https://github.com/cran/earth
Tip revision: 8724a4f35c66c4fac196b09beb8fb703d6caeaae authored by Stephen Milborrow on 15 June 2011, 18:00:33 UTC
version 3.1-1
version 3.1-1
Tip revision: 8724a4f
NEWS
Changes to Earth Package
------------------------
3.1-1 Jun 15, 2011
Documentation emendations.
We now issue a warning if user uses a CV arg to plot.earth but no CV data to plot.
The CV summary print no longer prints response name for single response models.
3.1-0 Jun 14, 2011
print.evimp now formats the results a little differently (more clearly).
"Reached min GRSq" and similar trace messages now also print the number of terms.
The min auto-calculated ylim in model selection plots is now clamped at -1.
Added the col.residuals, col.pch.max.oof.rsq, and col.pch.cv.rsq args to plot.earth.
Cross validation with wp no longer gives an error message.
Revised the documentation.
3.0-0 Jun 10, 2011
Created the vignette earth-notes.pdf which collects and extends
documentation that was previously in the help files.
Revamped cross validation. New argument "ncross" to earth.
Extended plot.earth, mostly for cross validation.
The default for evimp's "sqrt." argument is now TRUE.
plot.earth now uses lowess rather than loess (loess tends to issue ugly warnings).
Removed earth's Print.pruning.pass argument.
Earth now uses less memory if passed an x matrix of doubles. Earth's memory report
(with trace>=4) was not accurate in all cases and has been removed.
Tweaked the Author: entry in DESCRIPTION for better results from citation().
Other minor touchups.
2.6-2 Apr 25, 2011
Moved plotmo.methods.earth.R to here so the plotmo package is independent of earth.
Modified test scripts to conform to R 2.13.0's way of printing numbers.
2.6-1 Apr 13, 2011
Fixed an issue of dependency on the plotmo package.
2.6-0 Apr 12, 2011
Moved plotmo to the plotmo package, and added "depends plotmo" to earth's DESCRIPTION
Added the Exhaustive.tol arg as a work-around for leaps.exhaustive error code -999
(Thanks to David Marra for help tracking this down.)
The "Exhaustive pruning" pacifier is now printed based on the number of subsets
Warnings from leaps routines are now treated as errors (because ret val is bad with warning)
Replaced n=2 and similar in calls to eval with an explicit environment
The decision to use eval.subsets.xtx is now more automatic and less obtrusive
The response y is now named in certain situations where it used to be unnamed
Removed annoying warning "specified nprune 20 is greater than the number of model terms"
Some code tidying
2.5-1 Mar 25 2011
Modified handling of illegal arguments
2.5-0 Mar 24 2011
Changes to plotmo:
The arguments were reordered (moved the most important arguments first).
The ycolumn arg is now called nresponse and handled more consistently.
The degree2="all" setting is now replaced by all2=TRUE, likewise for degree1.
The default for the type argument is now object dependent.
The cex parameter is now supported, and text is a little larger for most plots.
The degree2 graph titles now have a space for readability.
There is some minor backwards incompatibility in the minor arguments.
The plotmo graphs are now ordered on the variable order, for all model classes.
Plotmo now handles a wider range of object classes.
Factor predictors are now plotted in degree2 plots.
Miscellaneous other touchups.
2.4-8 Mar 05 2011
plotmo now handles vector colors better
plotmo is now better at plotting lda and qda models
Added the jitter.response argument to plotmo
Moved plotmo method functions into a new file, plotmo.methods.R.
2.4-7 Feb 02 2011
Intercept-only models are now better supported, esp. for earth-glm models.
Martin Renner and Keith Woolner provided the impetus for this change.
Legend arguments are now handled better in plot.earth.models.
A vector legend.text is now handled correctly and you can use
values like "topleft" in legend.pos (thanks to Gavin Simpson at ECRC).
The elements of cv.list in earth's returned value are now named,
and plot.earth.models(model$cv.list) thus has better legends.
Cumulative distrib plots in plot.earth.models now use the jitter arg, and
plot.earth's (pointless) jitter argument has been removed.
A few code and doc touchups were also made.
