Releases: gavinsimpson/analogue
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 aspdf()
.Stratiplot()
now handles a matrix as argumentx
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 and
expm1` 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 functionPlot3d
andplot3d.prcurve
is deprecated and if called needs to use the full function name. This change is to makeanalogue
easier to install on MacOS X as nowrgl
is not needed to install analogue. If you want to plot the principal curve in an interactive 3d view, you'll need to getrgl
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 classcrossval
.timetrack
had several improvements including a newprecict
method, which allows further points to be added to an existing timetrack, apoints
method to allow the addition of data to an existing timetrack plot, and theplot
method can create a blank plotting region allowing greater customisation.prcurve
getspredict
andfitted
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
, andLocation
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 settingncomp
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 thedata
andordination
components of the returned object. Note this function is now deprecated; see earlier note above. -
predict.pcr
was incorrectly calling the internal functionfitPCR
with the:::
operator.
DEPRECATED:
plot3d.prcurve
is deprecated. Functionality is in new functionPlot3d
.
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.