Code

Middle task tutorials #58

Code

Merged

avallecam merged 82 commits intomainepiverse-trace/tutorials:mainfrom middle_task_1epiverse-trace/tutorials:middle_task_1Copy head branch name to clipboardFeb 2, 2024

+1,699-15

Commits

Commits on Jan 29, 2024

• Add first lesson on Epinow2

  

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• Add summary to quantify-transmissibility

  

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• Add citation for generation time

  

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• Update lesson times

  

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• Add second lesson on EpiNow2

  

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• Add section on incomplete observations

  

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• Fix typo in starting Rt dist values

  

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• Minor edits to text

  

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• Add section on regional estimates

  

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• Minor edits to text

  

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• Edits to text

  

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• Minor edits to text

  

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• Update config.yaml

  

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• Update renv.lock

  

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• Reorder sections across two tutorials

  

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• Rename second tutorial to create-forecast.Rmd

  

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• Update output definitions

  

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• Edits to lesson content

  

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• Tidy up example code

  

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• Fix typos

  

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• Fix copy and paste error

  

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• Add callout on Stan options

  

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• Add number of cores

  

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• Style code update

  

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• Update episodes/quantify-transmissibility.Rmd

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• Update episodes/quantify-transmissibility.Rmd

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• Update episodes/quantify-transmissibility.Rmd

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• Update episodes/quantify-transmissibility.Rmd

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• Update episodes/quantify-transmissibility.Rmd

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• Update episodes/quantify-transmissibility.Rmd

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• Apply suggestions from code review

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• Add note on EpiNow2 version

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• Remove note on relationship between R0 and Rt

  

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• Remove nowcast from heading

  

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• Add additional keypoint

  

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• Change of phrasing

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• Replace 'latent' with 'incubation'

  

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• Add glossary entries

  

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• Clarify the levels of uncertainty

  

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• Add callout on how delays can be specified for different data sources

  

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• Add probability thresholds to expected change callout

  

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• Rearrange results order and explain uncertainty pattern

  

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• Defining transmission speed/strength

  

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  a51bd39

• Update quantify-transmissibility.Rmd

  

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• Add callout on options for Rt for forecasting

  

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• Apply suggestions from code review

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• update language used in prerequisites

  

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• add data file for ebola case study challenge

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• add challenge for middle tasks

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• update exercise time

  

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• improve figure sizes

  

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• Fix typo

  

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• add project option to callout

  

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• update data formatting and callout

  

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• add growth rate to glossary

  

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• improve summaries

  

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• replace 'lesson' with 'tutorial'

  

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• add forecasting secondary observations section

  

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• fix typo

  

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• fix typo

  

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• style code

  

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• close renv lock bracket

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• install rcppparallel from rspm

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• add install rcppparallel from rspm

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• replace links to download and read ebola_cases

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• activate chunk output type console + stan params

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Commits on Jan 30, 2024

• remove the eval false tag to challenge chunks

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• replace paragraph with code within given gh-action

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Commits on Jan 31, 2024

• move read data for challenge within its solution

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• add new renv additions

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Commits on Feb 2, 2024

• use lintr addin to resolve local markers

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• use lintr addin to remove local warnings

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• add explicit data to forecast

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• fix typo

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• add details to rt_opts() description

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• fix typo for rt_opts() function

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• clarify the usage of a model different to default

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• clarify the assumed scenario

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• fix local options configuration with withr

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• reactivate chunks to allow running the solution

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• use chunk_output_type inline explicit to read data

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• simplify how to extract result from data.table object

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