- - - The 'jezioro' R package - - -
The free software programming language and environment R is integral to much of the work done at PEARL. To help introduce new PEARLites to this piece of software, I have started a general guide for the typical use of R in paleolimnological analyses, and I maintain the jezioro package.
The jezioro (polish for 'lake') R package is a collection of functions and datasets intended to simplify some of the work performed at PEARL. The package is primarily the work of myself, Josh Thienpont and Andrew Labaj, and the current version (0.20) contains ten functions and two calibration sets.
The package includes the following functions (along with example data to illustrate their use):
- cladCount - determine the number of individuals (and their relative abundances) represented in raw cladoceran subfossil data
- dipteranVWHO - harmonize appropriately formatted chironomid/chaoborid sample data with the Quinlan and Smol (2001, 2010) calibration set, construct the VWHO inference model described in Quinlan and Smol (2001, 2010), infer VWHO from the sample data, and perform an analog matching analysis between the sample data and the calibration set
- interpDates - interpolate dates for the undated intervals of a dated sediment core
- quickGAM - fit a GAM and perform the related analyses described in Simpson (2018)
- vrsChla - infer chlorophyll a concentration in lake sediment from visible reflectance measurements
- the 'binford' functions collectively calculate 210Pb dates for a sediment core using the methods described in Binford (1990), Schelske (1994), and Appleby (2001)
- binfordRho - determine water content and dry sediment density for freeze-dried intervals of a sediment core
- binfordActivity - calculate 210Pb, 214Bi, and 137Cs activities corrected for the efficiency of the gamma counter
- binfordDates - uses the unsupported fraction of 210Pb activity in sediment samples to calculate sediment ages via the Constant Rate of Supply (CRS) model
- the 'wiltse' functions test for homogeneity and coherence within a dataset. They are slightly modified versions of the 'brien' and 'decompose' functions described in Brendan Wiltse’s 2014 PhD thesis
- wiltseBrien - perform the Brien test (Brien et al. 1984) on variables contained within a data frame
- wiltseDecompose - build upon the Brien test by identifying homogenous and coherent subsets within the correlation matrix
The package also contains some commonly used calibration sets to facilitate the construction of transfer functions for application to individual sediment cores:
- tpHall1996 - the diatom-inferred TP calibration set of 54 south-central Ontario lakes described in Hall and Smol (1996)
- vwhoQuinlan2010 - the dipteran-inferred VWHO calibration set of 54 south-central Ontario lakes described in Quinlan and Smol (2001; 2010)
In addition, the chirInfo data set provides a table of several aspects of chironomid taxonomy/ecology to facilitate manipulation of chironomid data (e.g. sorting by littoral/profundal habitat preferences)
- - - Stratigraphy Plot Script (SPS) - - -
The stratigraphy plot script is an R script that aims to produce publication quality stratigraphic diagrams with minimal intervention. It builds upon the strat.plot function provided by the rioja R package.
The script is still a work in progress and currently requires extensive manual adjustment. Thus, it is not yet possible to embed it in a function/package. However, I have posted it here to provide a reference point for those working on their own plots.
