R code for development and application of the Temporal Response Surface method

This record contains R code to accompany the imidacloprid Temporal Response Surface paper (https://doi.org/10.1021/acs.est.4c14331), to allow other researchers access and apply to the method. The code can be applied to other compounds that also exhibit cumulative and delayed toxicity. The repo also includes code that allows the user to operationalise the method to calculate risk/impact to aquatic ecosystems that results from exposure to such compounds. The code components are as follows:Duration over threshold plotting.This code was developed to visually compare the duration and concentration of instream imidacloprid detections with the duration and concentration of toxicity data used to derive WQ guidelinesThe idea being, that if imidacloprid (and similar compounds) exhibit time dependent toxicity, then the toxicity test duration should approximate the duration of real-word exposure.If real world exposure is longer than that used to derive guidelines, then careful consideration must be made of the appropriateness of the toxicity data and any conversions used in the development of ecosystem protection guidelines 2. Ordinal regression for Daphnia magna and H. aztecaThe iterative development and testing of a regression model for D.magna that can predict effect concentration for days 1-100 of exposure 3. Ordinal regressions for Deleatidium sp.The iterative development and testing of a regression model for Deleatidium sp. that can predict effect concentration for days 1-100 of exposure 4. Ratio calculationsThis code calculates ratios that are then applied to the toxicity data in the Base SSD to create a temporally adjusted toxicity data set for every day from 1-100 days of continuous exposure.The resulting data set represents the observed and predicted effect concentration for all species in the SSDThe results replicate an experiment where the species were each exposure to imidacloprid for 100 consecutive days, with effect concentration calculated accordingly 5. IMI (imidacloprid) temporal SSD developmentThis code uses the ssdtools R package to derive an SSD for each day of temporally adjusted toxicity dataThe resulting SSDs represent toxic effects resulting from 1-100 days of continuous exposure of the ecosystem to imidacloprid 6. PC (protective concentration)plotting code for Figure 11 in S8: Change in TRS protective concentrations over time 7. Exposure duration codeCalculates exposure duration on time-series monitoring dataRule set: if Concentration