jezioro: jezioro

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

Description

The jezioro package is a collection of functions and datasets intended for use in paleolimnological analyses by members of the Paleoecological Environmental Assessment and Research Laboratory (PEARL).

Details

Package:	jezioro
Type:	Package
Version:	0.20
Date:	2020-09-04
License:	GPL (>= 2)
LazyLoad:	no

jezioro contains the following functions

• cladCount determines the minimum number of individuals (and their relative abundances) represented in raw cladoceran subfossil count data

• dipteranVWHO harmonize appropriately formatted chironomid count data with the calibration set described in Quinlan and Smol (2001, 2010), construct the described VWHO model, infer VWHO from the chironomid sample data using the model, and perform an analog matching analysis between the sample data and the calibration set

• interpDates interpolates dates for undated intervals of a dated sediment core

• quickGAM fit a GAM and perform the related analyses described in Simpson (2018)

• vrsChla infers sediment chlorophyll a concentrations from measurements of visible reflectance

• binfordRho calculates percent water and dry sediment density for individual freeze-dried intervals from a sediment core (values are interpolated for intervals that were not freeze-dried)

• binfordActivity determines corrected 210Pb, 214Bi and 137Cs activities from the appropriate Region of Interest (ROI) values (i.e. output from the gamma counter) and generates a plot of the activities vs. sediment depth

• binfordDates uses the output of binfordRho and binfordActivity to calculate 210Pb dates for a sediment core using the constant rate of supply (CRS) model

• wiltseBrien performs a Brien's test on a correlation matrix to test whether changes in the underlying variables are coherent

• wiltseDecompose uses the Brien's test iteratively to identify homogenous and coherent subsets within a correlation matrix

NOTE:
binfordRho, binfordActivity and binfordDates are intended to be run in sequence, as the output from binfordRho and binfordActivity provide the input for binfordDates:

jezioro contains the following data sets:

• chirInfo a data frame summarizing ecological informatoin for individual chironomid taxa n example input file for cladCount (rows are subfossils, columns are samples)

• cladCountInput an example input file for cladCount (rows are subfossils, columns are samples)

• dipteranVWHOInput an example input file for dipteranVWHO

• vrsChlaInput an example input file for vrsChla with sediment intervals as rows and spectrophotometer measurements for wavelengths 650-700 nm, measured every 2 nm

• binfordRhoInput an example input file for binfordRho formatted as if sediment intervals were subsampled prior to freeze-drying (i.e. into scintillation vials)

• binfordActivityInput an appropriately formatted input file for binfordActivity

• wiltseInput an example input file for wiltseBrien and wiltseDecompose (rows are sediment intervals, columns are PCA axis-1 scores for the dominant diatom species in 8 lakes)

• tpHall1996 the diatom-TP calibration set described in Hall and Smol (1996)

• vwhoQuinlan2010 the dipteran-VWHO calibration set described in Quinlan and Smol (2001, 2010)

Author(s)

Adam Jeziorski, Joshua Thienpont, Andrew Labaj, Brendan Wiltse

Maintainer: Adam Jeziorski <[e-mail]>

References

Hall RI, Smol JP (1996) Paleolimnological assessment of long-term water-quality changes in south-central Ontario lakes affected by cottage development and acidification. Canadian Journal of Fisheries and Aquatic Sciences 53: 1-17

Simpson GL (2018) Modelling Palaeoecological Time Series Using Generalised Additive Models. Frontiers in Ecology and Evolution DOI:10.3389/fevo.2018.00149

Quinlan R, Smol JP (2001) Chironomid-based inference models for estimating end-of-summer hypolimnetic oxygen from south-central Ontario shield lakes. Freshwater Biology 46: 1529-1551

Quinlan R, Smol JP (2010) Use of Chaoborus subfossil mandibles in models for inferring past hypolimnetic oxygen. Journal of Paleolimnology 44: 43-50.

Examples

#load example cladoceran count data and the calculate number of individuals and relative 
#abundance of each taxon present
data(cladCountInput)
cladCount(cladCountInput)

#load example vrsChla measurements and infer chlorophyll a values
data(vrsChlaInput)
vrsChla(vrsChlaInput)

#load binfordRhoInput data and calculate the percent water of the sediment samples freeze
#-dried in "Whirlpak" bags, while defining custom values for bag weight and core diameter
data(binfordRhoInput)
binfordRho(binfordRhoInput, bagwt=3.75, subsample=FALSE, coreD=3.81)

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