metric.scores: Score metrics

In BioMonTools: Biomonitoring and Bioassessment Calculations

Score metrics

Description

This function calculates metric scores based on a Thresholds data frame. Can generate scores for categories n=3 (e.g., 1/3/5, ScoreRegime="Cat_135") or n=4 (e.g., 0/2/4/6, ScoreRegime="Cat_0246") or continuous (e.g., 0-100, ScoreRegime="Cont_0100").

Usage

metric.scores(
  DF_Metrics,
  col_MetricNames,
  col_IndexName,
  col_IndexClass,
  DF_Thresh_Metric,
  DF_Thresh_Index,
  col_ni_total = "ni_total",
  col_IndexRegion = NULL
)

Arguments

DF_Metrics	Data frame of metric values (as columns), Index Name, and Index Region (strata).
col_MetricNames	Names of columns of metric values.
col_IndexName	Name of column with index (e.g., MBSS.2005.Bugs)
col_IndexClass	Name of column with relevant bioregion or site class (e.g., COASTAL).
DF_Thresh_Metric	Data frame of Scoring Thresholds for metrics (INDEX_NAME, INDEX_CLASS, METRIC_NAME, Direction, Thresh_Lo, Thresh_Mid, Thresh_Hi, ScoreRegime , SingleValue_Add, NormDist_Tail_Lo, NormDist_Tail_Hi, CatGrad_xvar , CatGrad_InfPt, CatGrad_Lo_m, CatGrad_Lo_b, CatGrad_Mid_m, CatGrad_Mid_b , CatGrad_Hi_m, CatGrad_Hi_b).
DF_Thresh_Index	Data frame of Scoring Thresholds for indices (INDEX_NAME, INDEX_CLASS,METRIC_NAME, ScoreRegime, Thresh01, Thresh02 , Thresh03, Thresh04, Thresh05, Thresh06, Thresh07 , Nar01, Nar02, Nar03, Nar04, Nar05, Nar06).
col_ni_total	Name of column with total number of individuals. Used for cases where sample was collected but no organisms collected. Default = ni_total.#'
col_IndexRegion	Name of column with relevant bioregion or site class (e.g., COASTAL). Default = NULL. DEPRECATED

Details

The R library dplyr is needed for this function.

For all ScoreRegime cases at the index level a "sum_Index" field is computed that is the sum of all metric scores. Valid "ScoreRegime" values are:

* SUM = all metric scores added together.

* AVERAGE = all metric scores added and divided by the number of metrics. The index is on the same scale as the individual metric scores.

* AVERAGE_100 = AVERAGE is scaled 0 to 100.

FIX, 2024-01-29, v1.0.0.9060 Rename col_IndexRegion to col_IndexClass Add col_IndexRegion as variable at end to avoid breaking existing code Later remove it as an input variable but add code in the function to accept

Value

vector of scores

Examples

# Example data

library(readxl)
library(reshape2)

# Thresholds
fn_thresh <- file.path(system.file(package = "BioMonTools"),
                       "extdata",
                       "MetricScoring.xlsx")
df_thresh_metric <- read_excel(fn_thresh, sheet = "metric.scoring")
df_thresh_index <- read_excel(fn_thresh, sheet = "index.scoring")

#~~~~~~~~~~~~~~~~~~~~~~~~
# Pacific Northwest, BCG Level 1 Indicator Taxa Index
df_samps_bugs <- read_excel(system.file("extdata/Data_Benthos.xlsx"
                                        , package = "BioMonTools")
                            , guess_max = 10^6)

myIndex <- "BCG_PacNW_L1"
df_samps_bugs$Index_Name   <- myIndex
df_samps_bugs$Index_Class <- "ALL"
(myMetrics.Bugs <- unique(
  as.data.frame(df_thresh_metric)[df_thresh_metric[,
                                  "INDEX_NAME"] == myIndex, "METRIC_NAME"]))
# Run Function
df_metric_values_bugs <- metric.values(df_samps_bugs,
                                       "bugs",
                                       fun.MetricNames = myMetrics.Bugs)

# index to BCG.PacNW.L1
df_metric_values_bugs$INDEX_NAME <- myIndex
df_metric_values_bugs$INDEX_CLASS <- "ALL"

# SCORE Metrics
df_metric_scores_bugs <- metric.scores(df_metric_values_bugs,
                                       myMetrics.Bugs,
                                       "INDEX_NAME",
                                       "INDEX_CLASS",
                                       df_thresh_metric,
                                       df_thresh_index)

# QC, table
table(df_metric_scores_bugs$Index, df_metric_scores_bugs$Index_Nar)
# QC, plot
hist(df_metric_scores_bugs$Index,
     main = "PacNW BCG Example Data",
     xlab = "Level 1 Indicator Taxa Index Score")
abline(v = c(21,30), col = "blue")
text(21 + c(-2, +2), 200, c("Low", "Medium"), col = "blue")

BioMonTools documentation built on Nov. 5, 2025, 7:18 p.m.