README.md

In shiggo/jezioro: Tools for Paleolimnological Analyses at the Paleoecological Environmental Assessment and Research Laboratory

jezioro

The jezioro R package is a collection of functions and datasets intended for use by members of the Paleoecological Environmental Assessment and Research Laboratory (PEARL). The package is maintained by Adam Jeziorski, and contains contributions from Adam Jeziorski, Joshua Thienpont, and Andrew Labaj.

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: performs the GAM fitting procedure and 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, 137Cs, and 214Bi activities corrected for the efficiency of the gamma counter * binfordDates: use 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: diatom-inferred TP calibration set of 54 south-central Ontario lakes described in Hall and Smol (1996) vwhoQuinlan2010: 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)

Documentation

The package also contains two guides/vignettes:

• The user guide provides detailed information on the functions and data sets within the package as well as examples of their use.

• A general guide to the use of R at PEARL is an ongoing attempt to provide an overview of the most commonly used functions and packages relevant to the analyses performed at PEARL.

Dependencies

The package requires an R version >= 3.5.0.

The function dipteranVWHO depends on analogue, plyr, and rioja.

The function quickGAM depends on ggplot2, gratia, and mgcv.

Several other dependencies are related to the various examples in the general guide vignette and include: dplyr, knitr, magrittr, mapproj, rgdal, and rmarkdown.

Installation

The most recent version of the jezioro package can be downloaded from the "release" tab. Both source code and compiled binaries (for windows + macOS/linux) are available there as assets. These binaries can then be installed as "a local file".

Alternately, jezioro can be installed directly into a local R environment from the github repository using the devtools package. However, note that this method will not provide a local copy of vignettes/guides.

library("devtools")
install_github("shiggo/jezioro")

shiggo/jezioro documentation built on Sept. 7, 2020, 7:34 p.m.