LRA

R package for the Landscape Reconstruction Algorithm

This program calculates the REVEALS model [Sugita, 2007][2]. The calculation is possible for a single site or a combination of multiple sites. The function enables using deposition models for peatlands and lakes, and two dispersal models (Gaussian plume model [Prentice, 1985][1], Lagrangian stochastic model taken from the DISQOVER package [Theuerkauf,et al. 2016][3]).

Date (version)  : v0.1.2, 22 May 2024
Author          : Petr Kuneš
Email           : petr.kunes@natur.cuni.cz
Citation        : Abraham, V., Oušková, V., & Kuneš, P. 2014. Present-day vegetation helps quantifying past land cover in selected regions of the Czech Republic. PLoS ONE 9: e100117.

How do you install the package from GitHub?

1. First, you need to install the devtools package. Run R and then type

   install.packages("devtools")
   

2. Load the devtools package.

   library(devtools)
   

3. Install the disqover package.

   install.packages("https://github.com/MartinTheuerkauf/disqover/raw/8c9bd9bc08515e3f1a8b63464951c728cc673d0b/disqover_0.9.13.tar.gz", repos = NULL, type = "source")
   

4. In most cases, you just use install_github() function.

   install_github("petrkunes/LRA")
   

5. Load the LRA package

   library(LRA)
   

6. Run the example REVEALS calculation

   REVEALS.mult.sites <- REVEALS(list(PC_Cerne, PC_Prasilske, PC_Rybarenska), avg, alvc, 3, 100000, "gpm neutral")
   

References:

[1]: Prentice, I.C. 1985. Pollen representation, source area, and basin size: Toward a unified theory of pollen analysis. Quaternary Research 23: 76–86.

[2]: Sugita, S. 2007. Theory of quantitative reconstruction of vegetation I: pollen from large sites REVEALS regional vegetation composition. Holocene 17: 229–241.

[3]: Theuerkauf, M., Couwenberg, J., Kuparinen, A., & Liebscher, V. 2016. A matter of dispersal: REVEALSinR introduces state-of-the-art dispersal models to quantitative vegetation reconstruction. Vegetation History and Archaeobotany 25: 541–553.