[Analogue-commits] r393 - pkg/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 13 22:08:43 CET 2013
Author: gsimpson
Date: 2013-12-13 22:08:43 +0100 (Fri, 13 Dec 2013)
New Revision: 393
Added:
pkg/inst/NEWS.Rd
Modified:
pkg/inst/ChangeLog
Log:
add a NEWS.Rd file containing highlights on the upcoming 0.12-0 release
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2013-12-13 05:35:20 UTC (rev 392)
+++ pkg/inst/ChangeLog 2013-12-13 21:08:43 UTC (rev 393)
@@ -4,6 +4,9 @@
* Preparing for the 0.12-0 release.
+ * NEWS: analogue now has an `inst/NEWS.Rd` file highlight the major
+ changes in the upcoming 0.12-0 release.
+
Version 0.11-6
* distance3: removed - redundant attempt to improve `distance()`.
Added: pkg/inst/NEWS.Rd
===================================================================
--- pkg/inst/NEWS.Rd (rev 0)
+++ pkg/inst/NEWS.Rd 2013-12-13 21:08:43 UTC (rev 393)
@@ -0,0 +1,148 @@
+\name{NEWS}
+\title{Latest changes to the \pkg{analogue} package}
+\encoding{UTF-8}
+
+\section{Changes in version 0.12-0}{
+
+ \subsection{General summary}{
+
+ \itemize{
+ \item Version 0.12-0 represents a major update of \pkg{analogue},
+ including the addition of new functionality and long-required
+ improvements to the computation of dissimilarity matrices which
+ now uses faster C code.
+
+ \item Several of the dependencies are now only imported into the
+ namespace for \pkg{analogue}. As a result, existing code that did
+ not already load these packages will need to be updated to load
+ them via a call to \code{library()}.
+
+ \item Highlights of the release are listed below. For a full
+ record of changes made during the development leading up to this
+ release see the ChangeLog in the package sources.
+ }
+
+ } % general
+
+ \subsection{New Features}{
+
+ \itemize{
+ \item Dissimilarities are now computed using fast C code in
+ function \code{distance()}. The new functions are tested against
+ the old code (now available as function \code{oldDistance()}) to
+ ensure the new code performs correctly.
+
+ \item Fitting principal curves to palaeo data and working with the
+ fitted objects is now much easier.
+
+ \code{prcurve()} now returns each of the fitted smooth models as
+ part of component \code{smooths}, allowing further examination of
+ the the individual fits.
+
+ There are now methods for \code{lines()} and \code{points} to
+ allow greater flexibility in producing plots of the fitted
+ principal curve. A \code{scores()} method to extract ordination
+ scores for prcinipal curves is also available. A \code{resid()}
+ method is also available to return various types of residuals for
+ the principal curve.
+
+ \code{smoothGAM()} is a new plugin smoother function for use with
+ \code{prcurve()}, which allows GAMs to be used as smoothers fitted
+ to individual variables. It is significantly slower than
+ \code{smoothSpline()}, but can handle non-Gaussian responses. The
+ underlying models are fitted using \code{gam()} from \pkg{mgcv}.
+
+ As principal curves are smooth curves in high-dimensions it makes
+ sense to view them in 3D. \pkg{analogue} has a function for that:
+ the \code{plot3d.prcurve()} method uses the underlying
+ functionality of the \pkg{rgl} package to provide an interactive
+ 3D representation of the data and the fitted principal curve.
+
+ \code{prcurve()} also returns the fitted ordination and the
+ original data, making it much easier to predict where passive
+ samples should lay and simpler to plot the curve.
+
+ \item New function (and S3 generic), \code{sppResponse()} for
+ species responses along gradients. Currently the only supplied
+ method is for the results of \code{prcurve()} fits, where the
+ function returns the fitted response curves along the principal
+ curve. A \code{plot()} method is also available.
+
+ \item \code{logitreg()} can now fit the logistic regression via
+ Firth's bias reduction method. This helps in cases where there is
+ complete or quasi-complete separation, and for cases where there
+ are far more no-analogues than analogues.
+
+ \item This release sees much improved functionality for fitting
+ principal component regression calibration models where the data
+ are subject to an "ecologically meaningful" transformation (such
+ as the Hellinger transformation). Models fitted with \code{pcr()}
+ can be cross-validated using the new \code{crossval()} method, and
+ predictions from the fitted model can be computed using the
+ \code{predict()} method. Both ensure that the transformation is
+ applied to the test or new data samples in the appropriate manner.
+
+ \item New function \code{rankDC()} to compute the rank correlation
+ between gradient distances (e.g. environmental variables) and
+ distances in species composition. Has both base and Lattice
+ graphics plot methods (the latter via \code{dotplot()}).
+
+ \item \code{Stratiplot()} gains two new arguments: \code{labelAt}
+ and \code{labelRot}, which allows control of the placement and
+ rotation of variable labels on the panels of the plot when not
+ using the strip.
+
+ \item The \code{plot()} method for \code{timetrack()} now allows
+ the plotting of linear combination or weighted average site
+ scores.
+
+ \item The \code{fitted()} method for \code{timetrack()} now has
+ argument \code{which}, replacing the original \code{type}.
+
+ \item There is a new \code{scores()} method for objects eturned by
+ \code{timetrack()}.
+
+ \item \code{analog()} gains a method allowing it to work directly
+ on objects of class \code{"distance"}, as returned by
+ \code{distance()}. This avoids recomputing the dissimilarity
+ matrix if a suitable one is already available.
+ }
+
+ } % new features
+
+ \subsection{Bug Fixes}{
+
+ \itemize{
+ \item \code{chooseTaxa()} no longer drops empty dimensions if the
+ conditions supplied result in a single species being
+ returned. Reported by Michael Burstert.
+
+ A warning about presence of \code{NA}s when \code{na.rm = TRUE}
+ was supplied is also fixed.
+
+ \item The \code{formula} method of \code{timetrack()} was not
+ well-implemented for various reasons, and could result in the
+ species data not being transformed and other mistakes.
+
+ The new code takes a one-sided formula describing the constraints
+ for the underlying ordination, and variables in this formula will
+ be searched for in the data frame supplied as argument \code{env}.
+
+ \item \code{predict.wa()} would sometimes produce a 1-column
+ matrix during the deshrinking step, which would result in an
+ error. This empty dimension is now dropped so that a vector is
+ always returned from the deshrinking function.
+
+ }
+
+ } % deprecated
+
+ %% \subsection{DEPRECATED}{
+
+ %% \itemize{
+ %% \item
+
+ %% }
+
+ %% } % deprecated
+}
\ No newline at end of file
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