Merging features from package `MIST`

including:

features for vector-autogressive models for species interactions
features for specifying fishing mortality
features for estimating biological reference points and population status relative to these

Added simulate feature and options to combine data types

Three main updates to CPP file:

V4.2.0 -- fixed bug occurring when specifying a constant intercept
V4.3.0 -- added new options for distributions/link-functions when combining multiple data types
V4.4.0 -- added simulate feature to improve simulation-testing options

Added V4.1.0...

... which adds feature to compute GMRF normalization constant during outer-optimizer but not during inner-optimizer. However, preliminary testing suggests that this feature does not speed up VAST. Also modifies/adds a few plotting features.

Added tools for expanding compositional data

Including calculate_proportion as well as new options for internally calculating standard errors for proportions (which is not advisable unless the number of proportions is small, given that the calculation is no longer separable among categories)

Added option for independent factors

via input FieldConfig[X]="IID", where X={1,2,3,4}, which requires CPP Version="VAST_v2_6_0". Also includes new option for "Binned-Poisson" data as used by REEF for citizen-science data collections.

Added user manual and `Rerun_Fn`...

... where the latter is designed to allow exploration of counter-factuals where covariates, age-structure, or spatio-temporal residuals are turned off to attribute distribution shift to different mechanisms.

Added Poisson-process link function

This release adds a new "Poisson-process link function", accessed using ObsModel[2]=1, which links the encounter probability and positive catch-rate components of the delta model

Added continuous-integration and unit-testing

Stable version, with continuous-integration and unit-testing comparisons to confirm identical parameter estimates as SpatialDeltaGLMM package at https://github.com/nwfsc-assess/geostatistical_delta-GLMM/ when analyzing data for a single species.

Initial public release

This release includes unit-testing to automatically confirm that it gives identical results to SpatialDeltaGLMM for single-species runs, and also has unit-testing for a 5-species Eastern Bering Sea example