WaterBase

This is an R package for reproducing the Waterbase data analysis and the results for manuscript.

Data

• Raw data handling is located in ./data-raw
• User would need to set up a folder containing downloaded data files from the water base website: Waterbase_v2019_1_S_WISE6_SpatialObject_DerivedData_repaired.csv and Waterbase_v2020_1_T_WISE6_AggregatedData.csv, those can be downloaded from the Water Framework Directive website.
• The primary source for toxicity benchmarks (BMs) was the set of species sensitivity distributions (SSDs) from Posthuma et al. (2019). This dataset consisted of parameters (median and standard deviation of log-transformed toxicity data) of log-normal SSDs for 12386 chemicals based on chronic (NOEC or EC10) endpoints (Posthuma et al., 2019b). Details about the SSDs, underlying ecotoxicological data, and quality assurance can be found elsewhere (Posthuma et al., 2019b). If you would like to obtain the raw SSD data file, please either contact Posthuma or the authors of the article.

Reproduce the Results in the Manuscript

Installing

install_github("Bayer-Group/WaterBase")

Data Selections and Curation

Note that this step has been done inside the package and the pre-processed water base data is a data object Data.AggBySiteID.2 included in the WaterBase package. You can use data("Data.AggBySiteID.2") to load the data object. Also, the chemical classes are defined in the data object chemclass.

The detailed pre-processing of the data including data selection and curation are included in the file

vignettes/articles/Stepwise-Curation_WB_v2.Rmd`. 

The file below include processing the the chemicalclass information.

data-raw/DATASET_class.R

Tables and Figures in the Manuscript

The figures and tables in the manuscript can be reproduced using the following R markdown file. The generated figures are saved in inst/manuscript_2022

vignettes/articles/Manuscript_Prep_2022_article.Rmd

Sensitivity analysis is documented in

vignettes/articles/Sensitivity.Rmd

Tables and Figures in the Supplemental Materials

The figures and tables in the supplemental information can be reproduced using the following R markdown files. The generated figures are saved in inst/manuscript_2022 and inst/manuscript_maps, tables are in inst/SM

vignettes/Manuscript_Supplemental.Rmd
vignettes/articles/Manuscript_supp_summaries.Rmd

Authors

• Ismael M. Rodea Palomares - Ismael M. Rodea Palomares
• Zhenglei Gao - Zhenglei Gao

Acknowledgments

• Thanks to Arnd Weyers & Markus Ebeling for their valuable inputs.