spMC News

CHANGES IN spMC 0.3.11

  NEW FEATURES:
    o the logical argument `entropy` is introduced in the function
      sim(), sim_ck(), sim_ik(), sim_mcs() and sim_path(). Entropy
      and standardized entropy are introduced to study the 
      uncertainty of the predicted values.

    o the package logo man/figures/logo.svg was included.
    
    o it was added a README.md file.
    
    o the files man/spMC-package.Rd, man/setCores.Rd, man/quench.Rd,
      man/sim.Rd, man/sim_ck.Rd, and man/sim_ik.Rd have been updated.
    
    o it was removed a reference in inst/CITATION.

  BUG FIXES:
    o fixed a minor bug in the function `embedTProbs` of the file
      `spMC.c` to avoid possible divisions by zeros.

CHANGES IN spMC 0.3.10

  BUG FIXES:
    o a more consistent use of PROTECT has been implemented for the
      function `bclm` in the file `spMC.c` (line 1552).

CHANGES IN spMC 0.3.9

  BUG FIXES:
    o the order of the macros $(LAPACK_LIBS) and $(BLAS_LIBS) was 
      switched to be conformed with the new CRAN guidelines.

    o bibentry author fields in the inst/CITATION file are now
      following the standard "Given_1 Family_1 and Given_2 Family_2".

CHANGES IN spMC 0.3.8

  BUG FIXES:
    o sim_mcs() returns more accurate probabilities, and reliable
      predictions.

    o embed_MC() returns the transition probabilities that are now
      consistent with the tpfit() estimation methodology. An 
      additional attribute is added to deal with the counts.

CHANGES IN spMC 0.3.7

  BUG FIXES:
    o the argument "contour" in image.pemt() is now TRUE by default,
      and the contour plots are drawn according the rappresented
      probabilities.

CHANGES IN spMC 0.3.6

  BUG FIXES:
    o the example of the tpfit_me() function now provides consistent
      results.

CHANGES IN spMC 0.3.5

  BUG FIXES:
    o mlen() now returns more accurate results with "avg" method.

    o "transCount" consider all directions between couple of points.

    o the C code was fixed in order to be compatible with OpenMP 4.0.

    o the deprecated which.lines() function is now replaced by 
      which_lines() in all the examples of the manual.

CHANGES IN spMC 0.3.4

  BUG FIXES:
    o an uninitialized variable was fixed in the C procedure
      "transCount" when dealing with OpenMP 3.1.

    o unused variabels were removed from the C procedure "nsph2".

    o unused values were fixed in the C procedures "nsph2" and 
      "nsph".

CHANGES IN spMC 0.3.3

  NEW FEATURES: 
    o quench() function is introduced to reproduce the optimizations
      algorithms, which are required for removing spatial artifacts
      from the simulations.

    o transiogram() function computes also the log-odds standard error
      which will be used to draw confidence intervals for transition
      probabilities.

    o plot.transiogram() can draw confidence intervals around
      empirical transition probabilities.

  BUG FIXES:
    o transiogram() has increased accuracy on non-autotransition
      probabilities calculation.

    o pemt() has improved probabilities calculation for multiple
      directions.

  DEPRECATED AND DEFUNCT:
    o the arguments GA, optype and max.it in functions sim_ik() and
      sim_ck() are defunct. Simulation optimization is performed by
      the quench() function.

CHANGES IN spMC 0.3.2

  NEW FEATURES: 
    o pers.multi_tpfit() will produce perspective plots for 
      theoretical multidimensional transiograms.

    o perp.pemt() will produce perspective plots for 
      pseudo-empirical multidimensional transiograms.

    o sim(), sim_ck(), sim_ik(), sim_mcs() and sim_path() are now
      returning an object of class "data.frame" and "spsim".

    o tpfit(), tpfit_ml(), tpfit_ils(), tpfit_me(), multi_tpfit(),
      multi_tpfit_ml(), multi_tpfit_ils(), multi_tpfit_me(), mlen()
      and pemt() allows for the choice among serveral mean lengths 
      estimation method through the argument "mle".

    o transiogram() can also compute empirical probabilities for
      reversible chains throught the argument "reverse".

