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README.Rmd
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README.Rmd
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---
output: github_document
---
## CSCI
#### *Raphael Mazor, raphaelm@sccwrp.org, Marcus W. Beck, marcusb@sccwrp.org, Mark W. Engeln*
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/SCCWRP/CSCI?branch=master&svg=true)](https://ci.appveyor.com/project/SCCWRP/CSCI)
[![Travis-CI Build Status](https://travis-ci.org/SCCWRP/CSCI.svg?branch=master)](https://travis-ci.org/SCCWRP/CSCI)
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:
```{r, eval = FALSE}
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.
```{r, echo = F, warning = F, message = F}
devtools::load_all()
```
```{r}
#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)
```