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.
BUG FIXES
cleanup from the root
directory.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.
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.
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
embedTProbs of the
file spMC.c to avoid possible divisions by zeros.BUG FIXES
PROTECT has been implemented
for the function bclm in the file spMC.c (line
1552).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".
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.
BUG FIXES
"contour" in image.pemt() is
now TRUE by default, and the contour plots are drawn
according the rappresented probabilities.BUG FIXES
tpfit_me() function now provides
consistent results.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.
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".
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
GA, optype and
max.it in functions sim_ik() and
sim_ck() are defunct. Simulation optimization is performed
by the quench() function.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
"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().
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().