In SCCWRP/CSCI: Tools for California Freshwater Biotic Assessment

CSCI

Raphael Mazor, raphaelm@sccwrp.org, Marcus W. Beck, marcusb@sccwrp.org, Mark W. Engeln

R package materials to calculate the California Stream Condition Index (CSCI) based on O/E and pMMI scores using benthic macroinvertebrates.

Installation

Install the package as follows:

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

Citation

Please cite the package as follows:

Mazor, MD, Rehn, AC, Ode, PR, Engeln, M, Schiff, KC, Stein, ED, Gillett, DJ, Herbst, DB, Hawkins, CP. 2016. Bioassessment in complex environments: Designing an index for consistent meaning in different settings. Freshwater Science 35(1): 249-271.

Usage

The core function is CSCI which requires taxonomic and site level data.

devtools::load_all()

#A list of two data frames: bugs and stations
data(bugs_stations) 

# run the estimator
results <- CSCI(bugs = bugs_stations[[1]], stations = bugs_stations[[2]])

# see all the components of the report
ls(results)

# preview report components
lapply(results, head)