README.md

In SCCWRP/SQI: Calculate Stream Quality Index Scores From Stream Data

Marcus W. Beck, [e-mail], Raphael D. Mazor, [e-mail], Susanna Theroux, [e-mail], Kenneth C. Schiff, [e-mail]

Overview

This package provides functions to calculate a stream quality index using stream data. The index requires biological, chemical, and physical data.

Installing the package

The development version of this package can be installed from Github:

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

Usage

The core function is sqi():

head(sampdat)

## # A tibble: 6 x 19
##   MasterID    yr  CSCI  ASCI   IPI PCT_SAFN H_AqHab H_SubNat Ev_FlowHab
##   <chr>    <dbl> <dbl> <dbl> <dbl>    <dbl>   <dbl>    <dbl>      <dbl>
## 1 402M000~  2015 0.729 0.969  1.07     0.81    1        0.96       0.77
## 2 402M000~  2015 0.945 1.14   1        0.77    0.73     0.97       0.78
## 3 402M000~  2015 0.283 1.17   0.95     0.77    0.78     1          0.15
## 4 402M000~  2016 0.703 0.932  0.98     0.95    0.85     1          0.18
## 5 402M000~  2016 0.315 0.886  0.93     0.96    0.96     0.93       0.3 
## 6 402S095~  2012 0.948 1.04   1        0.82    0.82     0.93       0.77
## # ... with 10 more variables: XCMG <dbl>, blc <dbl>, bs <dbl>, hy <dbl>,
## #   ps <dbl>, indexscore_cram <dbl>, Cond <dbl>, TN <dbl>, TP <dbl>,
## #   SiteSet <chr>

sqi(sampdat)

## # A tibble: 267 x 28
##    MasterID    yr  CSCI  ASCI   IPI PCT_SAFN H_AqHab H_SubNat Ev_FlowHab
##    <chr>    <dbl> <dbl> <dbl> <dbl>    <dbl>   <dbl>    <dbl>      <dbl>
##  1 402M000~  2015 0.729 0.969  1.07     0.81    1       0.96        0.77
##  2 402M000~  2015 0.945 1.14   1        0.77    0.73    0.97        0.78
##  3 402M000~  2015 0.283 1.17   0.95     0.77    0.78    1           0.15
##  4 402M000~  2016 0.703 0.932  0.98     0.95    0.85    1           0.18
##  5 402M000~  2016 0.315 0.886  0.93     0.96    0.96    0.93        0.3 
##  6 402S095~  2012 0.948 1.04   1        0.82    0.82    0.93        0.77
##  7 403BA01~  2010 0.943 0.953  0.71     0.5     0.59    0.77        0.88
##  8 403M015~  2016 0.431 0.463  0.41     0.04    0.52    0.290       1   
##  9 403M015~  2015 0.664 0.974  0.96     0.64    0.92    0.85        0.85
## 10 403M015~  2015 0.761 1.10   0.97     0.77    0.93    0.8         1   
## # ... with 257 more rows, and 19 more variables: XCMG <dbl>, blc <dbl>,
## #   bs <dbl>, hy <dbl>, ps <dbl>, indexscore_cram <dbl>, Cond <dbl>,
## #   TN <dbl>, TP <dbl>, SiteSet <chr>, pChem <dbl>, pHab <dbl>,
## #   pChemHab <dbl>, BiologicalCondition <chr>,
## #   WaterChemistryCondition <chr>, HabitatCondition <chr>,
## #   OverallStressCondition <chr>, OverallStressCondition_detail <chr>,
## #   StreamHealthIndex <chr>

Metadata

Resources: paper Contact: Raphael Mazor

SCCWRP/SQI documentation built on April 10, 2022, 1:15 p.m.