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improved simulations and bug fixes - #14

Merged

harmsm merged 30 commits into

harmslab:mainfrom

harmsm:main

Jul 12, 2026

Merged

improved simulations and bug fixes#14
harmsm merged 30 commits into
harmslab:mainfrom
harmsm:main

Commits on Jun 25, 2026
- added genotype batching
  harmsm
  committed
  16aafa5
Commits on Jun 26, 2026
- fixed bug in growth prediction batching
  harmsm
  committed
  0c33d37
Commits on Jul 3, 2026
- fixing empirical theta correction bug
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  ca00115
- test fix
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  b0ca829
- fixed batching bug in thermo models
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  9965669
Commits on Jul 4, 2026
- added ability to pin dk_geno for calibration
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  a09e839
- oom fix for new posterior sampling
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  f4a8f28
- added k_ref fitting input
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  7e08327
- catch trailing example from last commit
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  1c29b5b
- wired base_growth file in
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  e9ed48e
- fixed bugs
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  3c9be7d
Commits on Jul 5, 2026
- moved presplit and base_growth into observer
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  6616643
- standardized observe variable naming and prior treatment
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  cfd309d
- updated claude
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  1c4723b
- cleaned up simulate code organization
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  f038394
- user now must specify lambda estimate for trans models
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  2d162ca
- implement condition-specific priors on growth param
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  128cd47
- clean up/bug fix in transformation_lambda
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  5893f82
- moved priors out of model_orch into components
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  22405db
- added growth parameter outputs to summary
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  3ab5f40
- added script to balance ln_cfu0 for mut classes
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  3a6cdee
- added new data input docs
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  19018b3
- doc/readme/docstring consistency update
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  36e4177
Commits on Jul 6, 2026
- fixed faulty simulate tile mixing code
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  ce25d73
- added poisson lam to summarize outputs
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  04f87ec
- updated grid calculator
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  6a6c67b
Commits on Jul 7, 2026
- added dk_geno pinning to calibration
  harmsm
  committed
  3aaa4c5
Commits on Jul 8, 2026
- more granular simulation control, parameter clamping
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  committed
  cc6c018
Commits on Jul 9, 2026
- added ability to simulate empirically informed data
  harmsm
  committed
  288ed3b
- added congressional de-attenuation to empirical
  harmsm
  committed
  0ff01d1

Commits

Commits on Jun 25, 2026

Commits on Jun 26, 2026

Commits on Jul 3, 2026

Commits on Jul 4, 2026

Commits on Jul 5, 2026

Commits on Jul 6, 2026

Commits on Jul 7, 2026

Commits on Jul 8, 2026

Commits on Jul 9, 2026