Changes to the earth package

5.3.3 Feb 16, 2024

Updates for R version 4.3.2.
For example, had to change "sort.unique" to "sort_unique".

On leaps.f, changed "IF (NBEST .GT. 0)" to "IF (NBEST .GT. -1)" in subroutines
FORWRD and BAKWRD in order to match corresponding changes in the leaps package.

Removed dependency on possibly orphaned package TeachingDemos.

5.3.2 Jan 26, 2023

Modified use of "bool" in the C code to conform to C23 (which predefines "bool").

Changed sprintf to snprintf to prevent a warning in the Debian build for CRAN.

Changed the "NEWS" filename to "", and changed it to markdown format.

Earth now issues an error if colnames in x are duplicated because of factor expansion.
Thanks to Jens Heumann at Jacobs Center UZH for spotting this.

5.3.1 July 19, 2021

Minor updates for R version 4.1.0:

o Updates to the test scripts for ordered factors.

o Update to the code that reports missing arguments.

5.3.0 Oct 10, 2020

Fixed a minor bug where occasionally, for binary variables,
earth put a 1 when it should have put a 2 into the dirs matrix.
The bug was invisible unless you accessed earth's dirs matrix directly.
In some circumstances this fix may cause earth to build slightly different
models (an internal boundary check for almost-zero in earth.c was modified).
Thanks to Max Kuhn for reporting this issue.

Updated the .c and .h files to use the more modern header
file <stdbool.h> where appropriate (i.e. when not in an R environment).
We now also check that sizeof(bool)==sizeof(Rboolean) when called from R.

Updated some trace prints in earth.c (only affects very high trace levels).

Test suite additions: Added test.earthc.gcc.bat and
test.earthc.clang.bat. Extended inst/slowtests/test.earthc.c to
include binary predictors. Added test.numstab.R to test models which
are known to give (slightly) different results with different
compilers. Extended the clang tests. We now use version VC16 (Visual
Studio 2019) of the Microsoft compiler. Miscellaneous other test updates.

Minor documentation updates.

5.2.0 Sep 15, 2020

Earth now has better support for models with unusual variable names:
for example, variable names with spaces in them, and formula terms
like "as.numeric(x1)".

Earth model selection graph:

  * The text "selected model" is now first in the menu.
  * Minor adjustments for vertical lines which overlay each other.
  * The graph with nprune or pmethod="cv" models is now a little clearer.

Better support for residual plots for earth-glm models.

By default, plotmo now plots the offset if specified in the
earth model formula.

Under certain circumstances when nprune was used with pmethod="cv", would issue an incorrect error message.
Fixed that with help from Boris Leroy at the
Museum national d'Histoire naturelle (Paris).

Earth objects now have a "modvars" field. See the help page for earth.object.
Earth objects no longer have a "" field, and the "namesx" field
is deprecated. These fields have been subsumed by the "modvars" field.

Updated the libraries shared with the earth and plotmo packages.
Support for unusual variable names (mentioned above) required a
fairly substantial change to the internal handling of formulas. It
also affected the code that selects which variables to plot in plotmo.
For easier maintenance, the source file earth.R was split into earth.R,, and earth.prune.R.  The new file naken.R was added for
handling model variables.

Extended the test scripts and updated them for R version 4.0.2.
Added new test files test.emma.R and test.ordinal.R.

Some documentation updates.

5.1.2 Nov 4, 2019

Changed the type of the "lindeps" argument of the Fortran subroutine
"SING" from LOGICAL to INTEGER, to satisfy a CRAN check.

Improved handling of linear dependencies in bx (before the backward pass),
although it is unlikely that such dependencies would exist in any earth model.

Improved error reporting in leaps routines, although it is unlikely that
such errors could occur in earth.

Updated test scripts for the new random number generator
that came with R version 3.6.0.

5.1.1 Apr 11, 2019

Earth now runs with R versions 3.4.0 or higher (whereas before
the R version had to be 3.5.0 or higher).  This restriction was lifted
after running the tests in earth/inst/slowtests on R version 3.4.0.

Minor updates to libraries shared with plotmo and rpart.plot.

5.1.0 Apr 3, 2019

Fixed a formatting bug in the trace output for cross validation.
Thanks to Dirk Eddelbuettel.

