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Align cfr notation 275 - #283

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Fix #275

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avallecam and others added 5 commits August 7, 2026 12:21
…st-delays

Use a consistent i/j convention (j = cumulative day, i = incidence day,
f_{j-i} = delay) in every double-sum equation, matching Nishiura et al.
2009. Fixes a f_{j-j} typo and incorrect sum bounds in the Day 1-3
worked examples, and adds index-meaning bullets where each formula
first appears.

Fixes #275

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Insert an intermediate line before each collapsed bracket, listing the
raw f_{j-i} subscripts for every (j,i) pair the sum bounds produce, so
the delay arithmetic is visible step by step. Add a note that since i
only ranges 0..j, j-i is always non-negative, so f is never evaluated
outside its defined domain.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Add the raw f_{j-i} pair-expansion line to Day 2 and Day 3, matching
the pattern already used in Day 0/Day 1. Reorder the collapsed and
numeric lines in Day 1-3 to start from c0 and ascend, instead of
descending from c_t, for a consistent reading order across all days.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Cross-references the delay-adjusted CFR derivation with the D_t /
expected-outcomes formulation from Garske et al. (2009, BMJ b2840),
and points the reader to the Day 0/Day 1 worked example for comparison.
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Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-middle/compare/md-outputs..md-outputs-PR-283

The following changes were observed in the rendered markdown documents:

 intro-cfr-adjust-delays.md | 164 +++++++++++++++++++++++++--------------------
 md5sum.txt                 |   6 +-
 severity-static.md         |   9 ++-
 3 files changed, 100 insertions(+), 79 deletions(-)
What does this mean?

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.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2026-08-07 15:05:48 +0000

@avallecam
avallecam requested a review from Degoot-AM August 7, 2026 15:03
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align all equation notation about CFR

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