Change in package structure: the ecogen class was adapted to the update of Adegenet to version 2.0.0.
A new slot ("A", including a data frame with allelic frequencies), replaces the GENIND slot of previous EcoGenetics
versions. The program uses now an internal (modified) version of the "genind" class, adapted for internal use
(temporal objects in internal processes).
eco.format, replacing the deprecated functions "aue.idig" and "aue.char2num".
eco.convert, allowing conversion among genetic data (loci matrix, alleles matrix, loci list and alleles list).
eco.2columns was deprecated and included as a conversion case in eco.convert.
A generic system of accesors is implemented for all the objects included in the package.
In this version, the G data frame can be optionally stored in a pre-processed format. Default option
generates, for codominant data, a matrix with removed separators and missing data conversion
to NA and remotion of non informative alleles. An option for ordering the alleles is also
available. For dominant data, the pre-process consists of the remotion of non informative alleles
and monomorphic loci (in default option, loci with polymorphism level < 5%).
The function eco.append has been deprecated. An improved version of the function has been
developed with accessors (accessor ecoslot.OUT(object)) and square brackets (object[["OUT"]])
Most of the functions included were adapted for genetic data of any ploidy levels.
Bugs correction: eco.2genepop - problem in the "POP" argument of the output file corrected.
Minor changes in dependences.
Updated examples. Improved help files and overview of the package -help("EcoGenetics").
This version has improvements in the modular design of the package.
Many functions of the version 1.1.0 were adapted to an improved S4
structure. Three main functions for autocorrelation analysis were
generated: eco.gsa, eco.lsa and eco.correlog, replacing the deprecated
eco.moran, eco.geary, eco.joincount, eco.localmoran,
eco.getisord and eco.autocor.
New functions: eco.detrend, eco.2spagedi, aux.image2df, aux.filter.
New functionalities: partial Mantel test, partial Mantel correlograms,
cross-correlation, cross-correlograms and local-Geary's C.
Incorporation of new and improved examples.
Bugs in the Getis-Ord (internal) function and in eco.mantel were corrected.
Leandro Roser [aut, cre],
Juan Vilardi [aut],
Beatriz Saidman [aut],
Laura Ferreyra [aut],
Thibaut Jombart [ctb] (author of included adegenet code),
Winston Chang [ctb] (author of the multiplot function included under
the name grf.multiplot)