Changes to the plotmo package
-----------------------------

--- 3.3.1  Nov 24, 2016

When choosing which variables to plot for randomForest models,
variable importance is now calculated using a more correct measure,
viz. one of IncMSE or IncNodePurity (regression models), or
MeanDecreaseAccuracy or MeanDecreaseGini (classifications models).
The second option is used if importance=TRUE was used when building
the model.  Use trace=1 when calling plotmo to which measure of
importance is used.

The plot_gbm function now displays the gray vertical line at the
correct position when n.trees is specified.

Documentation touchups.

--- 3.3.0  Nov 11, 2016

Added support for partial dependence plots (the pmethod argument).

Extended the vignette with new chapters on partial dependence plots
and classification models.

Plotmo's nrug argument now supports quantiles.

The title on persp plots is now better aligned to the degree plot
titles.  The margins for persp plots are now more optimal (they now
give bigger plots when do.par=FALSE and there are also degree1 plots).

Added support for e1071::predict.svm decision.values and probability
arguments.

Fixed error message when plot_gbm was used on multinomial models.
Fixed warnings in plot_gbm when gbm.ntrees is very small (less than 10).

--- 3.2.1  Oct 27, 2016

Added support for gbm package version 2.2.  See gbm.backcompat.R.

Extended linmod.R: support for no-intercept models, support for
'keep' argument, better handling of newdata in predict.linmod.
Also extended the tests for linmod.R in inst/slowtests.

--- 3.2.0  Sep 7, 2016

The functions plot_gbm and plot_glmnet are now exported and available
for the user.  These functions have been enhanced for this version.

Improved support for gbm and glmnet and related models.

The plotres function now works better with caret "train" models
(but caret support is still a bit minimal).

We now print "plotmo grid:" instead of just "grid:" for context when
it's printed from within a body of code.

Removed deprecated interface functions like get.plotmo.pairs.

Updated dot library functions for eventual move to a dots package.

Revamped the vignettes.

--- 3.1.5  Aug 26, 2016

The pt.cex argument now works correctly in plotres QQ plots.

Changed default colors in plot.glmnetx.  The colors stay in the order
they are passed to plot.glmnetx as we move down the rhs of the plot.

Extended test suite to include adabag package.

Fixed code in meta.R which assumed all.equal() always
returned TRUE or FALSE.

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

Updated and extended vignettes.

--- 3.1.4  Jul 29, 2015

Added support for the adabag package.

Added imports for standard grDevices, stats, and utils
functions, as now required by CRAN check.

Documentation updates. Thanks to Achim Zeileis for his feedback.

--- 3.1.3  Jun 24, 2015

Added plotmo.prolog.cv.glmnet (to handle missing "call" in cv.glmnet objects).
More work on the issue where vars on the rhs of formula are multidimensional.
Documentation updates.

--- 3.1.2  Jun 15, 2015

Added the new vignette "Guidelines for S3 Regression Models".
Documentation touchups.

--- 3.1.1  May 27, 2015

Removed references needed for old versions of earth.  Fixed a
gbm column naming issue.  Other minor code and document updates.

--- 3.1.0  May 6, 2015

Removed references to functions in old versions of earth.

Simplified the way xlim and ylim are calculated internally.

Simplified the way jitter is handled.

If type="probability" or similar, and the response has two
columns, nresponse now automatically defaults to column 2.

Added support for biglm objects.  The predict.biglm method
(unnecessarily) requires that newdata has a response column, so
plotmo adds a dummy response column before calling predict.biglm.

We now find the data argument for formula models even if the argument
is unnamed.

--- 3.0.0  Apr 29, 2015

Added the plotres function.

Reworked the internal functions that get the data from the model.

Reparameterized the argument list of plotmo, but maintained
backwards compatibility using the "dots" routines.

--- 2.2.1  Jan 7, 2015

If pch.response has type character, we now plot the
response points as text.

Earth models with no degree1 terms but with degree2 terms were
incorrectly labelled as intercept-only models.  Fixed that.

Changes to match changes to earth's predict.varmod interval argument.

--- 2.2.0  Dec 10, 2014

Fixed incorrect printing of some messages when trace=-1.

Expansions to check.index for earth.

Documentation touchups.

