NEWS

CHANGES IN VERSION 0.99.6
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* Implementing GitHub action workflows
* Adding testthat framework 
* Deprecating clonalCommunity 

CHANGES IN VERSION 0.99.5
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* Added geometric encoding using the BLOSUM62 matrix
* Trained classical and variational autoencoders for light/heavy chains with 1.5 million cdr sequences
 	- Architecture: 256-128-30-128-256
	- Parameters: 
		Batch Size = 64
		Latent Dimensions = 30
		Epochs = 100
		Loss = Mean Squared Error
	- Optimizers: Adam
	- Early stopping was set to patients of 10 for minimal validation loss and restoration of best weights
	- learn rate varied by models
	- classical auto encoders have batch normalization layers between the dense layers. 
    


CHANGES IN VERSION 0.99.4
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* Added chain.checker() function to allow for uncapitlized chain calls

CHANGES IN VERSION 0.99.3
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* Updated models for manuscript revision
 	- Architecture: 256-128-30-128-256
	- Parameters: 
		Batch Size = 64
		Learning Rate = 0.001
		Latent Dimensions = 30
		Epochs = 50
		Loss = Mean Squared Error
	- Optimizers: RAdam (for amino acid properties) and RMSprop (for OHE)
	- Early stopping was set to patients of 10 for minimal validation loss and restoration of best weights


CHANGES IN VERSION 0.99.2
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* Updated models to include radam optimization, early stop for min 10 epochs, and all trained on 800,000 unique cdr3s
* quietBCRgenes() now does not remove human Ig pseudogenes


CHANGES IN VERSION 0.99.1
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* Added detection of chain length to function call
* Added support for direct output of combineBCR()
* Modified quietBCR() to include constant regions and J-chains


CHANGES IN VERSION 0.99.0
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* Initial commit