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EHP_manuscript

This repository holds data, code, and plots for the Environmental Health Perspectives manuscript written with Dr. Scott Glaberman

Usage

  • Open the 02_orthogonal_regression.R script in Rstudio.
  • Run the code to see how the the orthReg function handles different comparisons.
    • The orthReg function takes three parameters, data, x, y
    • The data parameter should be set to the cleaned data data/processed/01_clean.csv, which was sourced from the master sheet in data/raw/Master_File.xlsx.
    • The x parameter is a vector with taxa, test_statistic, and duration_h for the taxa you want to be on the x-axis.
    • The y parameter is another vector of the same form as x, but it corresponds to what will fall on the y-axis.

Examples

# set working dir to base directory of repository
setwd(paste0(dirname(rstudioapi::getActiveDocumentContext()$path),"/.."))

# load functions
source("code/functions.R")

# load cleaned data
dat <- data.table::fread("data/processed/01_clean.csv")

# run the orthReg function on Rainbow trout and D. magna with specific test_statistics and durations. 
test1 <- orthReg(data = dat,
                x = c("Oncorhynchus mykiss", "LC50", "96"),
                y = c("Daphnia magna", "EC50", "48"))