epiverse-trace/tutorials-late

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Tutorials to learn accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling disease burden.

Stars: 2
Forks: 5
Open beginner issues: 0
Indexed issues: 50
Avg merge: 4m
Merged PRs (30d): 2

Dominant language: R
License: No license data
Last GitHub push: Aug 28, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

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50 open issues indexed

add section on comparing interventions using Vacamole model Open

epiverse-trace/tutorials-late#8 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add modelling interventions motivation section to modelling interventions introduction Open

enhancement

epiverse-trace/tutorials-late#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add introduction episode for the Late Task Open

epiverse-trace/tutorials-late#5 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add `testimonial` on good overview of uses of modeling durign epidemics Open

epiverse-trace/tutorials-late#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add `vaccination()` to challenge in `compare-vaccination` episode Open

epiverse-trace/tutorials-late#12 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
refer to blogs as explanation documentation Open

epiverse-trace/tutorials-late#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use of `{tracetheme}` in tutorails Open

epiverse-trace/tutorials-late#20 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add "outbreak analytics" to glossary file Open

bug

epiverse-trace/tutorials-late#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
update {epidemics} version in renv.lock to account for uncertainty Open

epiverse-trace/tutorials-late#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add link to why we transpose the matrix? Open

epiverse-trace/tutorials-late#27 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fix summary section in simulate transmission episode Open

epiverse-trace/tutorials-late#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
make reading contact data from socialmixr one episode Open

enhancement post-trial

epiverse-trace/tutorials-late#30 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add reference to other mathematical models to other diseases Open

enhancement post-trial

epiverse-trace/tutorials-late#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
misconception on rate of vaccination with duration of effect of vaccine Open

enhancement post-trial

epiverse-trace/tutorials-late#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add links to instructor materials Open

beta-stage enhancement post-trial

epiverse-trace/tutorials-late#33 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add readings in setup page for greater visibility before each session Open

enhancement post-trial upcoming-training

epiverse-trace/tutorials-late#35 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add namespace reminders Open

bug priority

epiverse-trace/tutorials-late#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
homogenize setup across websites Open

priority upcoming-training

epiverse-trace/tutorials-late#37 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
use {tracetheme} Open

enhancement

epiverse-trace/tutorials-late#38 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add link between epichains and epidemics about ebola model Open

epiverse-trace/tutorials-late#41 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add preparation callout box with papers of reference Open

documentation priority

epiverse-trace/tutorials-late#44 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add {simulist} callout box to use key time periods from {epidemics} Open

epiverse-trace/tutorials-late#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Episode suggestion: advanced content on editing models Open

epiverse-trace/tutorials-late#55 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add section on contactmatrix package to `contact-matrices` Open

epiverse-trace/tutorials-late#57 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
differential susceptibility scenario for measles case study Open

epiverse-trace/tutorials-late#58 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Primer box for compartmental model Open

epiverse-trace/tutorials-late#60 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
translate `simulating-transmission.Rmd` and `modelling-interventions.Rmd` Open

hackathon

epiverse-trace/tutorials-late#64 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fix alt text in setup and Rcpp in glossary Open

epiverse-trace/tutorials-late#65 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
clean glossary with repository exclusive entries Open

epiverse-trace/tutorials-late#66 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add the term "attack rate" as familiar with target audience Open

epiverse-trace/tutorials-late#67 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add one paragraph to assess for rate alpha Open

epiverse-trace/tutorials-late#71 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Episode feature suggestion: using epireview estimates Open

epiverse-trace/tutorials-late#75 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
use named child code chunks to avoid code replicates and minimize errors Open

bug priority

epiverse-trace/tutorials-late#80 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add external animations as pre-requisites as motivational reading Open

epiverse-trace/tutorials-late#92 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
new pipeline to access social contact matrix data Open

epiverse-trace/tutorials-late#116 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add translation reviewer Open

epiverse-trace/tutorials-late#120 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
replace parameters in code to reflect relationship with R0 Open

epiverse-trace/tutorials-late#125 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add video gif or animation on motivation page Open

epiverse-trace/tutorials-late#137 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add an explanation on herd immunity threshold Open

epiverse-trace/tutorials-late#141 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add whiteboard explanation on how the SEIR includes the C from contact matrices Open

epiverse-trace/tutorials-late#142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add ggplot contact matrix heatmaps to explain symmetry in contact-matrices episode Open

epiverse-trace/tutorials-late#146 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
clarify explanation of normalization of the contact matrix Open

epiverse-trace/tutorials-late#147 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
why `gh-pages` does not build website after merging PR Open

epiverse-trace/tutorials-late#165 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
sync readme rmd to md Open

epiverse-trace/tutorials-late#166 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
how to add the `actions` update workflow to other repos Open

epiverse-trace/tutorials-late#169 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
move text on normalization of matrices as extra episode Open

epiverse-trace/tutorials-late#171 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
make clean function with compartments as arguments Open

epiverse-trace/tutorials-late#173 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
No `NEWS.md` and PR template asks whether it's updated Open

epiverse-trace/tutorials-late#176 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add improvements Open

epiverse-trace/tutorials-late#181 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
replace `socialmixr::contact_matrix()` with piped `socialmixr::symmetrise()` Open

epiverse-trace/tutorials-late#184 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

epiverse-trace/tutorials-late

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