In SCCWRP/SQObioaccumulation: Run bioaccumulation model for SQO human health objectives

README

library(knitr)
opts_chunk$set(message = F, warning = F)

Install the package as follows:

install.packages('devtools')
library(devtools)
install_github('SCCWRP/SQObioaccumulation')
library(SQObioaccumulation)

devtools::load_all()

Run the bioaccumulation model with defaults:

# data inputs
data(biota)
data(constants)
data(contam)
data(mcsparms)

# calculated contaminant inputs
contamcalc <- cntcalc(contam, constants)

# run model
res <- bioaccum_batch(biota, contamcalc, constants)

# assign output to separate objects
cbiota <- res$cbiota
bsaf <- res$bsaf

Creat a summary table:

# summary table
indic_sum <- indic_sum_fun(cbiota, contamcalc)
indic_sum

Plot BSAF and tissue concentration estimates for a selected contaminant:

# plot of bsaf, cbiota by specific contaminant
plo_bsaf(bsaf, cbiota, 'alphaChlordane')

Make a table of BSAF and tissue concentration estimates for a selected contaminant:

# tabular summary of bsaf, cbiota by specific contaminant
tab_bsaf(bsaf, cbiota, 'alphaChlordane')

Run Monte Carlo simulations (MCS) with results from bioaccumulation model and additional inputs:

mcsres <- mcs_fun(1000, indic_sum, mcsparms, constants)

Summarize MCS results:

mcs_sum_fun(mcsres)

Plot cumulative distribution curves for MCS:

mcs_plo(mcsres, xmax = 3)

Get overall SQO assessment:

wgtavg <- wgt_avg_fun(mcsparms)
sqo_sum_fun(wgtavg, mcsres, constants)

SCCWRP/SQObioaccumulation documentation built on Dec. 31, 2021, 7:45 a.m.