Dear Emacs, please make this -*-Text-*- mode!
**************************************************
* *
* 1.1 SERIES NEWS *
* *
**************************************************
CHANGES IN R VERSION 1.1.2
CHANGES
o Changed the default clustering algorithm internally to the
"Mercator" contructor to use "hclust" instead of "pam".
CHANGES IN R VERSION 1.1.0
NEW FEATURES
o Incorporated tywo new "views": self-organizing maps (SOM) and
uniform manifold approximation and projection (UMAP).
CHANGES IN R VERSION 1.0.0
NEWS
o Updated versio number to coincide with publuication of manuscript.
CHANGES IN R VERSION 0.99.0
BUG FIX
o Updated vignette and manual pages in response to comments from
reviewer of manuscript.
CHANGES IN R VERSION 0.11.5
BUG FIX
o Added "flexmix" to dependency to work around a bug on CRAN's
fedora machines.
CHANGES IN R VERSION 0.11.3
NEW FEATURES
o Added 'print' and 'show' methods to the BinaryMatrix class. .
CHANGES IN R VERSION 0.11.2
NEW FEATURES
o Modified the Mercator constructor to accept an arbnitrary
distance matrix and not just a BinaryMatrix. Also included a
second vignette focusing on continuous data, with an extra
data set included to provide an illustration.
CHANGES IN R VERSION 0.11.0
NEW FEATURES
o Edited the binary vignette for clarification and better
examples.
CHANGES IN R VERSION 0.10.1
BUG FIX
o Fixed the bug with missing names on `clusters` slot. Again.
CHANGES IN R VERSION 0.10.0
NEW FEATURES
o Can now use `slot(object, "palette") <- ...1 to change the
palette associated with a Mercator object.
BREAKING CHANGES
o Mercator objects no longer have `colvv` or `symv` slots. To
` retain the old functionality, you must instead use the new
internal functions with same names; for example, write
`Mercator:::colv(object)` instead of `object@colv`.
CHANGES IN R VERSION 0.9.6
BUG FIXES
o Fixed a bug in "addVisualization" to make sure all matrices
have non-NULL rownames.
o Fixed a NAMESPACE/import bug. The 'scatter' method calls the
'smoothScatter' function from 'graphics'. This in turn calls a
hidden (unexported) function from 'grDevices' using three
colons (:::), which calls 'KernSmooth::bkde2D' without
importing anything. CRAN checks force my package to know this
internal implementation anhd import the function explicitly.
CHANGES IN R VERSION 0.9.5
BUG FIXES
o Fixed an igraph "jitter" bug in a test script.
CHANGES IN R VERSION 0.9.4
NEW FEATURES
o Added a new "barplot" method for the Mercator class, which
plots the silhouette widths in the colors already assigned to
clusters.
o Added a new "scatter" method for the Mercator class, which
displays some views as a smoothed scatter plot.
CHANGES IN R VERSION 0.9.2
NEW FEATURES
o Added a new "plot" method for the Mercator class, which
automatically sets the colors and symbols for different
views.
CHANGES IN R VERSION 0.9.1
BUG FIXES
o Fixed the bug in overcounting "redundant" or "unused" features.
CHANGES IN R VERSION 0.9.0
BREAKING CHANGES
o Deprecated the "recolor" function in favor of a new name, "setClusters".
CHANGES IN R VERSION 0.8.8
BUG FIXES
o Checked all the documentation; first version submitted to CRAN.
CHANGES IN R VERSION 0.8.7
BUG FIXES
o Fixed the "names" bug in using iGraph visualizations.
CHANGES IN R VERSION 0.8.2
FEATURES
o Added a (mostly) working vignette. (Is that a feature?)
CHANGES IN R VERSION 0.8.0
BREAKING CHANGES
o Renamed the "recoverCluster" function to "getClusters".
CHANGES IN R VERSION 0.7.8
BUG FIXES
o Fixed a NAMESPACE/DESCRIPTION issue to make it easier to work
with slots borrowed from other classes.
CHANGES IN R VERSION 0.7.7
BUG FIXES
o Worked around an issue in igraph, which doesn't like layouts
where nodes overlap.
CHANGES IN R VERSION 0.7.5
BUG FIXES
o Fixed a bug in igraph views, in order to work with more than
48 clusters.
CHANGES IN R VERSION 0.7.4
FEATURES
o Added a bunch of man pages (is that a feature?).
CHANGES IN R VERSION 0.7.2
BUG FIXES
o Fixed a bug in "downsample", where probabilities could be
greater than one.
CHANGES IN R VERSION 0.7.1
BUG FIXES
o Fixed a labeling bug in "recolor".
o Updated data objects to use "Mercator" rather than
"BinaryMatrix".
CHANGES IN R VERSION 0.7.0
BREAKING CHANGES
o Renamed the "DistanceVis" class to "Mercator".
o Renamed the whole package fromk "BinaryMatrix" to "Mercator"
BUG FIXES
o Fixed a "drop=FALSE" bug with subsetting "info" components
when they are single-column data frames.
CHANGES IN R VERSION 0.6.2
NEW FEATURES
o Added a "recoverCluster" function to the "DistanceVis"
class. May eventually be converted to a "predict" method.
BUG FIXES
o Fixed a "drop=FALSE" bug with subsetting "info" components
when they are single-column data frames.
CHANGES IN R VERSION 0.6.0
NEW FEATURES
o Added new automatically computed graph layouts based on MDS
and t-SNE.
CHANGES IN R VERSION 0.5.0
NEW FEATURES
o Added a new visualization, based on igraph.
CHANGES IN R VERSION 0.4.0
INCOMPATIBLE CHANGES
o Decided that the "recolor" function should be called
"remapColors", since the point is to make color assiognments
for two different distance metrics compatible
NEW FEATURES
o Added a **new** function called "recolor", which allows you
to change the stored color assignments based on a new
clustering using the same distance metric.
CHANGES IN R VERSION 0.3.0
INCOMPATIBLE CHANGES
o Decided that the BinaryMatrix class needs to carry along
information about both rows and columns, and not just
columns. As a results, changed the name of te "featresa" slot
to "columnInfo, and added a parallel "rowInfo" slot.
NEW FEATURES
o Added a transpose ("t") operator for a BinaryMatrix.
CHANGES IN R VERSION 0.2.0
NEW FEATURES
o Removed the (temporary) "CML.rda" file and replaced it with two
smaller subsets, "CML1000.rda" and "CML500.rda". Restructured
the appropriate test scripts to use the smaller data sets so
they run faster. Note that both subsets were created using
the "downsample" function.
CHANGES IN R VERSION 0.1.1
NEW FEATURES
o Added a "[" method to the DistanceVis class. Note the slowest
part of this method presently is subsetting the hierarchical
clusters, since it is implemented using the "prune" routine in
"dendextend", which removes one leaf at a time.
o Added a "recolor" function thast allows you to make the
color-and-symbol assigments for different distance matrices
behave "as consistenbtly as possible".
o Added a "downsample" function based on Peng Qiu's idea in the
SPADE package. The point is to take a subsample that
deliberately does *not* preserve the popultion distribution.
Instead, it samples fewer items fromt he most dense areas ofg
the distribution in order to preserve samples of as many
clusters as possible.
BUG FIXES
o Fixed a bug in the definiton of the Goodman-Kruskal
similarity measure, where half a term (inside a "max"
computation) had been accidentally omitted.
CHANGES IN R VERSION 0.1.0
NEW FEATURES
o Initial version. Classes BVinaryMatrix and DistanceVis,
although the first may be misleading and the second is a lousy
name. Both may change by version 1.0.
BUG FIXES
o Numerous.