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Herold 2020 example use of MIMIC #66

Merged
merged 15 commits into from
Jul 8, 2024
Merged

Herold 2020 example use of MIMIC #66

merged 15 commits into from
Jul 8, 2024

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Fontanapink
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@Fontanapink Fontanapink commented Jul 8, 2024 •
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Pull Request To-Do List

Description of the changes:

I have done the following to make this PR ready for review:

  • I have re-based my branch on the latest master branch
  • I have added necessary documentation (if appropriate)
  • I have commented my code, particularly in hard-to-understand areas
  • I have assigned a reviewer to this PR

For the reviewer, make sure this PR meets these criteria before merging:

  • New code has comments
  • New code has tests (if appropriate)
  • New code has documentation (if appropriate)
  • New code has been reviewed by at least one other person

Fontanapink and others added 15 commits June 13, 2024 15:28
@Fontanapink
Fixed wrong labeling of x and y-axis
09d4d24
@Fontanapink
This push adds:
1027d93 
1) new examples using data imputation, metabolite and abundance inferences using MVAR
2) small change in plotting of heatmaps
@Fontanapink
furthered the examples in the HErold-Metabolite example
d665fa0
@Fontanapink
Added .nc to attributes
96c5898
@Fontanapink
updated Herold example
bafd15e
@Fontanapink
adding some model posteriors
9813baa
@Fontanapink
Adding Herols posterior changes
076a065
@Fontanapink
Added MVAR posterior
85108cd
@Fontanapink
Trying to optimize the data imputer
f3b8774 
First try using t-student likelihood
@Fontanapink
This is with 2 * F + k * np.log(n) = BIC and searching for the MIN…
e3ff086 
… BIC
@Fontanapink
This example is constraining the kernel (covariance matrix) to matern…
add4a10 
… and RBF typical of time-series data
@Fontanapink
Added new data examples
5af0d4d
@Fontanapink
model posterior
5a611f5
@Fontanapink
added infered data
091c547
@actions-user
Update requirements.txt and format code
2a24d22
@Fontanapink Fontanapink merged commit eae663e into master Jul 8, 2024
@Fontanapink Fontanapink deleted the HeroldExample branch July 8, 2024 11:32
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@Fontanapink @actions-user