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example-complex-scenario-hub's Introduction

example-complex-scenario-hub

This repository is in development.

This repository serves as an example of a scenario modeling hub, modeled after the US Scenario Modeling Hub or the European COVID-19 Forecast Hub. Researchers from these teams have created the Consortium of Infectious Disease Modeling Hubs to provide a recommended set of standards and documentation for building and maintaining collaborative modeling hubs.

It is recommended that new Hubs create a Hub repository by buiding on the hubTemplate repository.

example-complex-scenario-hub's People

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luciecontamin avatar shauntruelove avatar elray1 avatar micokoch avatar kathsherratt avatar annakrystalli avatar

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example-complex-scenario-hub's Issues

update example mode output file(s) to our format

In looking at this file, I noticed that we'll need to make some minor updates to get it to match the file format that we've landed on. The main thing I noticed is that we will need an output_type column with values "sample", and then we could basically rename the current sample column to output_id.

Update authors

Use definition below
Definitions of roles (Author, maintainer, contributor, etc…)

Going forward, ensure that PRs from new contributors include an update to authorship roles (for R packages, in description file)

Clean up target metadata specification for "prop X" target

See current metadata draft here.

A couple of minor things to resolve:

  • What is a good target_name (imagine that this will be used as a label on a plot)
  • What is the target_description (one-sentence description of the target)
  • Is this a weekly step ahead target?
  • What are the appropriate target_units and target_type for a target that is a proportion?

clean up tasks.json

A couple of things I noticed about the draft tasks.json file we put together:

  1. Currently, quantile levels are listed here, under #/$defs/task_ids/quantile/quantile. This is not technically wrong in the sense that the reference can be resolved without issue. But it may be confusing to readers because quantiles are not a task id, but are rather a part of the output representation specification.
  2. We should add a boolean "round_id_from_variable": false flag

[ORG NAME CHANGE]: Update repo to hubverse-org organisation name

❗ Please do not merge anything into main until the 19th June

  • Create new branch called to-hubverse from latest dev branch (most likely related to the v3 schema PRs). (Make sure to pull first). If none exist, branch off from main.
  • Find and replace Infectious-Disease-Modeling-Hubs with hubverse-org throughout repo.
  • Upgrade config to v3 schema
  • Replace origin remote to point to the new organisation
    git remote set-url origin https://github.com/hubverse-org/<REPO_NAME>.git
    # Check remotes
    git remote -v
    url <- paste0('https://github.com/hubverse-org/', basename(getwd()), '.git')
    usethis::use_git_remote(name = "origin", url, overwrite = TRUE)
    # Check remotes
    usethis::git_remotes()
  • Push and open PR to original branch.

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