Update model function names #55

amanda-minter · 2023-11-07T09:06:05Z

Function names in {epidemics} are now model_X() following this PR

Function names in `{epidemics}` are now `model_X()`

github-actions · 2023-11-07T09:06:21Z

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-55

The following changes were observed in the rendered markdown documents:

 compare-interventions.md                        |   5 +--
 fig/simulating-transmission-rendered-plot-1.png | Bin 14897 -> 14781 bytes
 md5sum.txt                                      |   8 ++--
 model-choices.md                                |  16 ++++----
 modelling-interventions.md                      |  41 ++++---------------
 simulating-transmission.md                      |  50 +++++++-----------------
 6 files changed, 35 insertions(+), 85 deletions(-)

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If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

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⏱️ Updated at 2023-11-09 13:33:19 +0000

avallecam · 2023-11-08T19:14:16Z

I will need more time to look into this. Possibly on Friday or next Monday. Does it work for you?

amanda-minter · 2023-11-09T09:09:36Z

Please take a look as soon as you can, this is high priority as it affects the live site examples and is a blocker for @CarmenTamayo to review the materials.

avallecam

Is the replacement of model_ebola_r instead of the model_ebola_cpp is coherent?

From the vignette, in the "Run epidemic model" subtitle:

We run the model using the function model_ebola_r(). While there is a C++ equivalent of this model, it was not found to be much faster than the R-only version, and is not made available to users.

episodes/model-choices.Rmd

Function names in `{epidemics}` are now `model_X()`

avallecam · 2023-11-09T12:48:17Z

I did the step of "Update with rebase" here on GitHub. So if you need to make new changes locally, probably you need to pull content first? Let me know if this generates any issues.

…e/tutorials into update-model-names

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

Function names in `{epidemics}` are now `model_X()`

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

…e/tutorials into update-model-names

avallecam · 2023-11-09T14:50:13Z

I see a "branch cannot be rebased due to conflicts". I'm afraid that if it is not possible to resolve conflicts, then we should "squash and merge" for this one, again.

I think I will avoid the "Update with rebase" option in GitHub, and we as developers can do the rebasing in the local repos only by running git pull origin main to rebase the feature branch. I'll update on this in a separate issue/PR.

amanda-minter · 2023-11-09T15:01:10Z

I see a "branch cannot be rebased due to conflicts". I'm afraid that if it is not possible to resolve conflicts, then we should "squash and merge" for this one, again.

I think I will avoid the "Update with rebase" option in GitHub, and we as developers can do the rebasing in the local repos only by running git pull origin main to rebase the feature branch. I'll update on this in a separate issue/PR.

Thanks Andree, I will have to squash and merge this PR

Auto-generated via {sandpaper} Source : f8d1060 Branch : main Author : Amanda Minter <[email protected]> Time : 2023-11-09 15:01:14 +0000 Message : Update model function names (#55) * Update model function names Function names in `{epidemics}` are now `model_X()` * Update model function names Function names in `{epidemics}` are now `model_X()` * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Add checklist link * Update model function names Function names in `{epidemics}` are now `model_X()` * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Add checklist link --------- Co-authored-by: Andree Valle Campos <[email protected]>

Auto-generated via {sandpaper} Source : 6a660e9 Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2023-11-09 15:04:45 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : f8d1060 Branch : main Author : Amanda Minter <[email protected]> Time : 2023-11-09 15:01:14 +0000 Message : Update model function names (#55) * Update model function names Function names in `{epidemics}` are now `model_X()` * Update model function names Function names in `{epidemics}` are now `model_X()` * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Add checklist link * Update model function names Function names in `{epidemics}` are now `model_X()` * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Update episodes/model-choices.Rmd Co-authored-by: Andree Valle Campos <[email protected]> * Add checklist link --------- Co-authored-by: Andree Valle Campos <[email protected]>

Update model function names

126d18d

Function names in `{epidemics}` are now `model_X()`

amanda-minter requested a review from pratikunterwegs November 7, 2023 09:06

github-actions bot pushed a commit that referenced this pull request Nov 7, 2023

differences for PR #55

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pratikunterwegs removed their request for review November 7, 2023 10:33

amanda-minter requested a review from avallecam November 7, 2023 14:01

avallecam requested changes Nov 9, 2023

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Update model function names

25860d3

Function names in `{epidemics}` are now `model_X()`

avallecam force-pushed the update-model-names branch from 126d18d to 25860d3 Compare November 9, 2023 12:35

github-actions bot pushed a commit that referenced this pull request Nov 9, 2023

differences for PR #55

df83d46

amanda-minter and others added 4 commits November 9, 2023 13:12

Merge branch 'update-model-names' of https://github.com/epiverse-trac…

0655697

…e/tutorials into update-model-names

Update episodes/model-choices.Rmd

f82be3b

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

Update episodes/model-choices.Rmd

32129b3

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

Update episodes/model-choices.Rmd

e55cf73

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

github-actions bot pushed a commit that referenced this pull request Nov 9, 2023

differences for PR #55

9930960

Add checklist link

bcb9a3c

github-actions bot pushed a commit that referenced this pull request Nov 9, 2023

differences for PR #55

e870c2f

amanda-minter and others added 5 commits November 9, 2023 13:28

Update model function names

1bfd8a7

Function names in `{epidemics}` are now `model_X()`

Update episodes/model-choices.Rmd

180f0c5

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

Update episodes/model-choices.Rmd

10f2f1e

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

Update episodes/model-choices.Rmd

797c716

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

Add checklist link

2be9104

amanda-minter force-pushed the update-model-names branch from bcb9a3c to 2be9104 Compare November 9, 2023 13:28

Merge branch 'update-model-names' of https://github.com/epiverse-trac…

0f1d2ca

…e/tutorials into update-model-names

github-actions bot pushed a commit that referenced this pull request Nov 9, 2023

differences for PR #55

737a212

avallecam approved these changes Nov 9, 2023

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amanda-minter merged commit f8d1060 into main Nov 9, 2023
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amanda-minter deleted the update-model-names branch November 9, 2023 15:01

avallecam mentioned this pull request Nov 22, 2023

update contributing file: how-to's, requirements, references, format #35

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avallecam mentioned this pull request Dec 2, 2023

add steps on how to keep feature branch updated with main #81

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Update model function names #55

Update model function names #55

amanda-minter commented Nov 7, 2023

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amanda-minter commented Nov 9, 2023

Update model function names #55

Update model function names #55

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