epiverse-trace/howto

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Collection of reproducible how-to guides of Outbreak data analysis tasks using R packages.

Stars: 4
Forks: 2
Open beginner issues: 0
Indexed issues: 76

Dominant language: R
License: CC-BY-4.0
Last GitHub push: Jul 25, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted
PR merge metrics: No merged PRs in 30d

Open All

76 open issues indexed

add a contributing file Open

enhancement

epiverse-trace/howto#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add styler workflow Open

epiverse-trace/howto#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add gh-pages workflow Open

epiverse-trace/howto#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
update projection howto to use Rt from the last two weeks Open

documentation priority

epiverse-trace/howto#4 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add entry on how to calculate sub-national cfr? Open

enhancement midterm

epiverse-trace/howto#5 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add about the effect of code linking with downlit when using {packagename} Open

documentation

epiverse-trace/howto#7 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
share on projects about transversal multiple package examples Open

collaboration priority

epiverse-trace/howto#8 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add package-method assumptions in "steps in detail" section Open

enhancement

epiverse-trace/howto#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
make the copy button active always Open

documentation priority

epiverse-trace/howto#10 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add branching process howto Open

enhancement midterm

epiverse-trace/howto#11 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add data input, methods, data outputs in "ingredients" section Open

documentation priority

epiverse-trace/howto#12 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add R0 howto Open

enhancement midterm

epiverse-trace/howto#13 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add reference links to all entries Open

documentation priority

epiverse-trace/howto#14 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
update finalsize howto Open

enhancement midterm

epiverse-trace/howto#15 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add pending steps in details Open

documentation priority

epiverse-trace/howto#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add condition to add only scripts connecting multiple packages Open

documentation midterm

epiverse-trace/howto#18 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
use consitent terms Open

documentation midterm

epiverse-trace/howto#19 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add a qmd howto template file Open

collaboration documentation

epiverse-trace/howto#21 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add sivirep + incidence + epico script pipeline Open

enhancement midterm

epiverse-trace/howto#23 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
embrace the ecosystem Open

documentation midterm

epiverse-trace/howto#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
replace ingredients and steps after replace epidist_db with epiparam + as_epidist Open

epiverse-trace/howto#25 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add render and publishing command steps in contributing file Open

epiverse-trace/howto#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
how to keep the howto repository reproducible? Open

enhancement question

epiverse-trace/howto#27 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
replace how to use distcrete class objects from epiparameter Open

bug

epiverse-trace/howto#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
use discussions tab to request for answers to complex questions after tutorials Open

priority

epiverse-trace/howto#29 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
change repo name to `recipes` Open

epiverse-trace/howto#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add: how to create an epidist object to feed epinow2? Open

enhancement

epiverse-trace/howto#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add: how to estimate the probability of a large outbreak? Open

enhancement

epiverse-trace/howto#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add: how to estimate the proportion of cases that generate 50% of transmission? Open

enhancement

epiverse-trace/howto#33 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add: how to reuse distribution delays to quantify the time-varying reproduction number (Rt)? Open

enhancement

epiverse-trace/howto#34 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add: how to use variable distributions (with uncertainty) from epiparameter to epinow2 Open

enhancement

epiverse-trace/howto#35 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
how to pass multiple `<epidist>` objects to one (or multiple) `{cfr}` data inputs Open

epiverse-trace/howto#36 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add: fitting severity and converting into epiparameter objects Open

epiverse-trace/howto#37 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
add workflow/pipelines summary figures in the "steps in detail" section Open

enhancement

epiverse-trace/howto#44 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fix dates to specific entry date intead of `last-modified` Open

bug

epiverse-trace/howto#48 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
relocate template.qmd to analyses/ folder Open

epiverse-trace/howto#49 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add entry on calculating cfr from epinow2 Open

enhancement

epiverse-trace/howto#52 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add {epidemics} summative assessments Open

enhancement

epiverse-trace/howto#53 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add epicontacts + fitdistrplus + superspreading Open

enhancement

epiverse-trace/howto#55 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add epichains summative Open

enhancement

epiverse-trace/howto#56 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add howto connecting epichains outputs to epicontacts + fitdistribplus Open

enhancement

epiverse-trace/howto#61 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
evaluate to keep or modify epiparameter entry Open

epiverse-trace/howto#64 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
render workflow on a monthly CRON job to identify breaking changes Open

enhancement

epiverse-trace/howto#65 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Issues with packages needing `gfortran` Open

epiverse-trace/howto#66 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
create reprex use case for godata Open

epiverse-trace/howto#70 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
review all functions to have their namespace with `::` Open

priority

epiverse-trace/howto#73 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
rename objects in `reproduction_number_serological_data.qmd` to differentiate the dataset of observed and estimated values. Open

midterm priority

epiverse-trace/howto#76 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
clarify data entry alternatives Open

midterm priority

epiverse-trace/howto#77 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
full repository review Open

priority

epiverse-trace/howto#82 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
move reconstruct cases to second in the order of index subtitles Open

documentation

epiverse-trace/howto#83 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

epiverse-trace/howto

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