spMC News

CHANGES IN spMC 0.3.15

• BUG FIXES

  • It was edited the file NAMESPACE for better loading S3 Methods on more recent versions of R.

  • Fixing the function declaration SEXP isOmp(); to SEXP isOmp(void); within the file src/spMC.c.

  • Fixing unprotected variable prob in src/spMC.c within the functions annealingSIM and geneticSIM.

CHANGES IN spMC 0.3.14

• BUG FIXES

  • It was removed the file cleanup from the root directory.

CHANGES IN spMC 0.3.13

• BUG FIXES

  • Fixing the prototype of the SEXP isOmp(); to SEXP isOmp(void); within the header file src/spMC.h.

  • The file R/setCores.R has been updated to allow the function suppressPackageStartupMessages() to suppress all startup messages.

  • The file man/spMC-package.Rd has an updated url to a digital archived book on the references.

  • Converted the file NEWS to NEWS.md.

CHANGES IN spMC 0.3.12

• BUG FIXES

  • The URLs and images in the file README.md have been fixed.

  • The file man/spMC-package.Rd has been corrected at the <img> attribute align using "float:right;" instead.

CHANGES IN spMC 0.3.11

• NEW FEATURES

  • 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.

  • the package logo man/figures/logo.svg was included.

  • it was added a README.md file.

  • 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.

  • it was removed a reference in inst/CITATION.

• BUG FIXES

  • 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

  • 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

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

  • 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

  • sim_mcs() returns more accurate probabilities, and reliable predictions.

  • 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

  • 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

  • the example of the tpfit_me() function now provides consistent results.

CHANGES IN spMC 0.3.5

• BUG FIXES

  • mlen() now returns more accurate results with "avg" method.

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

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

  • 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

  • an uninitialized variable was fixed in the C procedure "transCount" when dealing with OpenMP 3.1.

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

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

CHANGES IN spMC 0.3.3

• NEW FEATURES

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

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

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

• BUG FIXES

  • transiogram() has increased accuracy on non-autotransition probabilities calculation.

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

• DEPRECATED AND DEFUNCT

  • 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

  • pers.multi_tpfit() will produce perspective plots for theoretical multidimensional transiograms.

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

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

  • 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".

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

• UTILITIES

  • 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

  • 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.

  • tpfit(mle = FALSE) is deprecated.

  • tpfit_ml(mle = FALSE) is deprecated.

  • tpfit_ils(mle = FALSE) is deprecated.

  • tpfit_me(mle = FALSE) is deprecated.

  • multi_tpfit(mle = FALSE) is deprecated.

  • multi_tpfit_ml(mle = FALSE) is deprecated.

  • multi_tpfit_ils(mle = FALSE) is deprecated.

  • multi_tpfit_me(mle = FALSE) is deprecated.

  • mlen(mle = FALSE) is deprecated.

  • pemt(mle = FALSE) is deprecated.

• BUG FIXES

  • The polar transformation performed by the C procedure "nsph" was not much accurate, and computationally inefficient.

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

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

CHANGES IN spMC 0.3.1

• NEW FEATURES

  • 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).

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

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

• UTILITIES

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

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

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

  • pemt() returns pseudo-empirical multidimensional transiograms.

• DEPRECATED AND DEFUNCT

  • ck.sim() is defunct. Use sim_ck() instead.

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

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

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

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

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

  • imgMultiTransiogram() is defunct.

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

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

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

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

  • metpfit and multi.metpfit() are defunct.

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

  • multi.tpfit() is defunct.

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

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

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

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

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

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