Changes in version 0.1.5 (2025-12-10)                  

  - Vignette updated
  - changed default max.iters from 200 to 500.
  - now coco objects store information about optim.control arguments for
    full reproducibility.
  - introduce a two-step optimization approach for automatic model
    selection. See help(coco).

                 Changes in version 0.1.4 (2024-12-12)                  

  - Documentation polished

Enhances

  - GetNeg2loglikelihood, GetNeg2loglikelihoodTaper, and
    GetNeg2loglikelihoodTaperProfile now much faster (~35% faster)
  - cocoOptim:
      - new REML estimation for dense coco type.
  - now cpp functions cov_rns and cov_rns_taper include as special cases
    the well-known shapes when nu = 0.5, 1.5, and 2.5, yielding
    computational speed-ups.
  - now getCIs display names of covariate instead of index of Design
    Matrix.
  - now .cocons.check.info also checks for smoothness model and
    smooth.limits.

Changes

  - coco now accepts data.frame for locs argument, which is then
    converted to matrix.
  - getTrend now is called getSpatMean.
  - cocoPredict renamed output spatial mean vectors: trend is now called
    systematic, while mean is called stochastic.
  - cocoOptim :
      - reordering of arguments.
      - mle estimation method now called ml.
      - pmle estimation method now called pml.
  - getHessian :
      - mle to ml and pmle to pml.
  - getCIs now alpha argument reflects confidence level instead
    of 1-confidence level.

Fixes

  - fix a bug for plotOptimInfo when handling pml or reml objects.

                 Changes in version 0.1.3 (2024-10-15)                  

  - Vignette updates, watermark removed
  - Documentation polished
  - New holes_bm dataset with independent realizations and spatial trend

Enhances

  - added a NEWS.md file with version updates / modifications / enhances
    / etc
  - automatized delta for method plot for coco class.
  - Better visualization for plot(cocoOptim object, type = "ellipse")
  - coco:
      - now it is not necessary to provide all models for each source of
        nonstationarity. Those not specified will be set to those
        referenced with a stationary 0-mean model (i.e. tilt = 0 , aniso
        = 0, nugget = -Inf (because of log-parameterization)). If
        'smooth' is not specified, then it is set to 0.5.
  - cocoOptim:
      - "auto" option for ncores argument for cocoOptim, providing a
        convenient number of threads based on the number of parameters
        to estimate, available threads, and settings of the LBFGSB
        routine
      - "safe" argument, which prevents crashes due to ill-posed
        covariance matrices (Choelsky factorization error)
      - .cocons.check.convergence now checks and reports at which
        iteration ill-posed covariance matrices have been found during
        the optimization.
      - now "pmle" works with multiple independent realizations for coco
        types dense and sparse
      - safer parallel handling
  - getHessian more memory efficient
  - cocoSim:
      - if provided a fitted coco object, then pars argument can be NULL
        (default), and coco.object@output$par is used instead (and also
        type is set to diff).
      - more memory efficient
  - safer parallel handling for getHessian
  - polishing of neg2loglikelihood functions, leading to more efficient
    code
  - new and more polished internal functions to assess the validity of
    arguments (stopifnot() instead of if() stop())
  - getCondNumber optimized
  - small improvement over cpp functions

Changes

  - switched getPen as an internal function
  - method plot for coco objects shows rotation angle of the kernel
    w.r.t x-axis
  - GetSpateffects now provides angle w.r.t to x-axis
  - method "summary" for coco objecets (former "print" method)
  - more proper naming of objects inside functions
  - renaming of "cat.vars" to "skip.scale" + associated checks and
    optimization
  - getCondNumber removed, which can be replaced with kappa function
    from base R (i.e. kappa(getCovMatrix(coco.object),exact = TRUE))

                 Changes in version 0.1.2 (2024-09-06)                  

  - improve overall help files
  - add examples for coco, cocoOptim, cocoPredict, and cocoSim
  - update Vignette
  - some bug fixes and overall code polishing
  - smooth_limits from info from the coco function is now called
    smooth.limits to match the style of other arguments (no backward
    compatibility)
  - new names for C++ sparse covariance functions
  - add warnings of non-convergence of the LBFGSB for cocoOptim
  - bug fixes for coco "methods"
  - less redundant code