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Full review of tutorials-early website #127

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Closed

Full review of tutorials-early website #127

wants to merge 677 commits into from

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avallecam
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@avallecam avallecam commented Sep 17, 2024 •
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REMINDER: this is a Full review. Before merging, redirect this to main

Fix #110
Fix #128

This PR aims to collect edit suggestions for the tutorials-early repository.

All rendered content is in https://epiverse-trace.github.io/tutorials-early/

We encourage in-line specific changes in the files changed tab (read GitHub how-to guide steps 5 to 7)

avallecam and others added 30 commits March 30, 2024 16:46
@avallecam
clean entry sentence
216da8f
@avallecam
add incidence2 package as prep for rt episode
918edc8
@avallecam
fix writing using grammarly
65914cd
@Degoot-AM
importing packages quietly
9ec8cf7
@Degoot-AM
Merge branch 'main' into fix-read-describe-cases
e016c42
@avallecam @adamkucharski
add context on transmissibility package
ac49ebb 
Co-authored-by: Adam Kucharski <[email protected]>
@avallecam
use specific namespace for EpiNow2 dist_spec()
d8a5477
@avallecam @adamkucharski
fix typo
7e3fc38 
Co-authored-by: Adam Kucharski <[email protected]>
@avallecam @adamkucharski
clarify action
f8264f2 
Co-authored-by: Adam Kucharski <[email protected]>
@avallecam
clarify reference to model fit in figure
29cf9c0
@avallecam
make NA visible
5d67ec2
@avallecam
relocate lognormal distribution step to get_params
0038780
@avallecam
clarify the aim of epiparameter
3425871
@avallecam
rename episode
b39cd2b
@avallecam
relocate from time periods 2 distributions callout
8911139
@avallecam
fix NA expression in callout title
dfb3d0c
@avallecam
rephrase challenge to an open exploration of delay
654744d
@avallecam
relocate closure and specify challenges section
4eb3e89
@avallecam
clean redundant outputs
d5bde80
@avallecam
rewrite episode wrapup and episodes connection
e8ab04a
@avallecam
remove reduntant output in intro and rewrite text
3fd652e
@avallecam
move warning after all analysis steps
dc7e8e3
@avallecam
move discussion to a stand-alone callout
5e850d6
@avallecam
add lognormal step and code completion tip
d20cf52
@avallecam
move influenza challenge to functions episode
4eab703
@avallecam
move ebola challenge to end of episode
3f2204a
@avallecam
add detail to challenges
819b5dd
@avallecam
edits to pass lintr checks
7ca068e
@avallecam
copy rt episode in middle of delays episodes
0c06fbb
@avallecam
use incidence2 as input for epinow2
922fce3
@avallecam
replace object name for linelist data (fix #99)
f1bb9de
@avallecam
add question connecting lost tag and validation
42abbd5
@avallecam
use tibble outputs and remove head() (fix #100)
0a48cd3
@avallecam
remove trailing white spaces
5af712c
@avallecam
add hint solution to validate challenge (fix #120)
86499f4
@avallecam
add solution to error warning challenge (fix #115)
5cc9eb8
@avallecam
add extra paragraph to solution about safeguarding
7cfe91d
@avallecam
reorder tag, validate, safeguard before tags_df()
ec12828
@avallecam
add variable loss in the discussion box
964e127
@avallecam
fix writing of solutions and discussions
0e641b7
@avallecam
clean spaces between lines and chunks + typos
d136f4a
@avallecam
fix linting issues
02ab391
@avallecam
remove head() from episodes (fix #122)
146c506 
this included print()
@avallecam
move all package loading functions to introduction
197fc03
@avallecam
remove trailing white spaces and fix identation
481ee11
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⚠️ WARNING ⚠️

This pull request contains a mix of workflow files and regular files. This could be malicious. No preview will be created.

regular files:

  • .lintr
  • CODE_OF_CONDUCT.md
  • CONTRIBUTING.md
  • LICENSE.md
  • README.Rmd
  • README.md
  • config.yaml
  • episodes/clean-data.Rmd
  • episodes/data/Marburg.zip
  • episodes/data/ebola_2014_first_200_days.csv
  • episodes/data/ebola_cases.csv
  • episodes/data/ebola_line_cases.csv
  • episodes/data/simulated_ebola.csv
  • episodes/data/simulated_ebola_2.csv
  • episodes/delays-functions.Rmd
  • episodes/describe-cases.Rmd
  • episodes/fig/disease-reporting.jpg
  • episodes/fig/fig5a-normaldistribution.png
  • episodes/fig/incubation-period-serial-interval.jpg
  • episodes/fig/infectiousness-covid19.jpg
  • episodes/fig/pkgs-hexlogos-2.png
  • episodes/fig/pkgs-hexlogos.png
  • episodes/fig/report_demo.png
  • episodes/fig/reproduction-generation-time.png
  • episodes/fig/reproduction-number-pre-symptomatic.png
  • episodes/fig/rt-adjusting-delays.png
  • episodes/fig/seria-interval-fitted-distributions.jpg

workflow files:

  • .github/workflows/README.md
  • .github/workflows/lint.yaml
  • .github/workflows/sandpaper-version.txt

@avallecam
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Hi @CarmenTamayo, can we have your review of the episodes in tutorials early? I'll be able to incorporate edits next week from Wednesday 25th onwards.

@avallecam avallecam mentioned this pull request Sep 23, 2024
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avallecam
avallecam commented Sep 30, 2024
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adding review edit suggestions

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@avallecam avallecam removed the request for review from CarmenTamayo September 30, 2024 20:15
This was referenced Sep 30, 2024
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closing given that this was redirected to main in #140

@avallecam avallecam closed this Sep 30, 2024
@avallecam avallecam mentioned this pull request Sep 30, 2024
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4 participants
@avallecam @Degoot-AM @Karim-Mane @Bisaloo