2.4-6 Jan 26 2011
Made the following changes to plotmo:
We now print the fixed grid values unless trace < 0.
The degree1 and degree2 arguments now have an "all" option.
We now have better support for rpart objects
The cex arg is now also used for response values (with cex.response!=0).
Added cex.lab argument.
For factor predictors we now print the factor levels vertically along the x axis.
Fixed crossed type.gcv and type.rss args in plot.evimp.
Fixed residuals.earth to handle vector responses correctly.
(Thanks to Gavin Simpson at UCL for providing fixes for the above bugs.)
plot.evimp now doesn't use on.exit(par(no.readonly=TRUE)), so we
now allow subsequent plots on the same page with mfrow != c(1,1).
Did the usual document touchups.
Minor cleanups for R check (partial arg matches).
2.4-5 Oct 30 2010
Plotmo now better handles the "data" argument for earth.formula models.
(Thanks to Keith Woolner for spotting that this was previously incorrect.)
2.4-4 Oct 6 2010
NAs are now allowed in the data passed to predict.earth. The predicted value
will be NA unless the NAs are in variables that are unused in the earth model.
2.4-3 Sep 29 2010
For certain data we were seeing duplicated term names for cuts that
are very close to each other. To avoid this you can now use
options(digits) to increase the number of significant digits used
when forming term names. (Thanks to Keith Woolner for spotting this.)
2.4-2 Aug 28 2010
We now give the correct error message for attempted cross validation of
paired binomial responses (which is not yet supported).
Labels on the largest residuals in plot.earth graphs are now slightly
better positioned (using plotrix::thigmophobe.labels).
plotd now handles qda objects in the same manner as lda objects
Other doc touchups.
2.4-0 Nov 8 2009
This version of earth will build models SLIGHTLY DIFFERENT FROM PRIOR VERSIONS,
because I fixed a bug in the calculation of minspan and endspan.
Use minspan=-1 for backwards compatibility.
(Thanks to Gints Jekabsons for spotting this.)
2.3-5 Oct 7 2009
Fixed bug where glm.control args were ignored under certain circumstances
(Thanks to Jérôme Guélat for letting me know about this.)
2.3-4 Sep 21 2009
. Fixed bug where predict.earth of a earth-glm model under R 2.9.0 and higher
incorrectly gave the message: Object of type 'closure' is not subsettable
(Thanks to Thomas Brockmeier for help tracking this down.)
. plotd now correctly ignores the vline if vline.col=0
. Doc touchups
2.3-2 Mar 23 2009
Extended plotd
Doc touchups
2.3-1 Feb 26 2009
Doc touchups
Added leaps::: prefix needed for new version of the leaps package
Added style="max" to summary.earth
Added labels param to plotd
Reordered some of earth's arguments
2.3-0 Feb 18 2009
Added the plotd function
Removed some restrictions on type="class" in predict.earth
Added sqrt. argument to evimp
Added more grid lines to cumul density plot in plot.earth
Added a help page section on interpreting the graphs in plot.earth
Miscellaneous other touchups to code and docs
2.2-3 Feb 2 2009
Added levels to the return value
Added type=class and thresh arguments to predict.earth
Thanks to Max Kuhn for suggesting these improvements
2.2-2 Jan 30 2009
Doc touchups
Cross validation MaxErr is now signed
2.2-1 Jan 22 2009
Added cross validation i.e. the nfold and stratify parameters.
We now scale y before the forward pass, for better numeric stability in
the forward pass with very big or very small y's.
For the old behaviour, set earth's new argument scale.y=FALSE.
Added get.pairs.bagEarth so plotmo prints degree2 plots for caret:bagEarth models.
Changes internal to earth.c:
High values of trace argument are treated differently
ServiceR (to allow interrupts) is called more consistently for large datasets
Delta RSS handling is simplified
Changed some var names for consistency
The last two were a byproduct of experimental changes to earth that
were not included in this release.
Changed documentation to American English.
2.1-2 Nov 18 2008
Touched up evimp help page.
