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sdmTMB 0.6.0

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@seananderson seananderson released this 30 May 19:55
  • Pass several arguments to DHARMa::plotQQunif().

  • Add silent option in simulate.sdmTMB(). Setting it to FALSE allows
    monitoring simulations from larger models.

  • Fix bug in est_non_rf1 and est_non_rf2 columns when all the following
    conditions were true:

    • predicting on new data
    • using a delta model
    • including IID random intercepts or time-varying coefficients
      See #342. Thanks to @tom-peatman for the issue report.
  • Fix delta-gamma binomial link printing for type = 'poisson-link' #340

  • Add suggestion to use an optimized BLAS library to README.

  • Add warning if it's detected that there were problems reloading (e.g., with
    readRDS()) a fitted model. Simultaneously revert the approach to
    how reloaded models are reattached.

  • Move log_ratio_mix parameter to 2nd phase with starting value of -1 instead
    of 0 to improve convergence.

  • Fix bugs for nbinom1() and nbinom2_mix() simulation.

  • Allow profile argument in the control list to take a character vector of
    parameters. This move these parameters from the outer optimization problem to
    the inner problem (but omits from the from the Laplace approximation). See
    documentation in TMB. This can considerably speed up fitting models with many
    fixed effects.

  • Add theoretical quantile residuals for the generalized gamma distribution.
    Thanks to J.C. Dunic. #333

  • Add "poisson-link" option to delta-mixture lognormal.

  • Fix bug in simulation from Poisson-link delta models.

  • Simplify the internal treatment of extra time slices (extra_time). #329
    This is much less bug prone and also fixes a recently introduced bug. #335
    This can slightly affect model results compared to the previous approach if
    extra time was used along with smoothers since the 'fake' extra data
    previously used was included when mgcv determined knot locations for
    smoothers.