update late tasks from feedback #85

amanda-minter · 2023-12-12T13:04:21Z

update late task tutorials after feedback, fixes #60, #63, #73, epiverse-trace/tutorials-late#6

Store all results and then extract infectious compartment for plotting

and clarify reduction is performed within the model functions

github-actions · 2023-12-12T13:04:37Z

❌ DANGER ❌

This pull request has modified workflows that created output. Close this now.

Co-authored-by: Andree Valle Campos <[email protected]>

avallecam

I agree with your previous edits.

I made a follow-up question on the edges of the diagrams.

I rewrote the edit suggestion in learning objectives from simulating-transmission.Rmd. If agreed, for consistency this can also be applied to modeling-interventions.Rmd and compare-interventions.Rmd:

In modeling-interventions.Rmd

From:
- Learn how to implement pharmaceutical and non-pharmaceutical interventions
To:
- Add pharmaceutical and non-pharmaceutical interventions to an {epidemics} model

In compare-interventions.Rmd:

From:
- Understand how to compare intervention scenarios
To:
- Compare intervention scenarios

episodes/simulating-transmission.Rmd

Co-authored-by: Andree Valle Campos <[email protected]>

avallecam · 2023-12-19T19:17:29Z

update late task tutorials after feedback, fixes #60, #63, #73, epiverse-trace/tutorials-late#6

@amanda-minter since the core edits to solve the issues in the first comment are already approved, I'll approve my review. Feel free to resolve any additional discussion here or reference them in new issues.

avallecam

update late task tutorials after feedback, fixes #60, #63, #73, #79

@amanda-minter since the core edits to solve the issues in the first comment are already approved, I'll approve my review. Feel free to resolve any additional discussion here or reference them in new issues.

…iagram

amanda-minter · 2023-12-21T14:04:56Z

Fixes #100

Auto-generated via {sandpaper} Source : 5c76e4e Branch : main Author : Amanda Minter <[email protected]> Time : 2023-12-21 14:05:03 +0000 Message : update late tasks from feedback (#85) * Extend challenge in 'Choosing an appropriate model' * Edit to accounting for uncertainty example Store all results and then extract infectious compartment for plotting * Add detail to Ebola case study challenge * update glossary entries * Add callout on ODE solver * clarify purpose of concept dependencies * Updates from review * Remove infection object * Update simulating-transmission.Rmd * Update model-choices.Rmd * Add exercise to `compare_interventions.Rmd` * update modelling interventions after review * Update renv.lock * update plots * make uncertainty plots consistent across episodes * fix broken link * making plots consistent across tutorials * update summary and key points * update plots and add challenge * update introduction * move contact matrix callout and clarify reduction is performed within the model functions * add callout on intervention types * update introduction and reorder text in other sections * update PI section * style code * spell check * Update compare-interventions.Rmd * Apply suggestions from code review Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/modelling-interventions.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * add dropdown menus to make section more interactive * add reminder about transmissibility calculation * link to latent period * update model terms * add note on flow diagram * add callout on model rates * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * update tutorial objectives * distinguish parameter definitions from process descriptions in flow diagram * Update model-choices.Rmd * remove pak call from set up * Update renv.lock --------- Co-authored-by: Andree Valle Campos <[email protected]>

Auto-generated via {sandpaper} Source : 8ba98d6 Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2023-12-21 14:08:01 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 5c76e4e Branch : main Author : Amanda Minter <[email protected]> Time : 2023-12-21 14:05:03 +0000 Message : update late tasks from feedback (#85) * Extend challenge in 'Choosing an appropriate model' * Edit to accounting for uncertainty example Store all results and then extract infectious compartment for plotting * Add detail to Ebola case study challenge * update glossary entries * Add callout on ODE solver * clarify purpose of concept dependencies * Updates from review * Remove infection object * Update simulating-transmission.Rmd * Update model-choices.Rmd * Add exercise to `compare_interventions.Rmd` * update modelling interventions after review * Update renv.lock * update plots * make uncertainty plots consistent across episodes * fix broken link * making plots consistent across tutorials * update summary and key points * update plots and add challenge * update introduction * move contact matrix callout and clarify reduction is performed within the model functions * add callout on intervention types * update introduction and reorder text in other sections * update PI section * style code * spell check * Update compare-interventions.Rmd * Apply suggestions from code review Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/modelling-interventions.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * add dropdown menus to make section more interactive * add reminder about transmissibility calculation * link to latent period * update model terms * add note on flow diagram * add callout on model rates * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * update tutorial objectives * distinguish parameter definitions from process descriptions in flow diagram * Update model-choices.Rmd * remove pak call from set up * Update renv.lock --------- Co-authored-by: Andree Valle Campos <[email protected]>

Auto-generated via {sandpaper} Source : 5c76e4e Branch : main Author : Amanda Minter <[email protected]> Time : 2023-12-21 14:05:03 +0000 Message : update late tasks from feedback (#85) * Extend challenge in 'Choosing an appropriate model' * Edit to accounting for uncertainty example Store all results and then extract infectious compartment for plotting * Add detail to Ebola case study challenge * update glossary entries * Add callout on ODE solver * clarify purpose of concept dependencies * Updates from review * Remove infection object * Update simulating-transmission.Rmd * Update model-choices.Rmd * Add exercise to `compare_interventions.Rmd` * update modelling interventions after review * Update renv.lock * update plots * make uncertainty plots consistent across episodes * fix broken link * making plots consistent across tutorials * update summary and key points * update plots and add challenge * update introduction * move contact matrix callout and clarify reduction is performed within the model functions * add callout on intervention types * update introduction and reorder text in other sections * update PI section * style code * spell check * Update compare-interventions.Rmd * Apply suggestions from code review Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/modelling-interventions.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * add dropdown menus to make section more interactive * add reminder about transmissibility calculation * link to latent period * update model terms * add note on flow diagram * add callout on model rates * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * update tutorial objectives * distinguish parameter definitions from process descriptions in flow diagram * Update model-choices.Rmd * remove pak call from set up * Update renv.lock --------- Co-authored-by: Andree Valle Campos <[email protected]>

