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Animal to Manure connection quarto update#3147

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Animal to Manure connection quarto update#3147
elle-andreen wants to merge 4 commits into
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@elle-andreen

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Translating "Animal to Manure connection" scientific documentation section and accompanying resources to quarto format.

@elle-andreen
elle-andreen requested a review from LisaM-kiwi July 16, 2026 19:19
@@ -0,0 +1,3 @@
Class , Description

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I created a connections table under resources/table_data to keep the file tree clean.
I also updated the paths in the document.


The Animal module is responsible for calculating manure excretion mass and composition based on animal attributes, ration composition and intake, and other factors. The Animal module must then pass this manure on to the Manure module, where manure nutrient gains and losses are quantified through field application or export. The Animal module currently calculates manure excretion at the pen level (i.e., values representative of the total manure from animals in a single pen), and several additional steps must occur before manure information can be sent to the Manure module. These steps include:

- Splitting manure from individual pens into one or more user\*defined manure streams

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Should user*defined have backticks around it? I haven't seen this type of language in other parts of the scientific documentation ...

Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd
#### Stream Formation

**Bedding**
- Instance(s) of a ManureStream for each manure stream defined by the user that represent the attributes of the manure in the specific manure stream. ManureStream instances include the following variables (all in kg except for volume, m³ and manure methane potential, m³/kgVS):

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Should ManureStream have backticks like this ManureStream?

Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated
`_apply_bedding (pen.py)`


```{python}

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There are some random ? in the calculations column, I will investigate

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Is the ? a placeholder? I can't figure out what you are trying to do here ...

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I think they were commas that were replaced with ? due to CSV encoding issues. I've reverted them to commas and they should render correctly now once I push that commit!

### Required User Inputs
#### Classes

```{python}

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All the tables are missing table tags

Comment thread docs/scientific/quarto-scidoc/qmd/connections.qmd Outdated

@LisaM-kiwi LisaM-kiwi left a comment

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Hi Elle!
I've added comments throughout the files so you can see the changes that I plan to make before merging.
There is one thing regarding a table that I commented on that I need your input on.
Thanks!

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2 participants