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New example: MRSA community #32

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New example: MRSA community #32

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@gvegayon gvegayon commented Nov 18, 2024

This pull request includes several changes to the epiworld project, focusing on template parameter defaults, error message clarity, and the addition of a new community-hospital model example. The most important changes are summarized below:

Template Parameter Defaults:

  • Updated various template definitions to use EPI_DEFAULT_TSEQ as the default type for TSeq instead of int. This change improves code consistency and flexibility. (epiworld.hpp [1] [2] [3] [4]; include/epiworld/agent-meat-virus-sampling.hpp [5] [6] [7]; include/epiworld/misc.hpp [8]

Error Message Clarity:

  • Improved the clarity of an error message in the Model<TSeq>::operator() method by adding single quotes around the parameter name. (epiworld.hpp [1]; include/epiworld/model-meat.hpp [2]

Community-Hospital Model Example:

  • Added a new example model that simulates the interaction between community and hospital populations. This includes updates to the Makefile, a detailed README.md, and a new main.cpp file with the model implementation. (examples/14-community-hosp/Makefile [1]; examples/14-community-hosp/README.md [2]; examples/14-community-hosp/main.cpp [3]
  • Updated the main Makefile to include the new community-hospital example. (examples/Makefile examples/MakefileL11-R12)

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codecov bot commented Nov 18, 2024

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 83.96%. Comparing base (d177940) to head (31d8724).
Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
include/epiworld/model-meat.hpp 0.00% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##           master      #32   +/-   ##
=======================================
  Coverage   83.96%   83.96%           
=======================================
  Files          42       42           
  Lines        2763     2763           
=======================================
  Hits         2320     2320           
  Misses        443      443           

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@gvegayon gvegayon requested a review from apulsipher November 19, 2024 04:43
@gvegayon gvegayon marked this pull request as ready for review November 19, 2024 04:44
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Generally this looks good! There are a few changes to make, and some of the automated checks are failing. Of the checks, the Doxygen check seems to be the biggest concern. Do we need to fix that test or is that something you can fix on this branch?

```bash
root ➜ /workspaces/epiworld/examples/14-community-hosp (example-karim) $ make
g++ -std=c++17 -O3 -g main.cpp -o main.o
root ➜ /workspaces/epiworld/examples/14-community-hosp (example-karim) $ ./main.o
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I'd suggest updating this example to remove (example-karim) for additional clarity


An few key observations from this example.

1. **We have a sampling function that exclude population**. These two functions are used in the update functions so, when susceptible (in the community) sample, the sampling excludes individuals who are hospitalized. Likewise, hospitalized
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This last sentence appears to be incomplete, or at least I'm not following it. "Likewise, hospitalized..." what?

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I'm addressing this in #34.

#include "../../epiworld.hpp"

/***
* A concrete example would be a model that includes two populations.
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Should be reworded to "A concrete example with a model that includes two populations:"

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I'm addressing this in #34.

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Closing this in favor of #34.

@gvegayon gvegayon closed this Nov 22, 2024
@gvegayon gvegayon deleted the example-karim branch November 22, 2024 23:09
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2 participants