shipunov 1.11-1:
Cosine.dist() removed as it is not useful in the context of package;
SM.dist() can now ignore similarities in zeroes and discretize numerical variables;
new function Tctext() which is based on but more convenient than Tcoords() for labeling 'hclust' plots;
PlotBest.dist() and PlotBest.mdist() improved (and simplified);
plot.Jclust() now accepts 'pos' and 'offset' oprions for text;
help files improved.
shipunov 1.11:
Bclust() now accepts the pre-built list of 'hclust' objects;
plot.Jclust() now plots rectangle borders even if they go outside of plotting region;
new method plot.Bclust() for quick plotting boostrap values;
Bclust() is now able to count the relative matches;
new function SM.dist() for simple match distances;
Files() corrected so it now outputs file list if needed;
new data 'hrahn' and related multi-entry identification system;
Pleiad() now converts dissimilarities into similarities and can colorize negative correlations;
help files improved.
shipunov 1.10:
"PBSmapping" package is now imported, not suggested so it should be installed together with "shipunov";
Dotchart1(), Dotchart(), Linechart(), Ex.col(), Str() functions and corresponding help files improved;
Gower.dist() now controls the missing data in the output;
Tcoords() now outputs proper coordinates even if labels are not present;
new functions Polycenter() and Polyarea(), function Squares() re-worked;
Hulls() and Ellipses() output now "centers" and "outliers" as _attributes_, please note that this might affect older scripts;
Overlap(), Squares() and Pinhull() are improved, their option "Hulls=" removed;
Jclust() and Bclabels() updated;
new Fences() function which colorizes tips of "hclust" dendrogram.
shipunov 1.9:
Misclass(..., best=TRUE) reworked to speed up, everything is taken outside of cycles, "force=TRUE" now also runs experimental fast tabulate()-based code;
Biarrows() is now by default with "shift="auto"" so arrows start out of the center without scaling;
Bclabels() now prints bootstrap values as is;
Ellipses() and especially Overlap() re-worked, the last now allows to output symmetric and negative overlaps;
Hulls() improved to return point indices as row names;
new function Vicinities() which helps to find "most central" observations;
new function Pinhull() which allows to calculate polygon memberships, "membership overlaps", ellipse outliers and more;
help files improved
shipunov 1.8:
DESCRIPTION corrected;
Alldups() improved;
in Hulls() "match.color" changed to "match.colors" (hopefully, will not affect anything);
new function Tcoords() to calculate coordinates of tips in "hclust" and Ploth() plots;
Pleiad() and its documentation slightly corrected;
in Saynodynamite(), color is now simply "red";
help files improved;
Ditto() improved;
some corrections for R-4;
Ploth() improved to change, e.g., label font;
Misclass() corrected in case if there are more predicted than observed classes;
Misclass(..., best=TRUE) now uses recursive .permutations() modified from "gtools" package, it allowed to increase the maximal number of classes from 7 to 8 ;)
shipunov 1.7:
Plot.phylocl() now allows "cex" for all labels;
function Peaks() removed as it was not really useful;
Biarrows() improved;
seq_len() or seq_along() used instead of "1:...";
Files() corrected;
Cosine.dist() and Misclass() improved;
Alldups() extended to work with matrices and data frames;
help files improved
shipunov 1.6:
help files improved;
small bug in BootRF() and BootKNN() corrected;
BootKNN() now also handles Dnn();
Gradd(..., what="lines") now also plots decision boundaries;
help(Gradd) simplified and two packages removed from "Suggested";
functions Co.test() and Is.tax.inform.char() removed as very simple and rarely used;
compatibility established with new R "stringsAsFactors=TRUE";
new function Biarrows() to make biplot from any dimension reduction;
Plot.phylocl() can now keep monotypic clades.
shipunov 1.5:
Class.sample() now handles proportion and has uniform sampling option;
Rows() renamed into Pull();
Adj.Rand() can now use NAs;
help files improved;
plot.nnet() removed as it is now available as NeuralNetTools::plotnet();
Dev() removed as it is simple without function (see ?BootKNN and ?BootRF);
BootRF() improved;
help keywords updated;
Life() has now interactive mode;
Dotchart1() updated with new version from base R;
Miney() code completely re-worked;
DNN() can now use self-training.
shipunov 1.4:
Fill() improved;
new Ditto() function (reverse Fill());
Biokey() and Numranks() improved;
help files improved;
new Rows() function;
R() renamed into R.logo();
Life() improved;
Rpart2newick() and Biokey() now keep node labels;
MrBayes() changed after new version of "ips" package
shipunov 1.3:
Gradd() bug corrected;
VTcoeffs() improved;
Numranks() improved;
help files improved;
new "%-%" a.k.a. "minus names" function;
new Dnn() function;
new Rpart2newick() function;
new Cosine.dist() function;
MRH() updated;
Recode*() functions improved;
Bclust() improved
shipunov 1.2:
new Fill() function;
datasets are now integrated;
new MRH() function;
new "chaetocnema" and "haltica" datasets;
Ellipses() extended;
Points() and PPoints() extended;
new DNN() function for distance matrix based kNN;
new S.value() function;
K() and Misclass() extended;
MrBayes() extended to handle mixed analysis;
help files improved;
new Biokey() and Numranks() functions;
new datasets "plantago", "classifs" and "keys"
shipunov 1.1:
option "mad" added for pairwise.Eff();
Gen.cl.data() function to generate "scikit-learn"-like examples;
Misclass() is now able to search for the best table;
new Class.sample() function;
new Classproj() function;
Hulls(..., outliers=FALSE) now plots smoothed convex hulls and outputs outliers;
Overlap(..., Hulls=FALSE) might use non-Hulls() object;
Overlap2() removed;
new BestOverlap() function;
help files improved;
new Bclust() function and its allies;
new Updist() function;
Misclass(..., quiet=TRUE) now suppresses output;
"Rresults" script improved;
new Root1() function;
Draw.arrow() removed;
Histp() removed()
shipunov 1.0:
first release