| NEWS | R Documentation |
Bug fixes and minor improvement, merged package with age-depth functions and R implementation of Minchin's COMPAS.
Changes to the namespace mean that the rioja package needs to be loaded explicitly before some of the function will work properly.
agelme, predict.agelme and plot.fittedAgelme age-depth modelling functions from Heegaard et al (2005)
coverage.plot Diagnostic plot for reconstructions
centipede.plot Plot WA optima and tolerances
make.env, species, make.env Simulate species-environment relationships based on Minchin's (1983) compas.
rotate No longer needed as gstat now takes geodesic distance.
simulate.spatial Was a wrapper for krige(), now easier to use krige() directly.
randomTF and randomTFmm bug when partialling reconstructions out fixed
obs.cor bug when species not in same order in calibration set and fossil data fixed.
Bug fixes and minor improvement.
ModelMaker and randomTFmm allows models for randomTF to be fitted once and used for several reconstructions. This can be much faster, but does not work with MAT.
plot.palaeoSig p-value highlighted can be selected.
plot.obscor p-value highlighted can be selected.
randomTF Modified to accept predictions in a vector.
obs.cor bug when species not in same order in calibration set and fossil data fixed.
The package autocorTF has been merged with palaeoSig for ease of maintenance.
identify.obscor allows species names to be added to plots interactively.
obs.cor Now includes correlations with several different species weights
plot.obscor upgraded to allow the a choice of which abundance weighting is used, and the code for scaling points has been improved.
randomTF bug when partialling out reconstruction other than MAT now fixed.
The package autocorTF has been merged with palaeoSig for ease of maintenance.
RNE replaces function mat.rne, mat.he and mat.rd. RNE allows any of the transfer function methods in rioja to be used to find the dependence of transfer function performance on spatially close observations.
plot.RNE replaces plot.rne to work with the output of RNE.
obs.cor replaces the previous version of obs.cor, sim.cor and obscor.sig to make the function easier to use and more similar to randomTF
plot.obscor replaces the previous version of plot.obscor and plot.simcor to use the new output of obs.cor. The two plot types can be selected with the argument which.
jointsig: tests if two environmental variables have joint control on fossil assemblage composition.
plot.js: a plot function for jointsig
Hill.N2.core now calculates the Minimum, first quartile and median effective number of species for all fossil observations. This makes much more sense than the previous version, which conflated diversity in individual levels and turnover between levels.
plot.palaeoSig has been improved to give neater figures.
wajack was removed as WA is now implemented in rioja.
mat.h will be removed in the next release, when code for h-block resampling should be implimented in rioja.