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Releases: James-Thorson-NOAA/VAST

Fix MacOS and Ubuntu compile issue

13 Apr 23:11
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Fix MacOS and Ubuntu compile issue regarding calculation of new Schoeners-D overlap metric.

Improved EOF analysis, overlap metrics, and shapefile usage

11 Apr 19:42
dbe939c
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VAST release 3.4.0 matches FishStatsUtils 2.6.0 and these include several improvements including:

  1. Improved options for Empirical Orthogonal Function analysis
  2. New options for calculating relationships among variables including overlap e.g., Schoeners-D
  3. Options to define extrapolation-area based on user-supplied shapefile.

Adding two new CPP versions...

14 Jan 21:36
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... 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

10 Nov 01:19
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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...

11 Oct 21:38
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... 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

27 Sep 03:59
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Adding new formula interface that is backwards compatible, and allows for easier specification of density covariates

Adding S3 objects

25 Jul 19:55
9183b62
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And a few other small changes

Adding `fine_scale=TRUE` feature

10 May 13:57
66f0121
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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

02 Mar 23:14
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Adds several new features:

  1. 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.
  2. Xconfig_zcp which allows easier control of covariates and also allows for new "spatially-varying coefficient" models
  3. F_ct and B_cc which allow for specifying vector autoregression (i.e., multispecies Gompertz density dependence) and instantaneous fishing mortality, to merge features from the previous MIST package for MICE-in-space models

Fixed small bug in V2.0.0...

12 Nov 16:21
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... 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.