lowNoise: Simulated Floating Percentile Model Data, Low Random Noise in...

In RFPM: Floating Percentile Model

Simulated Floating Percentile Model Data, Low Random Noise in Toxicity Prediction

Description

Example dataset

Format

data.frame, containing 147 rows and 11 variables:

Al

aluminum concentration, mg/kg dry weight

As

arsenic concentration, mg/kg dry weight

Cu

copper concentration, mg/kg dry weight

Cd

cadmium concentration, mg/kg dry weight

Cr

chromium concentration, mg/kg dry weight

Fe

iron concentration, mg/kg dry weight

Pb

lead concentration, mg/kg dry weight

Hg

mercury concentration, mg/kg dry weight

Ni

nickel concentration, mg/kg dry weight

Zn

zinc concentration, mg/kg dry weight

Hit

logical; whether the sample was classified as toxic

Details

lowNoise 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; lowNoise is a single 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). Random normal noise was added to the lowNoise datasets by inputting eSD values into toxCRM equal to 10% of the range of chemical concentrations (chemical-specific). 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%.

References

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.

See Also

FPM, toxCRM, h.northport, perfect, highNoise

RFPM documentation built on Oct. 26, 2023, 1:08 a.m.