Data and R code for "New methods for quantifying the effects of catchment spatial patterns on aquatic responses"
This figshare item provides data and R code to reproduce the analysis in the following paper:
Weller, DE; ME Baker, and RS King. 2023. New methods for quantifying the effects of catchment spatial patterns on aquatic responses. Landscape Ecology. https://doi.org/10.1007/s10980-023-01706-x
This figshare item provides 14 files: five data files (.csv files), a list of models to be fitted by the R code (Modlist.csv), and seven files of R code (.R files). The file 0SpatialAnalysis.txt provides more information on the spatial analysis we used to generate distance distributions.
Data files
The five data files are
· subestPCB.csv
· cdist.csv
· hdist.csv
· ldist.csv
· tdist.csv
The file subestPCB.csv provides catchment id numbers, names, and average measured PCB concentrations from fish tissues for 14 study subestuaries. The remaining four files provide the distance distributions for commercial land, high-density residential land, low-density residential land, and all land. Each distance file has four columns, junk, count, catchment id, and distance. Information in the junk column is not used. Count provides land area as the number of 30 by 30 meter (0.09 hectare) pixels. The variable called distance provides the distance to the subestuary shoreline in decameters.
R code
The R codes reproduce the statistical analysis and most of the tables and figures from the published paper.
We ran the codes using Rstudio. We invoked Rstudio’s New Project … > Existing Directory option to establish the directory containing the data files and R codes files as an Rstudio project. Then we ran five R codes in sequence according to the initial numbers in the file names (1ReadData.R, 2FitModels.R, 3Tables.R, 4Figures.R, and 5FigureS3.R). Each program adds to the objects saved in the R workspace within the Rstudio project. Figures and tables are saved in the subdirectory FiguresTables.
The five numbered R files also use functions from two other files: DistWeightFunctionsV01.R and AuxillaryFunctionsV01.R.
The first R program expects the five data files (subestPCB.csv, cdist.csv, hdist.csv, ldist.csv, and tdist.csv) to reside in the same directory as the program and the Rstudio project.
Comments in the R files provide additional information on how each one works.