Fixed small memory leaks that sometimes occurred in the C code if error()
was invoked or the user hit ^C.  Changed the way memory is protected
in allowed.c to pacify CRAN rchk.  Thanks to Tomas Kalibera.
Changed the name of the fallback memory release function to FreeEarth
(it was FreeR) and made it suitable for use in environments other than R.

If nfold > 1 and keepxy = 2, we now use keepxy=TRUE on the fold models. This
allows and plotmo on the fold models e.g. plot(mod$cv.list[[3]]).
Also updated plotmo to remind user of this.

Tweaked the trace message that is issued when glm doesn't converge.

Documentation and test code updates.

5.0.0 March 20, 2019

Two-column binomial pair responses are now handled in a way that is more
consistent with glm() i.e. regression on the fraction_true, weighted by
the response rowsums.  We now support cross-validation of binomial
pair models.  The function expand.bpairs was added.  We no longer
supports multiple-response binomial-pair models, and the bpairs
argument is thus no longer necessary (i.e. we support a maximum of
one binomial-pair response; the fact that the response is a
binomial pair is automatically detected when family=binomial).

We now save some additional GLM stats with earth-glm models. Some error
message have been improved.  For earth-glm models now returns
the earth-glm coefficients (for these models, use,
type="earth") to get the internal earth model coefficients).

We now support "+" on the left side of formulas to specify multiple responses.
Scale.y now works as documented for multiple response models.

Fixed a bug where issued an incorrect error message under
certain conditions when a factor was passed as a string in the newdata.
(This was the same as the old predict.lm "xlevels" bug.)
Thanks to Meleksen Akin for help here.

Fixed a bug where sometimes logical variables weren't displayed by plotmo if
there were also factors in the model (you had to use all1=TRUE in plotmo).

The model plot now avoids displaying ".5" in the Number Of Terms axis.

Changes to some prints (mostly whitespace), for clarity.
Updates to the documentation and shared libraries.

4.7.0 Jan 2, 2019

Earth no longer ignores the offset term in formulas.
Thanks to Dag Johan Steinskog for help on this.

The names of factor arguments are now handled slightly differently in
the x argument for earth.default. This prevents a problem where plotmo
mistakenly mistook certain models for an intercept-only model.  (The
models in question are those built with earth.default with a factor
as the only column in the x matrix.)

The type arguments for and were tweaked.
For earth-glm models, now plots the "response" residuals.
For the behaviour of previous versions with earth-glm models, pass
type="earth" to to plot the earth (linear) residuals.

Added some extra information to summary(glm.model).
It now prints the AIC and the deviance ratio (defined analogously
to RSquared as 1 - deviance / null.deviance).

The function now includes summary of the weights and
offsets, if any.

For multiple-response models with weights, the weights are now
accounted for when calculating the per-response GRSq (and not
just for the overall GRSq).

With plotmo(earth.model, all1=TRUE) now really plots all variables,
(including variables that aren't used in the model).

Added "LazyData: yes" to the DESCRIPTION file.

Touch ups to documentation, code, and test scripts.  Minor changes
to prevent warnings when options(warnPartialMatchArgs=TRUE).

4.6.3 May 7, 2018

Earth's "allowed" argument was ignored when used with R version 3.5.0
(because of the byte compiler in that new version of R). Fixed that by
internally in earth invoking .Call("ForwardPassR") instead of .C("ForwardPassR").

The vignettes are now compressed with gs and qpdf as in tools::compactPDF,
(but that happens outside the standard CRAN build system).  It does mean
that the tar.gz file for earth is a little smaller (now 1342 kByte).

Made some internal changes to earth.c to quieten minor clang warnings.

4.6.2 Mar 20, 2018

Minor documentation updates for the Auto.linpreds argument.

4.6.1 Mar 1, 2018

Added support for package gam version 1.15 and higher (the S3 class of
gam objects changed from "gam" to "Gam" to prevent clashes with the
mgcv package).  Earth variance models now work with both the old and
new versions of gam.

4.6.0 Dec 14, 2017

Added the Auto.linpreds argument. See the earth help page for details.
Thanks to Ceyda Yazici for help on this.

Further extensions to argument handling with pmethod="cv"
(necessary when formula is a local variable in function calling earth.formula).

4.5.1 Jul 26, 2017

With pmethod="cv", you can now use arguments like "thresh" when earth
is called in a function for which "thresh" is a local variable.
Thanks to Matthew Watkins for help on this.

4.5.0 Apr 20, 2017

Removed trailing NULL entries in R_CMethodDef and R_FortranMethodDef to
match changes to Rdynload.c in R core source code above version 3.3.3.

