epsi: Empyrically-weighted Proportion of Sediment-sensitive...

In alexology/biomonitoR: biomonitoring indices and metrics

Empyrically-weighted Proportion of Sediment-sensitive Invertebrates index

Description

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This function calculates the Empyrically-weighted Proportion of Sediment-sensitive Invertebrates index (ePSI) according to the most recent version used in UK.

Usage

epsi(
  x,
  method = "uk",
  agg = FALSE,
  abucl = c(1, 9, 99, 999),
  exceptions = NULL,
  traceB = FALSE
)

Arguments

x	Results of aggregate_taxa().
method	The only avialble method is uk. Users can provide their own data.frame (see examples) with a column called Taxon and the column of scores called Scores.
agg	Default to FALSE. If set to TRUE epsi() will use the aggreation rules described in the details. It can also be a data.frame provided by the user containing the specification on how to aggregate taxa. This data.frame needs a column called Taxon containing the taxon to aggregate and a column called Correct_Taxon with the aggregation specifications. Used when users want to aggregate some taxonomic levels while using their own data.frame of scores (provided via method).
abucl	Log abundance categories. Tresholds are set to 1, 9, 99, 999.
exceptions	Taxa that need to be exluded from the calculation. This option can be useful, for instance, to exclude an alien species belonging to an autochthonous family. agg cannot be TRUE when a data.frame is provided as method.
traceB	If set to TRUE a list as specified below will be returned.

Details

epsi() implementation take into account composite taxa as follow:

1. Tipulidae (inc. Limoniidae, Pediciidae & Cylindrotomidae)

2. Siphlonuridae (inc. Ameletidae)

3. Hydrophilidae (inc. Georissidae, Helophoridae & Hydrochidae)

epsi() automatically check for parent-child pairs in the scoring system, see the return section for a definition. All the information used for epsi() calculation can be retrieved with the function show_scores.

Value

If traceB is set to TRUE a list with the following elements will be returned:

• results Results of epsi().

• taxa_df The data.frame used for the calculation containing the abundance of taxa receiving a score.

• epsi_df The data.frame used for the calculation containing scores and abundance classes for each site.

• composite_taxa Taxa aggregated following the aggregation of the default method or set in agg.

• exceptions A data.frame containing the containing changes made by excluding the taxa included in exceptions.

• parent_child_pairs Parent-child pairs are not present in the default implementation of epsi. A data.frame if both a taxon and a parent taxon receive a score.

Acknowledgements

We thank Carol Fitzpatrick, Richard Chadd, Judy England and Rachel Stubbington for providing us with the most updated ePSI scores and algorithms.

References

Turley MD, Bilotta GS, Chadd RP, Extence CA, Brazier RE, Burnside NG, Pickwell AG. 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.

Turley MD, Bilotta GS, Krueger T, Brazier RE, Extence CA. 2015. Developing an improved biomonitoring tool for fine sediment: combining expert knowledge and empirical data. Ecological indicators 54, 82-86.

See Also

aggregate_taxa

Examples

data(macro_ex)
data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
epsi(data_agr)

# provide your own score sistem. Scores and aggregation rules are for example purpose only.

epsi_scores <- data.frame(
  Taxon = c("Ephemerellidae", "Leuctridae", "Chironomidae"),
  Scores = c(0.1, 0.5, 0.2)
)
epsi_acc <- data.frame(Taxon = "Ephemerellidae", Correct_Taxon = "Chironomidae")

epsi(data_agr, method = epsi_scores, agg = epsi_acc, traceB = TRUE)

alexology/biomonitoR documentation built on Oct. 10, 2024, 12:02 a.m.