch
-1. Ferry
-1. Scribe
-1. Analysis
-1. Presentation -Static
-1. Presentation -Interactive
-1. Metadata
+Patterns {#patterns}
+====================================
+
+Ellis
+------------------------------------
+
+Arch
+------------------------------------
+
+Ferry
+------------------------------------
+
+Scribe
+------------------------------------
+
+Analysis
+------------------------------------
+
+Presentation -Static
+------------------------------------
+
+Presentation -Interactive
+------------------------------------
+
+Metadata
+------------------------------------
diff --git a/ch-publication.Rmd b/ch-publication.Rmd
@@ -1,5 +1,11 @@
-# Publishing Results
+Publishing Results {#publication}
+====================================
 
-1. To Other Analysts
-1. To Researchers & Content Experts
-1. To Technical-Phobic Audiences
+To Other Analysts
+------------------------------------
+
+To Researchers & Content Experts
+------------------------------------
+
+To Technical-Phobic Audiences
+------------------------------------
diff --git a/ch-scaling-up.Rmd b/ch-scaling-up.Rmd
@@ -1,8 +1,12 @@
-# Scaling Up
+Scaling Up {#scaling-up}
+====================================
 
-1. Data Storage
-    1. Local File vs Conventional Database vs Redshift
-    1. Usage Cases
-1. Data Processing
-    1. R vs SQL
-    1. R vs Spark
+Data Storage
+------------------------------------
+1. Local File vs Conventional Database vs Redshift
+1. Usage Cases
+
+Data Processing
+------------------------------------
+1. R vs SQL
+1. R vs Spark
diff --git a/ch-scratch-pad.Rmd b/ch-scratch-pad.Rmd
@@ -1,8 +1,9 @@
-# Scratch Pad of Loose Ideas
+Scratch Pad of Loose Ideas {#scratch-pad}
+====================================
 
 
 Chapters & Sections to Form
------------------------
+------------------------------------
 
 1. Tools to Consider
     1. tidyverse

diff --git a/ch-security.Rmd b/ch-security.Rmd
@@ -1,6 +1,12 @@
-# Security & Private Data
+Security & Private Data {#security}
+====================================
 
-1. File-level permissions
-1. Database permissions
-1. Public & Private Repositories
-    1. Scrubbing GitHub history
+File-level permissions
+------------------------------------
+
+Database permissions
+------------------------------------
+
+Public & Private Repositories
+------------------------------------
+1. Scrubbing GitHub history
diff --git a/ch-team.Rmd b/ch-team.Rmd
@@ -1,11 +1,17 @@
-# Growing a Team
+Growing a Team {#team}
+====================================
 
-1. Recruiting
-1. Training to Data Science
-    1. Starting with a Researcher
-    1. Starting with a Statistician
-    1. Starting with a DBA
-    1. Starting with a Software Developer
-1. Bridges Outside the Team
-    1. Monthly User Groups
-    1. Annual Conferences
+Recruiting
+------------------------------------
+
+Training to Data Science
+------------------------------------
+1. Starting with a Researcher
+1. Starting with a Statistician
+1. Starting with a DBA
+1. Starting with a Software Developer
+
+Bridges Outside the Team
+------------------------------------
+1. Monthly User Groups
+1. Annual Conferences
diff --git a/ch-testing-and-validation.Rmd b/ch-testing-and-validation.Rmd
@@ -1,8 +1,14 @@
-# Testing, Validation, & Defensive Programming
+Testing, Validation, & Defensive Programming {#testing-and-validation}
+====================================
 
-1. Testing Functions
-1. Defensive Programming
-    1. Throwing errors
-1. Validator
-    1. Benefits for Analysts
-    1. Benefits for Data Collectors
+Testing Functions
+------------------------------------
+
+Defensive Programming
+------------------------------------
+1. Throwing errors
+
+Validator
+------------------------------------
+1. Benefits for Analysts
+1. Benefits for Data Collectors
diff --git a/ch-tools.Rmd b/ch-tools.Rmd
@@ -1,10 +1,18 @@
-# Considerations when Selecting Tools
-
-1. General
-    1. The Component's Goal
-    1. Current Skillset of Team
-    1. Desired Future Skillset of Team
-    1. Skillset of Audience
-1. Languages
-1. R Packages
-1. Database
+Considerations when Selecting Tools {#tools}
+====================================
+
+General
+------------------------------------
+1. The Component's Goal
+1. Current Skillset of Team
+1. Desired Future Skillset of Team
+1. Skillset of Audience
+
+Languages
+------------------------------------
+
+R Packages
+------------------------------------
+
+Database
+------------------------------------