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Changelog

Source: NEWS.md

palaeoSig 2.1-4

Fixing some documentation formatting issues for CRAN

palaeoSig 2.1-3

CRAN release: 2023-03-10

Vignettes work on a subset of data for speed.

palaeoSig 2.1-2

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.

palaeoSig 2.1-1

CRAN compliance version re CITATION

palaeoSig 2.1-0

Vignettes

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).

Rewrites

rne() is now several orders of magnitude faster.

bug fixes

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.

palaeoSig 2.0-8

Bug fix

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.

palaeoSig 2.0-7

CRAN release: 2023-01-26

Maintenance release to fix CRAN check error.

palaeoSig 2.0-6

Bug fix

MAT shortcut now works when autosim is set

palaeoSig 2.0-1

Lots of changes in this version

Breaking changes

  • In the plotting functions p.val becomes p_val and is not the p-value rather than the percentile of the null distribution
  • The functionality of modelMaker and randomTFmm (which can be used when a calibration set is used for many cores) is moved within randomTF

Other changes

  • Lot more sanity checks on inputs to randomTF and obs.cor
  • randomTF now accepts a vector for the environmemtal data
  • randomTF 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.

New functions

  • autoplot functions for the output of randomTF and obs.cor

Deleted functions

  • mat.h Deleted as rioja::MAT can now do h-block cross-validation
  • modelMaker and randomTFmm - this functionality is now implemented in randomTF

Changes in version 1.1-3

CRAN release: 2015-02-17

GENERAL

  • 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.

NEW FUNCTIONS

  • 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.

REMOVED FUNCTIONS

  • rotate No longer needed as gstat now takes geodesic distance.
  • simulate.spatial Was a wrapper for krige(), now easier to use krige() directly.

MODIFIED FUNCTIONS

  • randomTF and randomTFmm bug when partialling reconstructions out fixed

BUG FIXES

  • obs.cor bug when species not in same order in calibration set and fossil data fixed.

Changes in version 1.1-2

CRAN release: 2013-04-18

GENERAL

  • Bug fixes and minor improvement.

NEW FUNCTIONS

  • 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.

MODIFIED FUNCTIONS

  • plot.palaeoSig p-value highlighted can be selected.
  • plot.obscor p-value highlighted can be selected.
  • randomTF Modified to accept predictions in a vector.

BUG FIXES

  • obs.cor bug when species not in same order in calibration set and fossil data fixed.

Changes in version 1.1-1

CRAN release: 2012-06-20

GENERAL

  • The package has been merged with for ease of maintenance.

NEW FUNCTIONS

  • identify.obscor allows species names to be added to plots interactively.

MODIFIED FUNCTIONS

  • 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.

BUG FIXES

  • randomTF bug when partialling out reconstruction other than MAT now fixed.

Changes in version 1.1

GENERAL

  • The package has been merged with for ease of maintenance.

NEW and REWRITTEN FUNCTIONS

  • 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 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.

REMOVED FUNCTIONS

  • wajack was removed as WA is now implemented in .

FORTHCOMING CHANGES

  • mat.h will be removed in the next release, when code for h-block resampling should be implemented in .