analogue Version 0.17-0

This is mainly a maintenance release addressing issues flagged under R CMD check in R-devel. In addition, the following changes were made to the package:

• Stratiplot() now draws a plot on the current device and returns a "trellis" object invisibly. This fixes #13 and prevents a blank page being drawn in devices such as pdf().
• Stratiplot() now handles a matrix as argument x via an S3 method for class "matrix".
• tran() add a "none" transformation which just returns its input. This is useful if you are writing code and comparing transformations and need to temporarily turn them off.

analogue version 0.16-0

With the recent release of version 2.2-0 of vegan, I needed to make a quick release of analogue as the changes in vegan meant that analogue wouldn't install cleanly due to changes in vegan's namespace. As a result, there are few changes in this release.

The main change is that the rgl-based functions for working with principal curves, plot3d.prcurve() etc, have been removed from analogue and placed in their own package analogueExtra. This was motivated again by issues with getting rgl installed on some systems. Vegan removed its rgl-based functions into a new package vegan3d from version 2.2-0 onwards and now analogue follows suit.

There were some changes to tran():

• a new method colCentre to centre data by columns,
• more accurate log(x + 1) transformation and the reverse via new base R functions (methods log1p1 andexpm1` respectively).

Stratiplot() also got a new argument yticks which allows one to set the locations of the ticks on the y- (depth-, age-) axis.

analogue version 0.14-0 released to CRAN

Changes in version 0.14-0:

General summary:

• Version 0.14-0 is less of a major update than that provided by version 0.12-0 and sees a continuation of the changes to dependencies to have packaes in Imports rather than Depends.
• The main development of analogue now takes place on github and bugs and feature requests should be posted there. The Travis continuous integration system is used to automatically check the package as new code is checked in.
• There are several new functions and methods and a few bug fixes, the details of which are given below.
• The main user-visible change over 0.12-0 is the deprecation of the plot3d.prcurve method. The functionality is now in new function Plot3d and plot3d.prcurve is deprecated and if called needs to use the full function name. This change is to make analogue easier to install on MacOS X as now rgl is not needed to install analogue. If you want to plot the principal curve in an interactive 3d view, you'll need to get rgl installed first.

New Features:

• n2 is a new utility function to calculate Hill's N2 for sites and species.
• optima can now compute bootstrap WA optima and uncertainty.
• performance has a new method for objects of class crossval.
• timetrack had several improvements including a new precict method, which allows further points to be added to an existing timetrack, a points method to allow the addition of data to an existing timetrack plot, and the plot method can create a blank plotting region allowing greater customisation.
• prcurve gets predict and fitted methods to predict locations of new samples on the principal curve and extract the locations of the training samples respectively.
• evenSample is a utility function to look at the evenness of the distribution of samples along a gradient.
• Data sets Pollen, Biome, Climate, and Location from the North American Modern Pollen Database have been updated to version 1.7.3 of the data base.

Bug Fixes:

• The calculation of AUC in roc wasn't working correctly in some circumstances with just a couple of groups.

• crossval.pcr had a number of bugs in the k-fold CV routine which were leading to errors and the function not working.

  The progress bar was not being updated correctly either.

• predict.pcr was setting ncomp incorrectly if not supplied by the user.

• ChiSquare wasn't returning the transformation parameters required to transform leave-out data during crossvalidation or new samples for which predictions were required.

• plot3d.prcurve was not using the data and ordination components of the returned object. Note this function is now deprecated; see earlier note above.

• predict.pcr was incorrectly calling the internal function fitPCR with the ::: operator.

DEPRECATED:

• plot3d.prcurve is deprecated. Functionality is in new function Plot3d.

Package tarballs and binaries

The *.tar.gz file below is the official package tarball deployed to CRAN. This is useful for those running R under Linux or other Unix-alike OSes. The *.zip file is a windows binary build from Appveyor. As always, binaries for Windows and MacOSX are also available from CRAN, but may take a day or two to show up.