Releases: James-Thorson-NOAA/VAST
Fix MacOS and Ubuntu compile issue
Fix MacOS and Ubuntu compile issue regarding calculation of new Schoeners-D overlap metric.
Improved EOF analysis, overlap metrics, and shapefile usage
VAST release 3.4.0 matches FishStatsUtils 2.6.0 and these include several improvements including:
- Improved options for Empirical Orthogonal Function analysis
- New options for calculating relationships among variables including overlap e.g., Schoeners-D
- Options to define extrapolation-area based on user-supplied shapefile.
Adding two new CPP versions...
... i.e., CPP version 8.4.0 which changes the parameterization of the inverse-Gaussian distribution, and CPP version 8.5.0 which includes a new backdoor for forecasting EOF results using temporally unbalanced data. Also updating dependency on new FishStatsUtils release 2.5.0
Updating FishStatsUtils dependency to 2.3.4
Updating dependency on FishStatsUtils to version 2.3.4
, which fixes bug when fine_scale=TRUE
and observations only cover a portion of the extrapolation-grid, as identified and fixed by Cole Monnahan. Also adding the inverse-Gaussian distribution for positive catch rates.
Updating dependency on FishStatsUtils...
... to require installing FishStatsUtils version >= 2.3.2, to avoid use of FishStatsUtils versions 2.3.0-2.3.1, which had bugs in make_covariates(.)
Adding new formula interface
Adding new formula interface that is backwards compatible, and allows for easier specification of density covariates
Adding S3 objects
And a few other small changes
Adding `fine_scale=TRUE` feature
This release includes a substantial change to functionality in VAST, by now including variation in density occurring at finer spatial scales that the spatial resolution of knots. It does this by using bilinear interpolation (a "predictive process modelling" framework") to interpolate Gaussian Markov random fields from the location of knots to the location of samples and extrapolation-grid cells, and also by using a new interface to density covariates, replacing X_xtp
(the value of covariates at each knot) with two inputs X_itp
(the value of covariates at observations) and X_gtp
(the value of covariates at extrapolation-grid cells).
Version 2.1.0
Adds several new features:
Expansion_cz
which allows indices to be derived in new ways (besides previous default of area-expansion), e.g., via the area-expanded biomass of another modeled category.Xconfig_zcp
which allows easier control of covariates and also allows for new "spatially-varying coefficient" modelsF_ct
andB_cc
which allow for specifying vector autoregression (i.e., multispecies Gompertz density dependence) and instantaneous fishing mortality, to merge features from the previousMIST
package for MICE-in-space models
Fixed small bug in V2.0.0...
... wherein CPP V5.3.0 would crash R whenever FieldConfig[1] != FieldConfig[2]
or FieldConfig[3]!=FieldConfig[4]
and both FieldConfig[2]>0
and FieldConfig[4]>0
. This release adds no new features, and only fixes that bug.