Auto-generated via {sandpaper} Source : 2cfa2eb Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2023-12-26 00:33:43 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 5c76e4e Branch : main Author : Amanda Minter <[email protected]> Time : 2023-12-21 14:05:03 +0000 Message : update late tasks from feedback (#85) * Extend challenge in 'Choosing an appropriate model' * Edit to accounting for uncertainty example Store all results and then extract infectious compartment for plotting * Add detail to Ebola case study challenge * update glossary entries * Add callout on ODE solver * clarify purpose of concept dependencies * Updates from review * Remove infection object * Update simulating-transmission.Rmd * Update model-choices.Rmd * Add exercise to `compare_interventions.Rmd` * update modelling interventions after review * Update renv.lock * update plots * make uncertainty plots consistent across episodes * fix broken link * making plots consistent across tutorials * update summary and key points * update plots and add challenge * update introduction * move contact matrix callout and clarify reduction is performed within the model functions * add callout on intervention types * update introduction and reorder text in other sections * update PI section * style code * spell check * Update compare-interventions.Rmd * Apply suggestions from code review Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/modelling-interventions.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * add dropdown menus to make section more interactive * add reminder about transmissibility calculation * link to latent period * update model terms * add note on flow diagram * add callout on model rates * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/simulating-transmission.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * update tutorial objectives * distinguish parameter definitions from process descriptions in flow diagram * Update model-choices.Rmd * remove pak call from set up * Update renv.lock --------- Co-authored-by: Andree Valle Campos <[email protected]>

amanda-minter added 27 commits November 9, 2023 15:23

Extend challenge in 'Choosing an appropriate model'

c996ee7

Edit to accounting for uncertainty example

f6a9b22

Store all results and then extract infectious compartment for plotting

Add detail to Ebola case study challenge

214cdb4

update glossary entries

1743b9e

Add callout on ODE solver

ae255b8

clarify purpose of concept dependencies

47459f5

Updates from review

1c5c3a1

Remove infection object

c0bc550

Update simulating-transmission.Rmd

29a1ee2

Update model-choices.Rmd

fdde615

Add exercise to compare_interventions.Rmd

299839d

update modelling interventions after review

4ee6232

Update renv.lock

4687cd0

update plots

d02fe46

make uncertainty plots consistent across episodes

5b179ee

fix broken link

8710704

making plots consistent across tutorials

db46af2

update summary and key points

77a8e93

update plots and add challenge

e733715

update introduction

28ee601

move contact matrix callout

97b4e87

and clarify reduction is performed within the model functions

add callout on intervention types

5c9480e

update introduction and reorder text in other sections

84c2f34

update PI section

809388f

style code

e57dd29

spell check

495c831

Update compare-interventions.Rmd

01bd1e6

amanda-minter requested a review from avallecam December 12, 2023 13:04

github-actions bot pushed a commit that referenced this pull request Dec 12, 2023

differences for PR #85

238b2ff

Update episodes/simulating-transmission.Rmd

4420515

Co-authored-by: Andree Valle Campos <[email protected]>

avallecam requested changes Dec 19, 2023

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amanda-minter and others added 6 commits December 19, 2023 14:31

Update episodes/simulating-transmission.Rmd

1ca6148

Co-authored-by: Andree Valle Campos <[email protected]>

Update episodes/simulating-transmission.Rmd

f397811

Co-authored-by: Andree Valle Campos <[email protected]>

Update episodes/simulating-transmission.Rmd

699e179

Co-authored-by: Andree Valle Campos <[email protected]>

Update episodes/simulating-transmission.Rmd

d095420

Co-authored-by: Andree Valle Campos <[email protected]>

update tutorial objectives

ef0b11f

Merge branch 'main' into update-late-tasks

9c386ce

github-actions bot pushed a commit that referenced this pull request Dec 19, 2023

differences for PR #85

5d29bbb

avallecam approved these changes Dec 19, 2023

View reviewed changes

amanda-minter added 4 commits December 21, 2023 10:52

distinguish parameter definitions from process descriptions in flow d…

bb95beb

…iagram

Update model-choices.Rmd

c17cfb6

remove pak call from set up

547490c

Merge branch 'main' into update-late-tasks

6ee137f

github-actions bot pushed a commit that referenced this pull request Dec 21, 2023

differences for PR #85

0f887fc

Bisaloo mentioned this pull request Dec 21, 2023

update {epidemics} code and package version in renv.lock #100

Closed

Update renv.lock

49dc2a8

amanda-minter merged commit 5c76e4e into main Dec 21, 2023
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amanda-minter deleted the update-late-tasks branch December 21, 2023 14:05

avallecam mentioned this pull request Dec 21, 2023

use {webshot} package to print {Diagrammer} and {visNetwork} outputs #98

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update late tasks from feedback #85

update late tasks from feedback #85

amanda-minter commented Dec 12, 2023

github-actions bot commented Dec 12, 2023 •

edited

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avallecam commented Dec 19, 2023

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amanda-minter commented Dec 21, 2023

update late tasks from feedback #85

update late tasks from feedback #85

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amanda-minter commented Dec 12, 2023

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amanda-minter commented Dec 21, 2023

github-actions bot commented Dec 12, 2023 •

edited

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