4.4.9 Feb 19, 2017

Fixed missing terminal entry in rentries.c:fortranEntries.
Minor tweaks to C and Fortran files for clang and vcc warnings.

4.4.8 Feb 18, 2017

Minor updates to
  Fixed a problem which can occur when the new x is a vector.
  We return NA if variables are missing in newdata.
  Extended the tests for in the slowtests directory.

We now call R_init_earth (to quieten CRAN check complaints).
To do that, added the file rentries.c and made changes to ForwardPassR.

Minor documentation updates.  Added DOI references to Friedman's papers
in the help pages as requested by Uwe Ligges.

4.4.7 Oct 18, 2016

Updates to the documentation and to the libraries
shared with plotmo and rpart.plot.

4.4.6 Sep 5, 2016

Added ... to argument list for all plotmo.* functions
for compatibility with plotmo version 3.2.0 and higher.

Tweaked leaps.f to eliminate gfortran warnings about the
deprecated way that DO loops were terminated.

4.4.5 Aug 19, 2016

Fixed issue in earth.c with the latest gcc which calculates a
negative almost-zero GRSq (something like -1e-17).
This messed up the test scripts because it printed as -0.0000.

Merged the library source file lib.R with the plotmo and
rpart.plot packages's lib.R.

Updated cross-validation section in vignette.

4.4.4 Jan 08, 2016

Fixed error message when predicting with a weighted model with a factor variable.
Thanks to Damien Georges.

Added a few type casts needed for clang and for matrices bigger than 2GB.
Thanks to Todd Rudick.

Removed a leftover debug call to cat("gc\n").
Thanks to Dirk Eddelbuettel.

Updated some stale web links in the documentation.

4.4.3 Sep 26, 2015

Minor changes to satisfy CRAN checks.

The print_summary function now has special handling for lists.

The stopifnot.identifier function now allows ":" in identifier names.

4.4.2 Jun 24, 2015

In we no longer unnecessarily issue the message:
   variable 'foo' was fitted with type "nmatrix.1"
   but type "numeric" was supplied

4.4.1 Jun 17, 2015

Fixed an issue with earth's interaction with caret in certain
situations. Thanks to Alexios Ghalanos for help on this.

Documentation updates.

4.4.0 May 29, 2015

Changes to earth.c. The following changes mean that earth will
produce slightly different models from previous releases:

    o For minspan counting in interaction terms, we now only count cases
      that are supported by the parent term (i.e., cases that are in the zero
      part of the parent hinge are not counted).  This makes earth more
      robust against overfitting on the edges of the training predictor space.
      In previous versions, earth could create a hinge at the edge of the
      predictor space, then crank up the hinge coefficient to a huge
      value because of one or two outlying cases. This is now less likely.
      Thanks to Louise Corron at Universite Aix-Marseille for help
      characterizing this.

    o Modified the code for weighted models, mostly for consistency with
      non-weighted models.

    o Changed a numerical tolerance in FindKnot for better support of
      "sawtooth" responses (responses which sharply zigzag up and down as
      the predictor increases).  The numerical tolerance was changed because
      we were seeing a breakdown caused by the the strategy of "start at one
      end of the predictor range and search downwards for knots".  The
      asymmetrical nature of this search tends to honor potential knots at
      the high end of the predictor range at the expense of knots at the
      low end before numerical tolerances kick in.  Thanks to Greg Jensen
      at Columbia for help on this.

    o Other minor updates, particularly to trace prints. Values that
      are almost zero are now printed as zero, for more consistency
      in trace prints across different architectures.

The weights argument has now been comprehensively tested and the
warning "support of weights is provisional" is no longer issued.

Earth now supports pmethod = "cv", which uses cross-validation to
select the optimum number of model terms.
Thanks to the sabermetrician Jonathan Judge for help on this.

Earth now supports bigger models with less memory thrashing.  It calls
gc() internally where necessary.  Leverages are calculated only for
non-big models (since memory use peaks when calculating leverages).

The model selection plot has had various enhancements.

Various other minor code and documentation updates.

4.3.0 Apr 30, 2015

We now support data matrices bigger than 2GB.

The function now invokes plotres in the plotmo package.
Reparameterized the argument list of, but maintained
back-compatibility by using the "dots" routines.

Numerous minor code clean-ups.