2.1-0 Nov 15 2008
plotmo now has better support for factors and for glm models
na.action (always na.fail) is now handled as documented in earth.formula
Added style="bf" to format.earth and summary.earth
Fixed a few minor bugs and touched up documentation for evimp
2.0-6 Oct 30 2008
You can now pass only the needed subset of columns to predict.earth
Added plot.evimp
Removed spurious warning "Need as many rows as columns"
2.0-5 Jul 14 2008
Touched up documentation for format.lm.
2.0-4 June 22 2008
Touched up code and documentation for a zero thresh value.
2.0-3 June 22 2008
Zero values are now allowed for earth's "thresh" parameter (previously if
you used thresh=0, thresh was clamped internally to 1e-10).
Also, if thresh=0, the MAX_GRSQ forward pass condition is ignored.
The idea is to get as close to a big nk as possible
Changed "valid.names" argument of format.earth and format.lm to "colon.char"
which achieves the same end more simply.
2.0-2 June 15 2008
Added column names to results of mars.to.earth, allows use of evimp.
Added valid.names argument to format.earth and format.lm.
2.0-1 June 10 2008
Added "namesx" and "first" arguments to the "allowed" function.
evimp() for a scalar x now returns a matrix (I added a missing drop=FALSE).
2.0-0 June 07 2008
Added support for glms and factors (but plotmo does not yet support factors).
Added variable importance function "evimp".
Added response weights argument "wp" to earth.
Output of summary.earth has changed to better deal
with multiple response models, see the "style" argument.
Added namesx and namesx.org to earth's return value.
1.3-2 Mar 29 2008
Fixed two bad multiple response bugs:
a) for multiple reponse models, earth calculated the wrong null RSS and
therefore the wrong RSq and GRSq for the sub-models. (The total
RSq and GRSq were correct.)
b) the wrong betas were used when pruning multiple response models.
Also fixed a bug where summary.earth printed the wrong number
of cases for multiple response models.
1.3-1 Mar 22 2008
"update.earth" now has a "ponly" argument, to force pruning only.
Because of this change, the "ppenalty" argument to earth is no longer
needed and has been removed.
Revisited text of warnings after I was bamboozled by one of
my own warnings.
Tweaked legend positioning in plot.earth.models.
1.3-0 Mar 18 2008
Default minspan is now 0 (was 1) for compatibility with mda:mars and
Friedman's MARS paper (I've flip flopped on this one). This means
that models built with the default args will be little different to
before.
Earth's peak memory is now about 40% less.
Big models are now more responsive to ^C.
For multiple response models, we now print response names in most
places instead of just "Response N".
Removed get.nterms.per.degree and get.nused.preds.per.subset from
NAMESPACE and from help pages, to simplify user interface.
Fixed some niggling document issues and extended the FAQ.
1.2-2 Jan 2008
print.summary.earth now prints the call even for x,y interface to earth
plotmo now accepts x matrices without column names
Tweaked FindKnot and OrthogResiduals for speed
Removed a few shadowed variables in earth.c after running gcc -Wshadow
Clarified some paras in earth.Rd, reduced page width for better html display
1.2-1
Fixed a newvar.penalty bug introduced in previous release.
Added src/tests/test.earthmain.gcc.bat
More man page tweaks
1.2-0
Added linpreds, allowed, and Use.beta.cache arguments
Anova decomp is now more consistent
Added a few GPL headers
Reinstated the beta cache
More man page tweaks
1.1-5
Fixed bug reported by Joe Ritzer: long predictor names got munged in plotmo
Changed "class" to "response" throughout when used for the
predicted responses in the input y.
Man page tweaks based on user feedback.
1.1-4
Changed as.matrix to data.matrix in earth.default -- grep for FIXED
Extended earth.Rd slightly
1.1-2
Added my web page to DESCRIPTION and to some man pages
1.1-1
Changed \r\n to \n to pacify CMD CHECK
1.1-0
Default minspan is now 1 (was 0)
Fixed potential crash in PrintForwardStep if nTrace>1
Added a missing drop=FALSE to backward()
Minor code, comment, and man page fixups
1.0-8
Fixed bug where plotmo failed under these circumstances:
form <- Volume ~ .; a <- earth(form, data = trees); plotmo(a)
1.0-7
Minor change to summary.earth formatting. Man page fixes.
1.0-6 May 11 2007
Initial release