EMRR Coding Bookdown
Preface
1
Basics of R
2
Data Manipulation
3
Making Plots
3.0.1
Coding goals
3.0.2
Study overview
3.0.3
Metadata for data set
3.0.4
Helpful resources
3.0.5
Initial set up
3.0.6
Formatting the data set and making the first plot
3.0.7
Summarize the data in new tibble
3.0.8
Plot time series for each study site separately
4
Interactive Tools
4.1
Plotly - Interactive plotting
4.2
Leaflet
4.3
Mapview
5
Shiny
6
Spatial data and making maps
6.1
Load data
6.2
Get data into spatial form
6.2.1
Spatial projections
6.3
Basic Spatial Operations
6.4
Make maps
6.4.1
Basic maps
6.4.2
Add arrows and scale bars, dotted lines
6.4.3
Add labels to map
6.4.4
Add inset map
6.5
Basemaps
7
Functions
8
For Loops and Conditionals
8.1
For Loops
8.2
Conditionals
9
Data Exploration and QA/QC
9.1
1 Recommended Reference Material
9.2
2 Background
9.3
3 Prepare your data
9.3.1
Get data
9.3.2
Develop your questions
9.3.3
Manipulate data
9.4
4 Examine patterns and relationships between response and predictor
9.4.1
A) Data over time
9.4.2
B) Data over space
9.4.3
C) Variability of data and continuous-categorical relationships
9.4.4
D) Collinearity and relationships between continuous variables
9.4.5
E) Distribution of data
9.4.6
F) How balanced are your data?
9.4.7
G) Are there missing data?
9.5
5 Identifying Outliers
9.5.1
A) Tukey Outliers
9.5.2
B) Median Absolute Deviation Outliers
9.5.3
C) Run outlier tests
9.5.4
D) Treatment of outliers
9.6
6 Other QA/QC
9.7
7 References
10
Basic Stats
10.1
Parametric Stats
10.1.1
T-test
10.2
Non-parametric Statistics
11
GLM and GLMM
12
GAM and GAMM
13
Multivariate Stats
13.1
Load data
13.2
PCA
13.3
Cluster analysis
13.4
NMDS
13.5
PERMANOVA
13.6
CCA
13.7
Load packages
14
Time Series
15
GitHub
16
Useful Resources
17
Instructions
17.1
About
17.1.1
Usage
17.1.2
Render book
17.1.3
Preview book
17.2
Introduction
17.2.1
A section
17.3
Cross references and chapters
17.3.1
Chapters and sub-chapters
17.4
Captioned figures and tables
17.5
Parts
17.6
Footnotes and Citations
17.6.1
Footnotes
17.6.2
Citations
17.7
Blocks
17.7.1
Equations
17.7.2
Theorems and proofs
17.7.3
Callout blocks
17.8
Publishing
17.8.1
404 pages
17.8.2
Metadata for sharing
References
Coding Bookdown for EMRR
Chapter 1
Basics of R
Creating projects, file structure
Reading in data from csv, excel
Reading data from online
Writing data
Column formats (character, numeric, datetime, factor)
Datetimes