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@template with inline functions
(@template has been deprecated)..drawEllipse and .scorePlot to
avoid use of the plyr package which is retired.ChemoSpec and ChemoSpec2D gain the ability to
produce ggplot2 and/or plotly graphics, which
required changes here in ChemoSpecUtils. See the news files
for ChemoSpec and ChemoSpec2D for more
details.R r80087.... in sumSpectra
corrected to show how to pass tol to
check4Gaps. Affects ChemoSpec only at this
time.Col7 added to the color
options.rowDist, which supports a number of functions,
was overhauled to address confusion in the documentation, and in my
head, about distances vs. similarities. Also, different definitions
found in the literature were documented more clearly. The Minkowski
distance option was removed (ask if you want it back), code was cleaned
up, documentation greatly improved, an example was added and unit tests
were added. Plot scales were also corrected as necessary. Depending upon
which distance option is chosen, this change affects
hcaSpectra, plotSpectraDist,
sampleDist and hcaScores in package
ChemoSpec as well as hats_alignSpectra2D and
hcaScores in package ChemoSpec2D..shrinkLeaf now shrinks the size of leaf
labels more aggressively as the number of samples increases.ChemoSpec and
ChemoSpec2D.removeFreq.Spectra now accepts a formula for
rem.freq.sampleDist, distPlot,
sampleDist.Spectra and sampleDist.Spectra2D;
sampleDist.Spectra moved here from ChemoSpec
or created anew, with changes to the plot details for consistency
between the two classes..getLimits now knows how to handle negative values in
the formulas.sumSpectra.Spectra now respects/accepts the
... argument, used to pass tol. This was
accidentally disabled. ## Misc.chkSpectra methods now check for duplicated sample
names.plotScores now accepts user supplied values for
xlim and/or ylim; the default calculation is
still available.tinytest.rowDist(..., method = "cosine") now has a unit
test.dontrun sections in examples, needed for last
submission.getVarExplained handles this common task
for all data reduction methods.plotScree.mia was eliminated via the
introduction of .getVarExplained and small changes to
plotScree.default.conColScheme was moved from ChemoSpec to
ChemoSpecUtils so it could be readily available for
Spectra2D objects. It was also re-written in the style of
updateGroups for consistency and user-friendliness.colorSymbol was moved from
ChemoSpec to ChemoSpecUtils.plotScores was fixed. This was a long standing bug that
somehow escaped notice (dating to the first few months of
ChemoSpec!)..getVarExplained was returning the eigenvalues, not the
percent variance explained, for class(mia). This affected
scree plots for class(mia) in
ChemoSpec2D.plotScores was no longer including the percent variance
explained in score plots, if xlab and/or ylab
were not provided. Fixed.chkSpectra.Spectra2D would fail if there was only one
sample when checking to see if NAs were present in the same positions
across all data sets. Fixed.rowDist. The previous version was giving slightly wrong
answers.updateGroups now reports the old groups if
new.grps = NULL, as intended and claimed in the
documentation.plotScree now knows what to do with class
princomp..chkArgs since errors were introduced
via the most recent “fix”! Updated unit tests for the function, but even
more work should be done there. Using
HandyStuff::examplePage to look for errors and warnings.
None found..chkArgs(mode = 13) that was giving
an error in ChemoSpec::r_pcaSpectra.updateGroups..groupNcolor
(the problem seems to have been present from the very first version of
ChemoSpec). Reported by Reinhard Kerschner (many
thanks!).check4Gaps gap checking more robust, with better
examples and documentation. If no gap found, a data frame with one row
is returned. In turn, this required changes over in
.binData and binSpectra which are in
ChemoSpec. In addition, while check4Gaps still
accepts an argument tol no other functions are using it,
and a much more suitable default value is computed in
check4Gaps rather than being computed in another function
and passed here..chkArgs.sumSpectra output format.removeGroup and removeSample go full S3
dispatch for consistency among the three packages.ChemoSpec2D.hcaScores moved from ChemoSpec and
converted to S3 dispatch.chkArgs and associated unit tests added,
but it is not yet used in any of the other functions.Seems to work correctly on behalf of ChemoSpec and
ChemoSpec2D devel versions.
chkSpectra,
removeFreq, sumSpectra,
sumGroups.ChemoSpec2D for CRAN,
temporarily.ChemoSpec >= 5.0..groupNcolor added with argument mode.addLegend gets an example.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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