4.2.0 Jan 12, 2015
    o Changed the default color scheme to black and red (was black and lightblue)
      for consistency with plot.lm and similar functions, and for readability.
      A result of this change is that col.line is now once again called col.rsq.
    o The type="pearson" arg is now type="student", since the stddev
      estimated by the varmod now includes a leverage correction.
    o The versus arg now takes numeric values, and can be used to plot
      the residuals versus the response or the leverages.
    o Added "abs" to displayed spearman correlation text to minimize confusion.
    o The error handling for the versus argument is improved.

minspan and endspan:
    o The positioning of knots is now more symmetrical (in that we now have
      an equal number of skipped cases at each end of the predictor range).
    o We always allow at least one knot, even if endspan and minspan are such
      that no knots would normally be allowed (endspan and minspan overlap).
    o Added the Adjust.endspan argument to reduce the possibility of an
      overfitted interaction term supported by just a few cases on the
      boundary of the predictor space.

variance models:
    o Variance model residuals now use the predicted value instead of the
      mean out-of-fold values.  This is simpler, and gives better results
      in simulation.  A consequence is that the legal values for
      predict.varmod's type argument have changed.
    o The convergence criteria for residual model IRLS was modified and
      non-convergence is better reported.

The intercept-only RSS with weights is now calculated correctly in earth.c.
Weights are now better tested.

The Get.crit argument was removed from  No longer needed.

RSq's and GRSq's that are within 1e-5 of zero are now set to zero to facilitate
testing across machines in the presence of numerical error,  especially
when case weights are used.

Increased MaxAllowedRssDelta in earth.c because it was a bit too conservative.

Updated the vignettes and help pages, and some error messages.

4.1.0 Dec 17, 2014

Added clang to the slowtests suite, and cleaned up minor warnings issued by clang.

Forward pass termination messages are now similar in R and C code.

The internal variable "reason" is now named "termcond".

Documentation improvements.

4.0.0 Dec 12, 2014

Earth now supports prediction intervals.  See earth's new var.method
argument, and the new vignette.  The function now has
"interval" and "level" arguments.  The residual plot of now
shows prediction intervals if available.  The new version of plotmo
will also show earth prediction intervals.

Case weights are now supported but are not yet comprehensively tested.
The current implementation of case weights is slow.

The and function now print the reason
the forward pass terminated.

The ordering of terms in was changed slightly: within
term pairs, the term for "predictor less than hinge" is now placed
before the term for "predictor greater than hinge" (so for example,
h(16-Girth) is before h(Girth-16)}.  This was done to make model
interpretation slightly easier.

Predictors that are discovered to best enter linearly (no knot) are
now printed without a knot by, to make model
interpretation a little easier.  Also, their entry in the dirs matrix
is now 2, the same as predictors that are forced to enter linearly
by earth's linpred arg.

The minspan argument can now take negative values, to specify the
max number of knots per predictor (as opposed to the spacing between
the knots).

Earth now has an endspan argument.  The default endspan=0 gives
the previous behaviour.

The linpreds argument now accepts variables specified by name.

Earth now accepts nk=1 to force an intercept-only model (in previous
versions, nk had to be at least 3).

DUP is now always TRUE in internal calls to C function, to satisfy
CRAN checks.  Sadly, this means that the earth forward pass uses
more memory (because all the argument data is duplicated when
handing over to C).

The comprehensive (but slow) earth tests are now in inst/slowtests.
As always, the tests in earth/tests just do a basic test of
portability problems.

"cv.rsq" is now consistently "CVRSq".

In the earth C code, QR_TOL is now 1e-7 (was .01) to match
lm's use of tol=1e-7 for dqrdc2.

The GLM types for are now prefixed by "glm.",
and type="pearson" now returns the pearsonized residuals.

Various other minor tweaks, improvements to error messages, etc.

Changes to has some new arguments, including info,
  delever, pearson, level, and versus.

  The which argument now has extra values 5:8, to plot
  residuals vs log fitted values etc.

  The residuals plot now has a symmetrical y axis to make asymmetry
  in the point cloud more obvious (see the center argument).

  Graphics arguments to are moved down so the more
  important arguments are earlier. now has an xlim argument, and the ylim argument can
  now be used on any plot (not just the Model Selection plot),
  providing it is the only plot (length(which == 1).