  UTILITIES:
    o Other robust methods are implemented for computing more
      reliable mean lengths. The choice can be perfrome among
      the averaging method ("avg"), the maximum likelihood estimator
      ("mlk"), trimmed average ("trm") or trimmed median ("mdn").

  DEPRECATED AND DEFUNCT:
    o the arguments GA, optype and max.it in functions sim_ik() and
      sim_ck() are deprecated. They will be considered defunct from
      next version release.
    
    o tpfit(mle = FALSE) is deprecated.

    o tpfit_ml(mle = FALSE) is deprecated.

    o tpfit_ils(mle = FALSE) is deprecated.

    o tpfit_me(mle = FALSE) is deprecated.

    o multi_tpfit(mle = FALSE) is deprecated.

    o multi_tpfit_ml(mle = FALSE) is deprecated.

    o multi_tpfit_ils(mle = FALSE) is deprecated.

    o multi_tpfit_me(mle = FALSE) is deprecated.

    o mlen(mle = FALSE) is deprecated.

    o pemt(mle = FALSE) is deprecated.

  BUG FIXES:
    o The polar transformation performed by the C procedure "nsph"
      was not much accurate, and computationally inefficient.

    o Memory bugs were fixed for C procedures "getCKPrbs", 
      "getIKPrbs", "nsph" and "transCount".

    o colors correspondence between transiograms and legend was fixed
      in functions image.multi_tpfit() and image.pemt().

CHANGES IN spMC 0.3.1

  NEW FEATURES:
    o tpfit_ml(), tpfit_ils(), tpfit_me(), multi_tpfit_ml(), 
      multi_tpfit_ils(), multi_tpfit_me() and other functions are
      introduced for R-methods consistency (see list of deprecated
      and defunct functions).

    o multi_tpfit() and tpfit() may perform all the other estimation
      methods by the use of the new argument method.

    o sim() may simulate and predict with all the available methods.

  UTILITIES:
    o contour.pemt() display contours of the pseudo-empirical 
      multidimensional and superpose the contour lines of the 
      theoretical transition probabilities.

    o image.pemt() plot the pseudo-empirical multidimensional 
      transiograms, which where previously computed.

    o is.pemt() tests an object if it is of the class 'pemt'.

    o pemt() returns pseudo-empirical multidimensional transiograms.

  DEPRECATED AND DEFUNCT:
    o ck.sim() is defunct. Use sim_ck() instead.

    o embed.MC() is defunct. Use embed_MC() instead.

    o ik.sim() is defunct. Use sim_ik() instead.

    o ilstpfit() and multi.ilstpfit() are defunct. 

      Iterated least squares are available by the use of the functions
      tpfit_ils() or multi_tpfit_ils().

    o image.multi.tpfit() is defunct. Use image.multi_tpfit() instead.

    o imgMultiTransiogram() is defunct.

      Pseudo-empirical multidimensional transiograms are now computed 
      first by the function pemt() and then plotted through 
      image.pemt().

    o is.multi.tpfit() is defunct. Use is.multi_tpfit() instead.

    o is.multi.transiogram() is defunct. Use is.multi_transiogram()
      instead.

    o mcs.sim() is defunct. Use sim_mcs() instead.

    o metpfit and multi.metpfit() are defunct.

      Maximum entropy methods is available by the use of the functions
      tpfit_me() or multi_tpfit_me().

    o multi.tpfit() is defunct.

      Multidimensional version of tpfit() is available by the use of
      the function multi_tpfit().

    o path.sim() is defunct. Use sim_path() instead.

    o predict.multi.tpfit() is defunct. Use predict.multi_tpfit()
      instead.

    o print.multi.tpfit() is defunct. Use print.multi_tpfit() instead.

    o print.multi.transiogram() is defunct. Use 
      print.multi_transiogram() instead.

    o which.lines() is defunct. Use which_lines().
