analogue 0.14-0 released

Gavin Simpson

A couple of week’s ago I packaged up a new release of analogue, which is available from CRAN. Version 0.14-0 is a smaller update than the changes released in 0.12-0 and sees a continuation of the changes to dependencies to have packages 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 (sample) & species (variables).
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 predict() 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.

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 argument 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.
predict.pcr() was incorrectly calling the internal function fitPCR with the ::: operator.

Deprecated

plot3d.prcurve() is deprecated. Functionality is in new function Plot3d(). Note: in the next version of analogue, this functionality will be removed entirely and located in a new package analogueExtra.