biocore / biocore/BIRDMAn

How to include random variables in the formula

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#83 4 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
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25
Forks
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Description

Dear @gibsramen and @mortonjt,

I built a formula to look for the effects of two variables likely affecting tadpole gut microbiome: temperature (with 5 levels) and nitrate concentration (with three levels), but I also have two random variables (aquarium and PCRreplicate) that I don't know how to include as random variables. I see you included random variables in your model in the original BIRDMAn paper, but I couldn't find the formula anywhere (sorry if I missed it).

This is my formula at the moment (without the random variables):

`formula="C(Temperature, Diff, levels=['18C', '22C', '26C', '28C', 'Fluctuating'])*C(Nitrate, Diff, levels=['control','N50','N100'])"`

Thank you very much for the availability to help
Paula

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by comparing the provided formula with the random-effects model described in the original BIRDMAn paper. Done means clarifying or documenting how aquarium and PCRreplicate should be represented as random variables in the formula interface.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, machine-learning
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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