QPAD Book
Preface
About the book and the course
About the author
Installing R and RStudio
Installing required packages
Installing the book
How this works
Acknowledgments
1
Introduction
1.1
Design-based approaches
1.2
Model-based approaches
1.3
Our approach
2
Organizing and Processing Point Count Data
2.1
Introduction
2.2
Prerequisites
2.3
R basics
2.4
JOSM data set
2.5
Cross tabulating species counts
2.6
Joining species data with predictors
2.7
Explore predictor variables
2.8
Derived variables
3
A Primer in Regression Techniques
3.1
Introduction
3.2
Prerequisites
3.3
Poisson null model
3.4
Exploring covariates
3.5
Single covariate
3.6
Additive model
3.7
Nonlinear terms
3.8
Categorical variables
3.9
Multiple main effects
3.10
Interaction
3.11
Different error distributions
3.12
Count duration effects
3.13
Count radius effects
3.14
Offsets
4
Behavioral Complexities
4.1
Introduction
4.2
Prerequisites
4.3
Birds in the forest
4.4
Survival model
4.5
Vocalization events
4.6
Removal model
4.6.1
Real data
4.6.2
Time-invariant conventional model
4.6.3
Time-varying conventional removal model
4.7
Finite mixtures
4.7.1
Time-invariant finite mixture removal model
4.7.2
Time-varying finite mixture removal models
4.8
Let the best model win
4.9
Estimating abundance
5
The Detection Process
5.1
Introduction
5.2
Prerequisites
5.3
Distance functions
5.4
Distance sampling
5.5
Average detection
5.6
Binned distances
5.7
Availability bias
5.8
Estimating density with truncation
5.9
Unlimited distance
5.10
Replicating landscapes
5.11
JOSM data
6
Dealing with Recordings
6.1
Introduction
6.2
Prerequisites
6.3
Paired sampling
6.4
Paired data
6.5
Availability
6.6
Distance sampling
6.7
Scaling constant
6.8
Data integration
6.9
ABMI data
7
A Closer Look at Assumptions
7.1
Intro
7.2
Prerequisites
7.3
bSims runs
8
Understanding Roadside Surveys
9
Miscellaneous Topics
These are just reminders, to be deleted later
9.1
Binomial model and censoring
9.2
Optimal partitioning
9.3
Optilevels
9.4
N-mixture models
9.5
Estimating abundance
Péter Sólymos
Point count data analysis: How to violate assumptions and get away with it
Chapter 8
Understanding Roadside Surveys
directional diff in signal transmission