NEWS

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Mercator 1.1.2 (2022-06-30)

CHANGES

• Changed the default clustering algorithm internally to the "Mercator" contructor to use "hclust" instead of "pam".

Mercator 1.1.0

NEW FEATURES

• Incorporated tywo new "views": self-organizing maps (SOM) and uniform manifold approximation and projection (UMAP).

Mercator 1.0.0 (2021-02-12)

NEWS

• Updated versio number to coincide with publuication of manuscript.

Mercator 0.99.0 (2021-01-10)

BUG FIX

• Updated vignette and manual pages in response to comments from reviewer of manuscript.

Mercator 0.11.5 (2020-11-12)

BUG FIX

• Added "flexmix" to dependency to work around a bug on CRAN's fedora machines.

Mercator 0.11.3

NEW FEATURES

• Added 'print' and 'show' methods to the BinaryMatrix class. .

Mercator 0.11.2 (2020-08-24)

NEW FEATURES

• 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.

Mercator 0.11.0

NEW FEATURES

• Edited the binary vignette for clarification and better examples.

Mercator 0.10.1

BUG FIX

• Fixed the bug with missing names on 'clusters' slot. Again.

Mercator 0.10.0 (2020-03-06)

NEW FEATURES

• Can now use 'slot(object, "palette") <- ...1 to change the palette associated with a Mercator object.

BREAKING CHANGES

• 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'.

Mercator 0.9.6 (2020-01-08)

BUG FIXES

• Fixed a bug in "addVisualization" to make sure all matrices have non-NULL rownames.
• 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.

Mercator 0.9.5 (2019-08-29)

BUG FIXES

• Fixed an igraph "jitter" bug in a test script.

Mercator 0.9.4

NEW FEATURES

• Added a new "barplot" method for the Mercator class, which plots the silhouette widths in the colors already assigned to clusters.
• Added a new "scatter" method for the Mercator class, which displays some views as a smoothed scatter plot.

Mercator 0.9.2

NEW FEATURES

• Added a new "plot" method for the Mercator class, which automatically sets the colors and symbols for different views.

Mercator 0.9.1

BUG FIXES

• Fixed the bug in overcounting "redundant" or "unused" features.

Mercator 0.9.0

BREAKING CHANGES

• Deprecated the "recolor" function in favor of a new name, "setClusters".

Mercator 0.8.8 (2019-08-02)

BUG FIXES

• Checked all the documentation; first version submitted to CRAN.

Mercator 0.8.7

BUG FIXES

• Fixed the "names" bug in using iGraph visualizations.

Mercator 0.8.2

FEATURES

• Added a (mostly) working vignette. (Is that a feature?)

Mercator 0.8.0

BREAKING CHANGES

• Renamed the "recoverCluster" function to "getClusters".

Mercator 0.7.8

BUG FIXES

• Fixed a NAMESPACE/DESCRIPTION issue to make it easier to work with slots borrowed from other classes.

Mercator 0.7.7

BUG FIXES

• Worked around an issue in igraph, which doesn't like layouts where nodes overlap.

Mercator 0.7.5

BUG FIXES

• Fixed a bug in igraph views, in order to work with more than 48 clusters.

Mercator 0.7.4

FEATURES

• Added a bunch of man pages (is that a feature?).

Mercator 0.7.2

BUG FIXES

• Fixed a bug in "downsample", where probabilities could be greater than one.

Mercator 0.7.1

BUG FIXES

• Fixed a labeling bug in "recolor".
• Updated data objects to use "Mercator" rather than "BinaryMatrix".

Mercator 0.7.0

BREAKING CHANGES

• Renamed the "DistanceVis" class to "Mercator".
• Renamed the whole package fromk "BinaryMatrix" to "Mercator"

BUG FIXES

• Fixed a "drop=FALSE" bug with subsetting "info" components when they are single-column data frames.

Mercator 0.6.2

NEW FEATURES

• Added a "recoverCluster" function to the "DistanceVis" class. May eventually be converted to a "predict" method.

BUG FIXES

• Fixed a "drop=FALSE" bug with subsetting "info" components when they are single-column data frames.

Mercator 0.6.0

NEW FEATURES

• Added new automatically computed graph layouts based on MDS and t-SNE.

Mercator 0.5.0

NEW FEATURES

• Added a new visualization, based on igraph.

Mercator 0.4.0

INCOMPATIBLE CHANGES

• 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

• 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.

Mercator 0.3.0

INCOMPATIBLE CHANGES

• 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

• Added a transpose ("t") operator for a BinaryMatrix.

Mercator 0.2.0

NEW FEATURES

• 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.

Mercator 0.1.1

NEW FEATURES

• 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.
• Added a "recolor" function thast allows you to make the color-and-symbol assigments for different distance matrices behave "as consistenbtly as possible".
• 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

• Fixed a bug in the definiton of the Goodman-Kruskal similarity measure, where half a term (inside a "max" computation) had been accidentally omitted.

Mercator 0.1.0

NEW FEATURES

• 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

• Numerous.