--- 2.1.0  Nov 30, 2014

Added a vignette "Notes on the plotmo package".

Some more functions are now exported to allow
earth::plotmor to easily get the model data

Some documentation touchups as usual.

--- 2.0.0  Nov 19, 2014

Plotting of prediction or confidence levels is now more comprehensive.
We now allow both prediction and confidence intervals to be plotted
for those predict methods that support it on new data (currently only
lm).  The "se" argument is now deprecated and superseded by the
"limit" argument (you will get a warning).

Plotmo will now plot the model even if it is an intercept-only model.
Use int.only.ok=FALSE for the old behaviour (i.e., issue an error for
intercept-only models).

The "grid:" message in now printed for only multiple predictor models.
Remember that you can always suppress this message in any case with
trace=-1.

The xlim argument is now supported.  Typically only useful
if only one degree1 plot.

Plotmo now supports quantreg and quantregForest objects.

Basic support for the AMORE package has been provided.  Thanks to
Bernard Nolan and David Lorenz for this.  But this has been commented
out in the source code to avoid having "suggests(AMORE)" in the plotmo
DESCRIPTION file.  To use functions, search for AMORE in the plotmo
source code, and cut and paste the commented-out code into your
environmemt.

The default pch.response is now 20 (was 1).

The default cex.response is now NULL (meaning automatic, was 1).

Minor other changes to fix formatting of captions etc.

--- 1.3-3  Feb 4, 2014

Clerical changes to satisfy recent CRAN check requirements.

--- 1.3-2  Dec 1, 2011

You can now use trace=-1 to inhibit the "grid: " message.

Removed a call to .Internal(persp)

--- 1.3-1  Sep 16, 2011

Fixed an minor incorrect message introduced in the previous release.

--- 1.3-0  Sep 15, 2011

You can now specify variables by name in degree1 and degree2.
Suppressed annoying "Warning: surface extends beyond the box".
We no longer issue an incorrect err msg if data frame has an "AsIs" field.

--- 1.2-6

Removed an incorrect stopifnot.integer(y.column) in plotmo_y.wrapper

--- 1.2-5 Jun 11, 2011

Fixed an incorrect stop when trace>0 and x had no column names.
We no longer print the plot index in the plot title when all1 or
   all2 specified but also degree1 and degree2.
Added get.plotmo.default.type.fda
Touchups to the documentation.

--- 1.2-4 Apr 27, 2011

Removed hooks for the earth package (which are no longer necessary
with earth 2.6-2).  The file plotmo.methods.R was deleted.

Added the grid argument.

--- 1.2-3 Apr 17, 2011

This package no longer needs the earth package.  However the current
  earth (2.6-1) needs some hooks in this package to build.
  After earth 2.6-2 is on CRAN that will no longer be necessary,
  and the hooks will be removed from this package.
We now have better error reporting for bad y's.
We now have better jittering of response points with a binary response.

--- 1.2-0 Apr 12, 2011

Added ndiscrete arg (variables with a small number of levels
   are now plotted as "blocks", like factors).
Added smooth.col and related args (plotmo can add a loess line).
Made tweaks necessary because earth now imports this package.
Added dvalue and npoints args.
Added center arg (preliminary implementation).
Added basic support for lars, nnet, and knn3 models.
Jittering now works better.
We now jitter response points for factors and discrete variables by default.
plotmo is now faster:
   We cache the plot data to avoid calling predict twice for each plot
   For discrete vars and factors we only call predict for their original values
   ngrid1 is much smaller (ok to do that because of ndiscrete arg)
Better error reporting for illegal args.
Reduced the number of default colors (just grays and lightblue now).
Out-of-range values in image plots are now plotted in blue.
Fixed an issue where the wrong environment could be used.
Better error reporting for unsupported models.
Fixed handling of factors with non contiguous levels
Modified test scripts to conform to R 2.13.0's way of printing numbers
Numerous other document and code touch ups.

--- 1.0-1 Apr 01, 2011

plotmo was printing degree1 graphs for all used earth predictors,
not just those appearing in degree1 terms.  Fixed that.

plotmo was not handling all1=TRUE correctly for earth models with
factor predictors.  Fixed that.

--- 1.0-0 Mar 31, 2011

Initial release.  Moved plotmo from earth 2.5-1 to here.
