A new version of my R package palaeoSig has been approved by CRAN! It always feels like a major achievement to get everything working and pass all the tests.
The package provides some diagnostics to test whether quantitiative palaeoenvironmental reconstructions based on microfossil assemblages are likely to be robust.
So what’s new in version 1.1-3?
- Bug fixes. Partialling reconstructions out now works again.
- A new function for plotting the coverage of the fossil assemblages by the modern calibration set based on this blog post, and a centipede plot showing the weighted average and tolerance of the species in the calibration set.
- The package now includes slightly modified versions of the age-depth modelling procedure from Heegaard et al 2005 as I didn’t have a working version. I would generally be inclined to use a Bayesian sedimentation model (for example in OxCal or Bacon) as these are more powerful when there is some prior knowledge, but my tests show that these perform about as well as the mixed-effect model in Heegaard et al.
- Functions for simulating species assemblages along environmental gradients based on Minchin’s (1985) COMPAS are included. These are useful for generating realistic looking species sets with known properties to test statistical methods. I used an earlier version of these functions to test the effect of uneven sampling on transfer function. Gavin Simpson’s coenocliner is similarly motivated.
- Due to advances in the gstat library, in particular this package working with geodesic distances, some functions in palaeoSig for simulating surrogate autocorrelated environmental variables are now redundant and have been removed.
I meant to include functions for calculating segment-wise RMSEP, but forgot. That will have to go in the next version. If I get inspired, I’ll give some examples of how the package can be used over the next month or so.