Technical introduction to R_eff #59

Degoot-AM · 2024-11-02T20:15:01Z

It's worth adding new training materials on social contact matrices for deeper introduction to $R_{eff}$.
suggested by @adamkucharski: #51 (comment)

adamkucharski · 2024-11-03T07:28:39Z

Perhaps I could have been clearer - we've already got an episode on this via recently closed pull request #52

* add measles outbreak example * add effective R_0 * add HIT explanation for r_eff * add hit * rename file from md to Rmd format * remove quarto features to make Rmd to knit R code * replace bib tags with hyperlinks + remove bib file * clean middle dot spaces between words * delete associated quarto files * fix heading typos * fix mathbfcal rendering issue * clean package loading + add namespace * remove output chunk figures * remove extra quarto tags * fix local lintr checks * change incubation to latent * replacing \cdot with . * reducing math technicals * Fixing typos of SIER vs SEIR * clarifying distinction between incubation period and latent period. * remove normalization * assumptions vs biological facts. * updating fig1 caption * HIT vs R_eff * fixing a typo: compagain * add MMR's efficacy ref * replace `take off` witn `start spreading` * add measles R0 range ref. * intuition behind beta/gamma * relation between R0 and generation time. * more on final size * add logic behind HIT equation * add refer * gamma * some words to clarify this assumption * using vs uaing * more on R_eff * remove loading finalsize since it only used by namespace ::. * add issue #59 * add clarification * removing typo * remove shading * removed duplicated statement. * excluding vaccinated when using new_infections. * obs vs R0 * some checks * fixing typos * typos * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> --------- Co-authored-by: Andree Valle Campos <[email protected]>

Auto-generated via `{sandpaper}` Source : eb29b8f Branch : main Author : Abdoelnaser M Degoot <[email protected]> Time : 2024-11-20 20:50:03 +0000 Message : add measles outbreak example (#51) * add measles outbreak example * add effective R_0 * add HIT explanation for r_eff * add hit * rename file from md to Rmd format * remove quarto features to make Rmd to knit R code * replace bib tags with hyperlinks + remove bib file * clean middle dot spaces between words * delete associated quarto files * fix heading typos * fix mathbfcal rendering issue * clean package loading + add namespace * remove output chunk figures * remove extra quarto tags * fix local lintr checks * change incubation to latent * replacing \cdot with . * reducing math technicals * Fixing typos of SIER vs SEIR * clarifying distinction between incubation period and latent period. * remove normalization * assumptions vs biological facts. * updating fig1 caption * HIT vs R_eff * fixing a typo: compagain * add MMR's efficacy ref * replace `take off` witn `start spreading` * add measles R0 range ref. * intuition behind beta/gamma * relation between R0 and generation time. * more on final size * add logic behind HIT equation * add refer * gamma * some words to clarify this assumption * using vs uaing * more on R_eff * remove loading finalsize since it only used by namespace ::. * add issue #59 * add clarification * removing typo * remove shading * removed duplicated statement. * excluding vaccinated when using new_infections. * obs vs R0 * some checks * fixing typos * typos * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> --------- Co-authored-by: Andree Valle Campos <[email protected]>

Auto-generated via `{sandpaper}` Source : 5aca77b Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2024-11-20 20:56:03 +0000 Message : markdown source builds Auto-generated via `{sandpaper}` Source : eb29b8f Branch : main Author : Abdoelnaser M Degoot <[email protected]> Time : 2024-11-20 20:50:03 +0000 Message : add measles outbreak example (#51) * add measles outbreak example * add effective R_0 * add HIT explanation for r_eff * add hit * rename file from md to Rmd format * remove quarto features to make Rmd to knit R code * replace bib tags with hyperlinks + remove bib file * clean middle dot spaces between words * delete associated quarto files * fix heading typos * fix mathbfcal rendering issue * clean package loading + add namespace * remove output chunk figures * remove extra quarto tags * fix local lintr checks * change incubation to latent * replacing \cdot with . * reducing math technicals * Fixing typos of SIER vs SEIR * clarifying distinction between incubation period and latent period. * remove normalization * assumptions vs biological facts. * updating fig1 caption * HIT vs R_eff * fixing a typo: compagain * add MMR's efficacy ref * replace `take off` witn `start spreading` * add measles R0 range ref. * intuition behind beta/gamma * relation between R0 and generation time. * more on final size * add logic behind HIT equation * add refer * gamma * some words to clarify this assumption * using vs uaing * more on R_eff * remove loading finalsize since it only used by namespace ::. * add issue #59 * add clarification * removing typo * remove shading * removed duplicated statement. * excluding vaccinated when using new_infections. * obs vs R0 * some checks * fixing typos * typos * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update learners/BF_measles.Rmd Co-authored-by: Andree Valle Campos <[email protected]> --------- Co-authored-by: Andree Valle Campos <[email protected]>

Degoot-AM mentioned this issue Nov 2, 2024

add measles outbreak example #51

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Degoot-AM added a commit that referenced this issue Nov 2, 2024

add issue #59

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Technical introduction to R_eff #59

Technical introduction to R_eff #59

Degoot-AM commented Nov 2, 2024

adamkucharski commented Nov 3, 2024

Technical introduction to R_eff #59

Technical introduction to R_eff #59

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Degoot-AM commented Nov 2, 2024

adamkucharski commented Nov 3, 2024