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sdmTMB 0.3.0
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@seananderson seananderson released this 30 Jan 19:07
v0.3.0
d3744b8

  • Create the sdmTMBextra package to remove rstan/tmbstan helpers, which
    were causing memory sanitizer errors on CRAN.
    https://github.com/pbs-assess/sdmTMBextra

  • The following functions are affected:

    • predict.sdmTMB() now takes mcmc_samples, which is output from
      sdmTMBextra::extract_mcmc().
    • simulate.sdmTMB() now takes mcmc_samples, which is output from
      sdmTMBextra::extract_mcmc().
    • residuals.sdmTMB() now takes mcmc_samples, which is output
      sdmTMBextra::predict_mle_mcmc(). This only affects
      residuals(..., type = "mle-mcmc").

  • Move dharma_residuals() to
    sdmTMBextra to reduce heavy
    dependencies.

  • See examples in the Bayesian and residuals vignettes or in the help files for
    those functions within sdmTMBextra.

  • Various fixes to pass CRAN checks. #158

  • Fix memory issue highlighted by Additional issues CRAN checks. #158

  • 'offset' argument can now be a character value indicating a column name. This
    is the preferred way of using an offset with parallel cross validation. #165

  • Fix parallel cross validation when using an offset vector. #165

  • Add leave-future-out cross validation functionality. #156

  • Example data qcs_grid is no longer replicated by year to save package
    space. #158

  • Add message with tidy(fit, "ran_pars") about why SEs are NA.

  • Add anisotropy to print() #157

  • Fix predict(..., type = "response", se_fit = TRUE), which involves issuing
    a warning and sticking to link space. #140

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