Code

Dragons rework#51

Code

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Tess-LaCoil merged 21 commits intomastertraitecoevo/hmde:masterfrom dragons-reworktraitecoevo/hmde:dragons-reworkCopy head branch name to clipboardJan 1, 2025

+474-249

Commits

Commits on Dec 18, 2024

• Adding a finite mixture model analysis of the posterior estimates, and the Stan rk45 adaptive step size solver as an option to show it does better.

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• Corrected minus sign error in the DE for linear model. Added the int_method argument to the data structure for the linear model and the test script.

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• Rearranged vignette to be more consice and focus on the finite mixture model results for classification of clusters.

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Commits on Dec 19, 2024

• Added the ability to set the prior means for beta parameters to the linear model, testing to check that it is present. Default values are log(1) = 0, but the user can provide alternatives if desired.

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• Updated the assign data function to correctly work with the default values for priors in the linear model and included testing code to check that the default/provided prior values work properly.

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Commits on Dec 20, 2024

• Adding RK4 function for plotting.

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• Added option to specify standard deviation priors.

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• Updated data assignment and model names.

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Commits on Dec 21, 2024

• Added plotting for numerical estimation with 0.5 step size.

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• Finalised plotting for numerics.

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• Plots for RK45 analysis.

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Commits on Dec 22, 2024

• Added analytic solution to affine model.

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• Corrected error in analytic solution.

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• Change to analytic solution.

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Commits on Dec 23, 2024

• Reverted reparameterisation for affine DE as it didn't have the result I wanted. Restored affine terminology swap.

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Commits on Dec 24, 2024

• Minor changes to vignette.

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• Building some helper functions for the here be dragons vignette.

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• Updated analysis to include Canham testing.

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Commits on Dec 25, 2024

• Separated off the bimodal posterior analysis to a different repo to avoid cluttering this one.

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Commits on Dec 30, 2024

• Added required libraries back in.

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• Corrected testing for affine model to include the prior SDs.

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