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.github/workflows

.github/workflows

 
 

.gitattributes

.gitattributes

 
 

.gitignore

.gitignore

 
 

README.md

README.md

 
 

_config.yml

_config.yml

 
 

_toc.yml

_toc.yml

 
 

basic-model.md

basic-model.md

 
 

coalescence-time-basic.ipynb

coalescence-time-basic.ipynb

 
 

coalestr-features.md

coalestr-features.md

 
 

coalestr.py

coalestr.py

 
 

colab.png

colab.png

 
 

colab2.png

colab2.png

 
 

colab3.png

colab3.png

 
 

colab4.png

colab4.png

 
 

colab5.png

colab5.png

 
 

create-metapopulation.ipynb

create-metapopulation.ipynb

 
 

create-population.ipynb

create-population.ipynb

 
 

create-subpopulation.ipynb

create-subpopulation.ipynb

 
 

epidemiological-scenarios.md

epidemiological-scenarios.md

 
 

fws-compare-methods.ipynb

fws-compare-methods.ipynb

 
 

fws.png

fws.png

 
 

generation.md

generation.md

 
 

generation.png

generation.png

 
 

get-coalescent.ipynb

get-coalescent.ipynb

 
 

get-diversity.ipynb

get-diversity.ipynb

 
 

glossary.md

glossary.md

 
 

haplotype-homozygosity-equation.png

haplotype-homozygosity-equation.png

 
 

haplotype-homozygosity.ipynb

haplotype-homozygosity.ipynb

 
 

how-to-use-this-book.md

how-to-use-this-book.md

 
 

hw-hs.ipynb

hw-hs.ipynb

 
 

hwhs-simple.png

hwhs-simple.png

 
 

hwhs.png

hwhs.png

 
 

ibd.ipynb

ibd.ipynb

 
 

idealised-tg.png

idealised-tg.png

 
 

index.md

index.md

 
 

local-outbreak.ipynb

local-outbreak.ipynb

 
 

locus.md

locus.md

 
 

locus.png

locus.png

 
 

logo.png

logo.png

 
 

migration-simple.ipynb

migration-simple.ipynb

 
 

nucleotide-diversity.ipynb

nucleotide-diversity.ipynb

 
 

nucleotide-diversity.png

nucleotide-diversity.png

 
 

phi-t.png

phi-t.png

 
 

pi_w_checks.ipynb

pi_w_checks.ipynb

 
 

population-class.ipynb

population-class.ipynb

 
 

references.bib

references.bib

 
 

requirements.txt

requirements.txt

 
 

subpop-matrix.md

subpop-matrix.md

 
 

subpop-matrix.png

subpop-matrix.png

 
 

superinfection.md

superinfection.md

 
 

superinfection.png

superinfection.png

 
 

time-series.ipynb

time-series.ipynb

 
 

transient-scenarios.ipynb

transient-scenarios.ipynb

 
 

transition-probability.md

transition-probability.md

 
 

transition-probability.png

transition-probability.png

 
 

transmission-graph.md

transmission-graph.md

 
 

transmission-graph.png

transmission-graph.png

 
 

underlying-concepts.md

underlying-concepts.md

 
 

using-google-colab.md

using-google-colab.md

 
 

within-host-pi.ipynb

within-host-pi.ipynb

 
 

within-host.ipynb

within-host.ipynb

 
 

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This repo contains Jupyter notebooks and markdown files for the website d-kwiat.github.io/gtg.

It accompanies a paper on Modelling transmission dynamics and genomic diversity of a recombining parasite population that will be appearing soon on BioRxiv.

It utilises the Python module coalestr.

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