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fwdpy11 manual

Introduction

Installation and setup

Setting up user environments for installation
Installation
Deployment tools
Invoking Python
Citation

Short vignettes - operations on populations

Initializing a population
Properties of populations

Short vignettes - setting up the genetics

Introduction
Genetic maps
Distributions of effect sizes
Mutations with variable dominance
Neutral mutations during a simulation
Genetic values - mutations with direct effects on fitness
Genetic values - simulating phenotypes/traits.
Working example - parameters for simulating direct effects on fitness
Working example - parameters for the simulation of a trait

Short vignettes - simulation with tree sequence recording

Evolving with tree sequence recording
Recording data during a simulation
Finishing a simulation with msprime
Adding neutral mutations to a population with existing ancestry
Importing mutations from tskit

Short vignettes - demographic modeling

Introduction
Using demes to specify demographic models.

Short vignettes - varying fitness conditions across demes

Introduction
The multivariate Gaussian distribution
The multivariate lognormal distribution
“Custom” multivariate distributions
Special considerations for demes models
Advanced topics

Short vignettes - conditional models

Tracking user-specified new mutations
Selective sweeps
Incomplete selective sweeps

Longer vignettes - demographic models

Timing of events in demographic models

Longer vignettes - exporting data to tskit

Converting data to tskit format
Working with data in tskit format

Longer vignettes - complete examples

Background selection
Gaussian stabilizing selection with an optimum shift
Adaptation of a trait to different optima in different demes
Tracking mutations over time
Tracking mutations over time using sqlite3

Concepts

Definitions

Tutorials

Advanced topics

Objects and concepts

Different effect sizes of mutations in different demes
Conceptual overview of tree sequence recording
Data structures related to tree sequences
Time series analysis

Technical details

Details of demes integration
Technical overview of genetic value calculations
Writing “plugins” with C++

Data types and fuctions

Genetic values
DataMatrix and StateMatrix
Function documentation
Random number distributions
Adding random noise to genetic values
Mapping genetic values to fitness
Model parameters
Setting up genomic intervals
Module fwdpy11.tskit_tools
Module fwdpy11.conditional_models
Data types related to simulated populations

Examples

Adaptation to different optima with multivariate distribution of effect sizes
Snowdrift model in python
Example of time series analysis implemented in C++

Miscellany

Changelog
Developer’s guide
Publications using fwdpy11
Upgrade path
Literature cited

Repository
Open issue

Search

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By Kevin Thornton

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