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v1.0.0 - new CRAN release
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@jchiquet jchiquet released this 06 Jan 15:16
· 262 commits to master since this release
v1.0.0
a2fca0b

PLNmodels 1.0.0

Breaking changes

  • interface for controlling the fits now use list generated by dedicated functions

    • PLN_param() for PLN
    • PLNLDA_param() for PLNLDA
    • PLNnetwork_param() for PLNnetwork
    • PLNPCA_param() for PLNPCA
    • PLNmixture_param() for PLNmixture
      The use of 'control = list()' is deprecated: the code stop and send an error.

  • The regression coefficients are now denoted by B, not Theta, such as B = t(Theta).
    We keep on sending back Theta as a field of myPLN$model_par$Theta, but this will soon be deprecated

New features

  • added Barents fish data set
  • support for PLN when (inverse) covariance is known/fixed
  • estimator of the variance of the model parameters
    • integration of sandwich estimator of the variance-covariance of Theta when Sigma is fixed
    • variational estimation of the variance-covariance based on variational approximation of the Fisher information
    • jackknife estimation of the variance of Theta and Sigma
    • bootstrap estimation of the variance of Theta and Sigma
  • handle list of penalty weights in PLNnetwork
  • first support for torch optimizers (for PLN and PLNLDA)

Bug fixes

  • fix in objective functions of ve_step of standard PLN models
  • fix in objective functions of main of standard PLN models
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