Vignettes work on a subset of data for speed.
Arguments to autoplot() functions have changed so first is now
object rather than x to meet CRAN rules. This
probably does not effect anybody unless they had named the first
argument.
CRAN compliance version re CITATION
New vignette showing how to use a red-noise null model for
randomTF().
Changed h-block cross-validation to use sf package for
geographic data (rather than sp).
rne() is now several orders of magnitude faster.
In randomTF(), species and fossil data were
automatically transformed to matrices so this was done once, not in
every iteration. This sometimes failed with MAT. Now this step is
recommended in the help file.
Sometimes great-circle distances from a point to itself, calculated
with fields::rdist.earth(), are non-zero due to rounding
errors. This lead to them not being excluded in the h-block resampling
in rne() when the threshold distance was zero. Now the
diagonal of the distance matrix is set to zero, removing this
problem.
In randomTF(), if argument col was missing, all columns
of the reconstruction would be used, because lazy evaluation was not
done before use in a formula. Code now check col is set
when needed.
Maintenance release to fix CRAN check error.
MAT shortcut now works when autosim is set
Lots of changes in this version
p.val becomes
p_val and is not the p-value rather than the percentile of
the null distributionmodelMaker and
randomTFmm (which can be used when a calibration set is
used for many cores) is moved within randomTFrandomTF and
obs.corrandomTF now accepts a vector for the environmemtal
datarandomTF and obs.cor have a
permute argument that permutes the environmental variable
rather than simulating one from a uniform distribution. This is only
possible with a single environmental variable.autoplot functions for the output of
randomTF and obs.cormat.h Deleted as rioja::MAT can now do
h-block cross-validationmodelMaker and randomTFmm - this
functionality is now implemented in randomTFagelme, predict.agelme and
plot.fittedAgelme age-depth modelling functions from
Heegaard et al (2005)coverage.plot Diagnostic plot for reconstructionscentipede.plot Plot WA optima and tolerancesmake.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 fixedobs.cor bug when species not in same order in
calibration set and fossil data fixed.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.identify.obscor allows species names to be added to
plots interactively.obs.cor Now includes correlations with several
different species weightsplot.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.RNE replaces function mat.rne,
mat.he and mat.rd. RNE allows any
of the transfer function methods in 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
randomTFplot.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
jointsigHill.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 .mat.h will be removed in the next release, when code
for h-block resampling should be implemented in .