Procedures and Guidelines
Welcome
Copyright
UBCO Biology open materials
Why Procedures and Guidelines?
Structure
File and Data Management
1
File and Data Management
2
File Naming
2.1
Quick Reference
2.1.1
Lab reports and manuscripts
2.1.2
Figures and plots
2.1.3
Analysis
2.1.4
Data
2.2
What’s in a name
Human interpretable
Machine readable
2.3
An example
3
Directories
3.1
Working directory
3.2
Relative and Absolute Paths
Absolute paths
Relative paths
3.3
Set a Working Directory in RStudio
Preferred Method: Creating a Project
Create a New Project in a New Folder
Create a New Project in an Existing Folder
4
Directory Structures
4.1
Directory Hierarchies
4.2
Directory Naming
4.3
readme files and data dictionaries
General rules
File formats
4.4
Root folder readme
4.5
Data directory readme
4.6
Data dictionary
4.7
Example BIOL 116
Top Level folder
Data Folder
Analysis Folder
Figures Folder
Report Folder
Screenshot
4.8
Example BIOL 125
Day 1
Day 2
Day 3
Day 4-5
Day 6
5
Tidy data
5.1
Wide Data
5.2
Tidy Data
5.3
Side by Side Comparison
Wide Data
Tidy Data
Data Presentation
6
Figures & Tables
6.1
Tables
Example
6.2
Descriptive & Summary Statistics
6.3
Results of Statistical Tests
6.4
Figures
Examples
7
Sketches & Drawings
7.1
The Role of Sketches
7.2
Sketching Guidelines
General Guidelines
Organisms and Structures
Microscopes
7.3
Good Example Sketches
Example 1
Example 2
7.4
Poor Example Sketch
Writing and Citing
8
Markdown
8.1
How Markdown Works
8.2
What You Need to Get Started
VS Code
8.3
Prose
8.4
Structure
Headings
8.5
Emphasis and Style
Italics
Bold
Strikethrough
8.6
Code
8.7
Blockquotes
8.8
Lists
Ordered lists
Unordered lists
8.9
Tables
8.10
Links
8.11
Images
8.12
Markdown Flavours
9
APA Citations
9.1
In-text Citations
Narrative vs Parenthetical
Quick Format Guide
9.2
Reference List
Journal article with a DOI (1-2 authors)
Journal article with a DOI (3-20 authors)
10
Types of Sources
Primary Sources
Secondary Sources
Review Sources
11
Finding & Evaluating Published Evidence
11.1
Types of Evidence
11.1.1
Original Research
11.1.2
Secondary Research
11.1.3
Opinion & Commentary
11.2
Sources of Evidence
11.2.1
General
11.2.2
Health & Biological Processes
11.2.3
Niche
11.3
Google Scholar and AI Citation Searching
11.3.1
When to Use Which
11.4
Grey Literature
11.5
Searching Basics
11.5.1
Concepts
11.5.2
Boolean logic
11.5.3
Stemming & Wildcards
11.5.4
Phrase searching
11.6
Evaluating the Literature
12
APA Citations
12.1
In-text Citations
Narrative vs Parenthetical
Quick Format Guide
12.2
Reference List
Journal article with a DOI (1-2 authors)
Journal article with a DOI (3-20 authors)
13
Academic Integrity
14
Reference Management: Zotero
14.1
Installation & first launch
First launch
14.2
Browser plugin
14.3
Accounts & sync setup
Connecting Zotero Desktop with the Cloud
14.4
Adding citations
14.5
Renaming PDFs
14.6
Syncing to the cloud
Zotero Cloud
15
Copyright
R
16
ggplot
16.1
The Basic Graph
16.2
Labeling and captions
16.3
Size, shape & colour
16.4
More than one geom
16.5
More than one plot
16.6
Faceting a Plot
16.7
Cusomizing Look and Feel
Themes
Colours
Glossary
17
Glossary
Appendix
A1: Magnification of A Drawing
17.1
Object Size
17.2
Method 1: Estimation
Field of View Diameter
Estimating Object Size
17.3
Method 2: Ocular Micrometer
Calibrating the Ocular Micrometer
17.4
Drawing Size
17.5
Calculating Scale
Published with bookdown
Procedures and Guidelines
5.3
Side by Side Comparison
Wide Data
Site
Trout_Caught_Day_1
Trout_Caught_Day_2
Trout_Caught_Day_3
Mabel-lake
1
3
3
Postill-lake
3
4
5
Ellison-Lake
0
5
1
Tidy Data
Site
Day
Trout_Caught
Mabel-lake
1
1
Mabel-lake
2
3
Mabel-lake
3
3
Postill-lake
1
3
Postill-lake
2
4
Postill-lake
3
5
Ellison-lake
1
0
Ellison-lake
2
5
Ellison-lake
3
1