  Some args are deprecated or changed (you will get an
  informative message if you use them).  The changes were
  made for consistency with similar arguments elsewhere.
      --Old--        --New--
      col.rsq        col.line
      col.residuals  col.points
      nresiduals     npoints
      col.legend     use legend.pos=NA for no legend

  If 1 is in the "which" arg to, then ylim is used
  for the Model Selection plot, else it is used for the
  Residuals vs Fitted plot.

3.2-7 Jan 28, 2014

Tweaks to standalone version of earth for clean compiles with certain 64 GCC builds.
plot.evimp now works with intercept-only models.
Other minor tweaks to plot.evimp.
Clerical changes to satisfy recent CRAN checks.

3.2-6 Apr 15, 2013

Added style="C".
Included the leaps package files into the earth package, to prevent
  warnings from CRAN check about earth's use of internal leaps code.
  Removed "Depends: leaps" from earth's DESCRIPTION file.
Lin deps discovered by leaps are now slightly better handled.
Small changes to earth.c and earth.h for stand-alone builds.
Added sections to the FAQ on using earth for
  binary and categorical responses.
Added a section to the vignette on building a model
  based on cross validation results.
Removed trace=4 from so a non-problem is no longer
  reported due to minor numerical differences across architectures.
Reduced the number of digits printed in some of earth's trace messages.
  This makes trace results more consistent across different architectures
  (the ls digits are often in the numerical noise floor).
We now print a max of 20 columns of a matrix when tracing.
The legend.text arg of now works correctly.

3.2-3 Apr 27, 2012

Incorporated Glen Luckjiff's patch to fix"terms")
  failure when bx had just two columns.
We no longer call fflush when in an R environment.
The tests/ code now uses the tree rather than the ozone1 data,
  in an effort to get test consistency across different architectures.
Added .Rinstignore to drop inst/docs/figs files (prevents note in CRAN build).

3.2-2 Mar 14, 2012

We no longer pass R_NilValue from the R code to the C code.
Incorporated Olaf Mersmann's patch for POS_INF with the INTEL_COMPILER.
Code touchups for Microsoft Visual Studio 2010.

3.2-1 Jul 19, 2011

  Documentation touchups.

3.2-0 Jun 19, 2011

The PDF file is now a standard vignette (but with no executable code).
The "Importances" printed by are now a maximum of option("width") wide.
We no longer warn "effective number of GCV parameters >= number of cases"
   but instead set such GCVs to Inf, so GCVs are now always
   non-decreasing with the number of terms.  Documented as FAQ 12.11.
The earth C routines now print memory allocations if trace=1.5.
The pnTrace arg to ForwardPassR is now a double and called pTrace (allowing trace=1.5).
The default nk is now clipped at 200.  This limits the amount of memory
   needed in the forward pass for large x matrices.  Numerical limits
   will probably kick in before 200 are reached anyway.
We now force Use.beta.cache=FALSE with a message if the beta cache would
   be more than 3 GB. now warns if illegal arguments are passed.
Documentation touched up.

3.1-1 Jun 15, 2011

Documentation emendations.
We now issue a warning if user uses a CV arg to but no CV data to plot.
The CV summary print no longer prints the 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 args to
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, mostly for cross validation.
The default for evimp's "sqrt." argument is now TRUE. 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 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
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$cv.list) thus has better legends.

Cumulative distrib plots in now use the jitter arg, and'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 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  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 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 Jerome Guelat for letting me know about this.)

2.3-4 Sep 21 2009

. Fixed bug where 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
    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
Added sqrt. argument to evimp
Added more grid lines to cumul density plot in
Added a help page section on interpreting the graphs in
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
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 is now handled as documented in earth.formula
Added style="bf" to and
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
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 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, allows use of evimp.
Added valid.names argument to 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 has changed to better deal
   with multiple response models, see the "style" argument.
Added namesx and 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 printed the wrong number
of cases for multiple response models.

1.3-1 Mar 22 2008

"" 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

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

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 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 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


Fixed a newvar.penalty bug introduced in previous release.
Added src/tests/test.earthmain.gcc.bat
More man page tweaks


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


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.


Changed as.matrix to data.matrix in earth.default -- grep for FIXED
Extended earth.Rd slightly


Added my web page to DESCRIPTION and to some man pages


Changed \r\n to \n to pacify CMD CHECK


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


Fixed bug where plotmo failed under these circumstances:
    form <- Volume ~ .; a <- earth(form, data = trees); plotmo(a)


Minor change to formatting.  Man page fixes.

1.0-6 May 11 2007

Initial release