ipmr 0.0.5

ipmr 0.0.5

Contains a number of bug fixes and some new functionality. The latter are mostly related to PADRINO models, and shouldn't have too much of an effect on existing user-specified IPMs.

Features

• Adds return_sub_kernels argument to make_ipm() for *_stoch_param and all density dependent methods. This is due to the large RAM footprint that these objects can occupy, particularly for long running models. The default is FALSE, which will save considerable memory space. Can be set to TRUE for downstream analyses that require sub-kernels/iteration kernels.

• Prettier printing method for PADRINO objects/lists of user-specified models.

• Prettier warnings for left/right_ev()

• Depending on your view, this may be a bug fix: updates the log argument in lambda() so that it only changes the scale, NOT the calculation method. The prior behavior was documented, but unlikely to be intuitive, and so caused some confusion. Thanks to @Aariq for pointing this out.

• For stochastic IPMs, is_conv_to_asymptotic() and conv_plot() now check for convergence in stochastic lambda. That is, they use a cumulative mean log(lambda) over iterations after discarding a burn-in. Thanks to @Aariq for implementing this in #45.

• Adds experimental function make_ipm_report(). This function converts proto_ipm objects into Rmarkdown documents that, when rendered, contain the equations and parameters used to implement the model in Latex. See the function documentation for more details, and report bugs/notation quirks/preferences in the issue tracker.

Bug fixes

• Fixes bug in normalization of left/right eigenvectors in simple density independent stochastic models. (thanks to @Aariq)

• Fixes bug where "drop_levels" was not recognized in some parameter set indexed models.

• Fixes bug where parameter set levels were recycled in some cases.

• Fixes bug in lambda() where log = TRUE had no effect when the IPM was stochastic and type_lambda was 'last' or 'all'.

• Switched from all.equal to absolute tolerance. @Aariq in #52.

• Fixes bug where the value of lambda() was named for determinstic models and unnamed for stochastic models. @Aariq in #57.

• Fixes bug in make_ipm() where a user-specified sequence wasn't getting used correctly for certain model classes. @Aariq in #58.

• Warnings about NAs in data_list are no longer raised for model objects.