metric.scores: Score metrics

In leppott/MBSStools: MBSS tool suite for calculations and data manipulation

Score metrics

Description

This function calculates metric scores based on a Thresholds data frame. Can generate scores for 1/3/5 (ScoreRegime="135") for MD DNR MBSS FIBI and BIBI.

Usage

metric.scores(DF_Metrics, MetricNames, IndexName, IndexRegion, DF_Thresh)

Arguments

DF_Metrics	Data frame of metric values (as columns), Index Name, and Index Region (strata).
MetricNames	Names of columns of metric values.
IndexName	Nam of column with index (e.g., MBSS.2005.Bugs)
IndexRegion	Name of column with relevant bioregion/strata/site class (e.g., COASTAL).
DF_Thresh	Data frame of Scoring Thresholds (Index.Name, Index.Region, Metric, Direction, Thresh.Lo, Thresh.Hi, ScoreRegime)

Details

The function reads the upper limit as greater than or equal (>=). For this reason the Family BIBI thresholds were tweaked and so do not match the published values. The published values use greater than (>) and don't match the mathematical operation used in this function.

The inputs and outputs have been designed to mimic those used by MBSS staff.

The R library dplyr is needed for this function.

Value

vector of scores

Examples

# Metrics, Fish
#(generate values then score)s
myIndex <- "MBSS.2005.Fish"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Fish <- as.character(unique(thresh[thresh[,
"Index.Name"] == myIndex,"MetricName.Other"])))
# Taxa Data
myDF.Fish <- taxa_fish
myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish,
TRUE)
# View(myMetric.Values.Fish)
# SCORE
Metrics.Fish.Scores <- metric.scores(myMetric.Values.Fish, myMetrics.Fish,
"Index.Name", "FIBISTRATA", thresh)
# View Results
# View(Metrics.Fish.Scores)
# Add Narrative
myBreaks <- c(1:5)
myLabels <- c("Very Poor", "Poor", "Fair", "Good")
Metrics.Fish.Scores$IBI_Nar <- cut(Metrics.Fish.Scores$IBI
                                   , breaks=myBreaks
                                   , labels=myLabels
                                   , include.lowest=TRUE
                                   , right=FALSE
                                   , ordered_result=TRUE)
# QC, IBI Numeric vs. Narrative
table(Metrics.Fish.Scores$IBI, Metrics.Fish.Scores$IBI_Nar, useNA="ifany")

# Metrics, Index, Benthic Macroinvertebrates, genus
# (generate values then scores)
myIndex <- "MBSS.2005.Bugs"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Bugs.MBSS <- as.character(unique(thresh[thresh[,
"Index.Name"] == myIndex,"MetricName.Other"])))
# Taxa Data
myDF.Bugs.MBSS <- taxa_bugs_genus
myMetric.Values.Bugs.MBSS <- metric.values(myDF.Bugs.MBSS, "bugs",
myMetrics.Bugs.MBSS)
# View(myMetric.Values.Bugs.MBSS)
# SCORE
Metrics.Bugs.Scores.MBSS <- metric.scores(myMetric.Values.Bugs.MBSS,
myMetrics.Bugs.MBSS, "INDEX.NAME", "STRATA_R", thresh)
# View Results
# View(Metrics.Bugs.Scores.MBSS)
# Add Narrative
myBreaks <- c(1:5)
myLabels <- c("Very Poor", "Poor", "Fair", "Good")
Metrics.Bugs.Scores.MBSS$IBI_Nar <- cut(Metrics.Bugs.Scores.MBSS$IBI
                                   , breaks=myBreaks
                                   , labels=myLabels
                                   , include.lowest=TRUE
                                   , right=FALSE
                                   , ordered_result=TRUE)
# QC, IBI Numeric vs. Narrative
table(Metrics.Bugs.Scores.MBSS$IBI
      , Metrics.Bugs.Scores.MBSS$IBI_Nar
      , useNA="ifany")

# QC bug count
Metrics.Bugs.Scores.MBSS[Metrics.Bugs.Scores.MBSS[,"totind"]>120,
"QC_Count"] <- "LARGE"
Metrics.Bugs.Scores.MBSS[Metrics.Bugs.Scores.MBSS[,"totind"]<60,
"QC_Count"] <- "SMALL"
Metrics.Bugs.Scores.MBSS[is.na(Metrics.Bugs.Scores.MBSS[,"QC_Count"]),
"QC_Count"] <- "OK"
# table of QC_Count
table(Metrics.Bugs.Scores.MBSS$QC_Count)

# Metrics, MSW Index, Benthic Macroinvertebrates, family
myIndex <- "MSW.1999.Bugs"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Bugs.MSW <- as.character(unique(thresh[thresh[,
"Index.Name"] == myIndex,"MetricName.Other"])))
# Taxa Data
myDF.Bugs.MSW <- taxa_bugs_family
myMetric.Values.Bugs.MSW <- metric.values(myDF.Bugs.MSW, "bugs",
myMetrics.Bugs.MSW)
# View(myMetric.Values.Bugs.MSW)
# SCORE
Metrics.Bugs.Scores.MSW <- metric.scores(myMetric.Values.Bugs.MSW,
myMetrics.Bugs.MSW, "INDEX.NAME", "STRATA_R", thresh)
# View Results
# View(Metrics.Bugs.Scores.MSW)
# Add Narrative
myBreaks <- c(1:5)
myLabels <- c("Very Poor", "Poor", "Fair", "Good")
Metrics.Bugs.Scores.MSW$IBI_Nar <- cut(Metrics.Bugs.Scores.MSW$IBI
                                   , breaks=myBreaks
                                   , labels=myLabels
                                   , include.lowest=TRUE
                                   , right=FALSE
                                   , ordered_result=TRUE)
# QC, IBI Numeric vs. Narrative
table(Metrics.Bugs.Scores.MSW$IBI, Metrics.Bugs.Scores.MSW$IBI_Nar
, useNA="ifany")

leppott/MBSStools documentation built on April 8, 2024, 9:57 p.m.