Example dataset
data.frame containing 147 rows and 11 variables:
aluminum concentration, mg/kg dry weight
arsenic concentration, mg/kg dry weight
copper concentration, mg/kg dry weight
cadmium concentration, mg/kg dry weight
chromium concentration, mg/kg dry weight
iron concentration, mg/kg dry weight
lead concentration, mg/kg dry weight
mercury concentration, mg/kg dry weight
nickel concentration, mg/kg dry weight
zinc concentration, mg/kg dry weight
logical; whether the sample was classified as toxic
perfect provides a sample of simulated data that were developed to analyze variability and sensitivity of FPM.
Simulated datasets (n=1000) were originally developed for the analyses; perfect is a single example realization of the simulation.
Simulations were generated using the covariance matrix of h.northport sediment chemical concentrations and the
rmvnorm function from the splus2R package (Constantine and Hesterberg 2021). The Hit values were generated with toxCRM
using simulated concentrations of Cr, Cu, Fe, and Zn
as inputs. The inputs to toxCRM were based on empirical toxicity ranges (minimum and maximum effect levels) as well as
arbitrarily based on probable effect concentration (PEC) and threshold effect concentration (TEC) values from MacDonald et al (2000). Inflection points were
set equal to PECs, and steepnesses were set as the ratio of the PEC to the TEC.
Fe inputs were arbitrary chosen to reflect its low toxicity relative to Cr, Cu, and Zn (e.g., high inflection point and relatively low steepness).
The median toxicity output (for the 4 chemicals) was compared to a threshold of 75% with Hit == TRUE assigned to values below that level and
Hit == FALSE assigned to values >=75%.
Constantine W, Hesterberg T. 2021. splus2R: Supplemental S-PLUS Functionality in R. Version 1.3-3 (online). Updated January 30. Available from: https://cran.r-project.org/web/packages/splus2R/index.html. MacDonald DD, Ingersoll CG, Berger TA. 2000. Development and evaluation of consensus-based sediment quality guidelines for freshwater ecosystems. Arch Environ Contam Toxicol 39(5):20-31.
FPM, toxCRM, h.northport, lowNoise, highNoise