Depth diversity gradients of macrophytes: shape, drivers and recent shifts

Research Compendium

Anne Lewerentz¹*, Markus Hoffmann², Juliano Sarmento Cabral¹

¹ Ecosystem Modelling, Center for Computational and Theoretical Ecology (CCTB), University of Würzburg, Clara-Oppenheimer-Weg 32, 97074 Würzburg, Germany

² Limnological Station, Chair of Aquatic Systems Biology, Technical University of Munich, Germany

* Corresponding author: anne.lewerentz@uni-wuerzburg.de

This repository is a R package which includes all data, analysis files and results to reproduce the following publications given in the Journal reference.

Journal references

Release 0.9 corresponds to a Preprint:

• Lewerentz, A., Hoffmann, M., Sarmento Cabral, J. (2021). Depth diversity gradients of macrophytes: shape, drivers and recent shifts. Authorea. DOI: 10.22541/au.161893346.60777770/v1

Release 1.0 corresponds to the following publication:

• Lewerentz, A., Hoffmann, M., & Sarmento Cabral, J. (2021). Depth diversity gradients of macrophytes: Shape, drivers, and recent shifts. Ecology and Evolution, ece3.8089. https://doi.org/10.1002/ece3.8089

Data source

Source of all used raw data is: Bayerisches Landesamt für Umwelt, www.lfu.bayern.de (Published under Licence CC BY 4.0).

Structure of research compendium

• data-raw/: Raw datasets for biotic and abiotic data and R code to generate data in preparation files data/
• data/: Cleaned data used for the analysis
• analysis/: R code in .Rmd files to reproduce tables, figures and analysis of main file and Supplementary material
• R/: ggplot theme to reproduce layout of plots

How to reproduce the results

Install the package

To install the package in R follow this code:

#install.packages("devtools") # install devtools if you don't have it already
devtools::install_github("https://github.com/AnneLew/Lewerentz-etal_2021_Macrophytes-DDG")
library("MacrophytesDDG")

Run R scripts

To reproduce the results run the R scripts in the following order:

Order	Script Name	Description
1	data-raw/DATASET.R	Preparation of Community table for submerged macrophytes (Makroph_comm_S; Makroph) and Calculation of mean annual values for selected physical chemical measurements (Chem.Mean.YearDF)
2	data-raw/DATASETPrep.R	Calcuation of Biodiversity metrices & Depth diversity gradient matrices; Output datasets: MakrophS_ALL; Makroph_Lake_DepthS; Makroph_Depth; Makroph_Lake_ALL; PEAK; Chem_uniform_LOIx; PEAK_Chem_norm
3	analysis/analysis.Rmd	Reproduces figures, tables and analysis used in main manuscript
4	analysis/SupplementaryMaterial.Rmd	Reproduces figures, tables and analysis shown in SupplementaryMaterial