epiverse-trace/tutorials-middle

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Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated incidence data, superspreading from line list and contact data, and simulating transmission chains.

Stars: 3
Forks: 6
Open beginner issues: 0
Indexed issues: 79
Avg merge: 1m
Merged PRs (30d): 1

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: help wanted

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79 issues indexed so far

`day01` add `{epiparameter}` functions diagram concept map to episodes Open

delays-episode enhancement

epiverse-trace/tutorials-middle#90 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
make local copy of refresher on R probability functions for the normal distribution Open

bug delays-episode enhancement priority

epiverse-trace/tutorials-middle#89 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add how `cfr::cfr_static()` works in the inside using `cfr::estimate_outcomes()` Open

epiverse-trace/tutorials-middle#3 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
collect action items from GPT review Open

upcoming training

epiverse-trace/tutorials-middle#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add callout on ratio, rate or risk? Open

enhancement

epiverse-trace/tutorials-middle#5 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add callout for outbreak or epidemic? Open

epiverse-trace/tutorials-middle#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
replace one-country pandemic planning scenario figure with multilateral source Open

epiverse-trace/tutorials-middle#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
remake observed biased confirmed CFR figure Open

epiverse-trace/tutorials-middle#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
assess to fix the format of the output figure in `severity-static.Rmd` Open

epiverse-trace/tutorials-middle#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
check if figures are allowed to be used with only attribution (license) Open

delays-episode documentation hackathon priority

epiverse-trace/tutorials-middle#88 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
create figure or animation to show concept scenario for {cfr} Open

help wanted upcoming training

epiverse-trace/tutorials-middle#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
should we move severity heterogeneity challenge to howto? Open

upcoming training

epiverse-trace/tutorials-middle#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add glossary entries on MLE, severity, virulence Open

upcoming training

epiverse-trace/tutorials-middle#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add reference of: using continuous distribution rather than discrete in {cfr} Open

epiverse-trace/tutorials-middle#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
redraw figure to use presymptomatic instead of asymptomatic Open

delays-episode priority

epiverse-trace/tutorials-middle#86 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
redraw reporting delays figure for simple schematic Open

delays-episode priority

epiverse-trace/tutorials-middle#85 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add serial interval figure of proportion of backward contacts to `hint` Open

delays-episode upcoming training

epiverse-trace/tutorials-middle#84 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
contact tracing practical sheet Open

delays-episode

epiverse-trace/tutorials-middle#83 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add serial interval contact tracing figures Open

delays-episode enhancement

epiverse-trace/tutorials-middle#82 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
refer to blogs as explanation documentation Open

epiverse-trace/tutorials-middle#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
create challenge on estimate and forecast secondary Open

enhancement

epiverse-trace/tutorials-middle#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add link to instructos materials Open

post-trial priority

epiverse-trace/tutorials-middle#62 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
assess for homogeneous ggplot2 format across episodes Open

enhancement

epiverse-trace/tutorials-middle#63 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
evaluate to create an isolated episode on contact data using {epicontacts} Open

priority

epiverse-trace/tutorials-middle#65 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
evaluate extreme dispersion parameter for MERS Open

priority

epiverse-trace/tutorials-middle#66 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
collect offspring distribution and generation time to reuse in examples or assessments Open

help wanted

epiverse-trace/tutorials-middle#69 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add mention to the observation-delay variations for EpiNow2 and cfr Open

enhancement priority upcoming training

epiverse-trace/tutorials-middle#75 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
use {tracetheme} Open

enhancement

epiverse-trace/tutorials-middle#76 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
update {cfr} due to braking change in outputs Open

priority upcoming training

epiverse-trace/tutorials-middle#77 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
simplify all here paths to only one nested folder called `data/` Open

priority

epiverse-trace/tutorials-middle#78 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
prefer to use natural parameter for lognormal distribution Open

epinow2-cran priority upcoming training

epiverse-trace/tutorials-middle#81 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
should we use `stan = stan_opts(method = "vb")` to make github workflows faster to run? Open

enhancement epinow2-cran priority upcoming training

epiverse-trace/tutorials-middle#80 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add callout box about the likelihood profile and `p` = maximum likelihood Open

priority upcoming training

epiverse-trace/tutorials-middle#92 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fix lognormal mispecification of mean and sd to meanlog and sdlog Open

bug epinow2-cran priority upcoming training

epiverse-trace/tutorials-middle#94 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
create assessment connecting epiparameter with cfr and epichains Open

enhancement upcoming training

epiverse-trace/tutorials-middle#97 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add summary table of the R packages for epidemic reproduction number Open

documentation epinow2-cran priority upcoming training

epiverse-trace/tutorials-middle#98 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
change `|>` to `%>%` for consistency + steps to change shortcut in global options Open

epiverse-trace/tutorials-middle#102 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
specify which component to replicate: {dplyr} instead of {incidence2} Open

epiverse-trace/tutorials-middle#105 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
rearrange location of HFR challenge Open

epiverse-trace/tutorials-middle#106 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add cfr summative assessment scenario to workshop materials Open

question

epiverse-trace/tutorials-middle#112 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
review to move text to read on cfr methods after the coding assessments Open

epiverse-trace/tutorials-middle#113 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add link to catalog of distribution functions and Distribution Zoo Open

epiverse-trace/tutorials-middle#114 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add Posit Cloud emergency alternative in package installation section Open

enhancement epinow2-cran

epiverse-trace/tutorials-middle#116 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add best practices for estimating and reporting delay distributions Open

enhancement

epiverse-trace/tutorials-middle#117 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add callout box `finalsize::r_eff()` after quantifying transmission? Open

question

epiverse-trace/tutorials-middle#118 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add data wrangling challenge to get required input columns for `{cfr}` Open

enhancement

epiverse-trace/tutorials-middle#119 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add `sessioninfo::session_info()` as a function to report issues with package function Open

enhancement

epiverse-trace/tutorials-middle#120 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
replace figure on "evidence for variation in individual reproductive number" by Lloyd-Smith et al., 2005 Open

documentation priority

epiverse-trace/tutorials-middle#121 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add challenge about epiparameter output interpretation Open

enhancement

epiverse-trace/tutorials-middle#122 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
include epiparameter shinyapp in materials (tutorials, slides, challenges) Open

epiverse-trace/tutorials-middle#124 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

epiverse-trace/tutorials-middle

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