Description Usage Arguments Value Examples
View source: R/metric.values.R
This function calculates metric values for bugs, fish, and algae. Inputs are a data frame of taxa, SampleID, and community. NonUnique = taxa to be excluded from taxa metrics (i.e., ambiguous taxa in the sample) Benthic Macroinvertebrates Required fields: SampleID (provided by user), Count, NonUnique, FinalID, Order, Family, Tribe, Genus, FFG, TolVal, Habit, Voltinism, BCG_Atr FFG = CF, CG, SC, SH, PR Habit = BU, CB, CN, SP, SW Voltinism = multivoltine, semivoltine, univoltine Fish Required fields: SampleID (provided by user), Count, NonUnique, FinalID, Genus, Trophic, Lithophil, StWidAvg, StLength, MassTotal Trophic = Lithophil = Stratum = Tolerance = Metric names have a prefix and suffix. The prefix follows the naming convention listed below. The suffix is a short name of the group being measured. Only phylogenetic names are first letter caps. ni = number of individuals nt = number of taxa pi = percent of individuals pt = percent of taxa x = index
1 2 | metric.values(fun.DF, fun.SampID, fun.Community, fun.MetricNames = NULL,
boo.Adjust = FALSE)
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fun.DF |
Data frame of taxa (list required fields) |
fun.SampID |
Sample ID column name |
fun.Community |
Community name for which to calculate metric values (bugs, fish, or algae) |
fun.MetricNames |
Optional vector of metric names to be returned. If none are supplied then all will be returned. |
boo.Adjust |
Optional boolean value on whether to perform adjustments of values prior to scoring. Default = FALSE. |
data frame of SampleID and metric values
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | # Index, Benthic Macroinvertebrates, genus
myIndex <- "MBSS.2005.Bugs"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Bugs <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"]))))
# Taxa Data
myDF.Bugs <- taxa_bugs_genus
myMetric.Values.Bugs <- metric.values(myDF.Bugs, "SampleID", "bugs", myMetrics.Bugs)
View(myMetric.Values.Bugs)
# Index, Benthic Macroinvertebrates, family
myIndex <- "MSW.1999.Bugs"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Bugs <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"]))))
# Taxa Data
myDF.Bugs <- taxa_bugs_family
myMetric.Values.Bugs <- metric.values(myDF.Bugs, "SampleID", "bugs", myMetrics.Bugs)
View(myMetric.Values.Bugs)
# Index, Fish
myIndex <- "MBSS.2005.Fish"
# Thresholds
thresh <- metrics_scoring
# get metric names for myIndex
(myMetrics.Fish <- as.character(droplevels(unique(thresh[thresh[,"Index.Name"]==myIndex,"Metric"]))))
# Taxa Data
myDF.Fish <- taxa_fish
myMetric.Values.Fish <- metric.values(myDF.Fish, "SampleID", "fish", myMetrics.Fish, TRUE)
View(myMetric.Values.Fish)
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