calc_epsi: Empirically-weighted Proportion of Sediment-sensitive...

In aquaMetrics/macroinvertebratesMetrics: Macroinvertebrate Biotic indices

Empirically-weighted Proportion of Sediment-sensitive Invertebrates (E-PSI)

Description

A sediment-sensitive macro-invertebrate metric that provides a proxy to describe the extent to which the surface of river bed are composed, or covered by sediments. It can be calculated at Taxonomic Levels 2 & 5

Usage

calc_epsi(
  data,
  names = macroinvertebrateMetrics::column_attributes$name,
  questions = c("Taxon abundance", "Taxon Abundance"),
  taxa_list = "TL2",
  log_abundance = TRUE,
  metric_cols = macroinvertebrateMetrics::metric_cols
)

Arguments

data	Dataframe with at least three columns itemSAMPLE_ID - unique idenftier for each sample itemTAXON - Taxon name that matches to macroinvertebrateTaxa dataset itemRESULT - Numeric log abundance category
names	Optional, user provided list of column names different to those used in 'column_attributes' to match with input data
questions	Optional, user provided 'question' default is 'Taxon abundance', which filters only abundance values.
log_abundance	If RESULT column in ecologyResults not log category then set to FALSE. This will calculate log value from your numeric abundance.
taxaList	The taxonomic level the sample(s) have been identified at according to specificed taxa lists as described in WFD100 Further Development of River Invertebrate Classification Tool. Either "TL2" - Taxa or "TL5" - Taxa list 5.

Value

Dataframe with itemSAMPLE_ID itemANALYSIS_NAME itemDETERMINAND itemRESULT

References

Turley, Matt & Bilotta, Gary & Chadd, Richard & A Extence, Chris & E Brazier, Richard & Burnside, Niall & Pickwell, Alex. (2016). A sediment-specific family-level biomonitoring tool to identify the impacts of fine sediment in temperate rivers and streams. Ecological Indicators. 70. 151-165. 10.1016/j.ecolind.2016.05.040.

Examples

sample <- demo_data
calc_epsi(data = sample, taxa_list = "TL2")

aquaMetrics/macroinvertebratesMetrics documentation built on Feb. 3, 2024, 2:35 a.m.