life: Lotic-invertebrate Index for Flow Evaluation index

In alexology/biomonitoR: biomonitoring indices and metrics

Lotic-invertebrate Index for Flow Evaluation index

Description

\Sexpr[results=rd, stage=render]{ lifecycle::badge("maturing") }

This function calculates the Lotic-invertebrate Index for Flow Evaluation index (LIFE).

Usage

life(
  x,
  method = "extence",
  abucl = c(1, 9, 99, 999, 9999),
  agg = FALSE,
  fs_scores = NULL,
  exceptions = NULL,
  traceB = FALSE
)

Arguments

x	Result of aggregate_taxa().
method	Possible choices are extence and life_2017. A custom data.frame containing the scoring system can be provided by the user.
abucl	Log abundance categories. Treshold are set to 1, 9, 99, 999 and 9999 as in the original paper of Extence et al. (1999).
agg	This option allows the composite family approach. It can be FALSE, TRUE or a data.frame. If FALSE no aggregation will be performed, while if TRUE aggregation will be performed according to the rules described in Details. A data.frame containing the aggregation rules can be provided by the user. This data.frame needs a column called Taxon containing the taxon to aggregate and a column called Correct_Taxon with the aggregation specifications. agg cannot be TRUE when a data.frame is provided as method.
fs_scores	Scores (fs) for different abundance categories of taxa associated with flow groups 1-4. A custom data.frame can be provided by the user.
exceptions	Taxa that to be excluded from the calculation. This option can be useful, for instance, to exclude an alien species belonging to an autochthonous family.
traceB	if set to TRUE a list as specified below will be returned.

Details

Lotic-invertebrate Index for Flow (LIFE) was originally proposed by Extence et al. (1999). biomonitoR implements the Extence et al. (1999) version called extence and the version currently used in UK called life_2017. If agg is set to TRUE the following composite families are used for extence:

1. Psychomyiidae (inc. Ecnomidae)

2. Rhyacophilidae (inc. Glossomatidae)

3. Ancylidae (inc. Acroloxidae)

4. Gammaridae (inc. Crangonyctidae)

5. Planariidae (inc. Dugesidae)

6. Hydrobiidae (inc. Bithyniidae)

while for life_2017 the following are used:

1. Hydrophilidae (inc. Georissidae, Helophoridae, Hydrochidae)

life() automatically check for parent-child pairs in the scoring system, see the return section for a definition. All the information used for LIFE 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 life().

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

• abu_df The data.frame containing scores and abundance classes for each site.

• life_df The data.frame used for the calculation containing scores for each site.

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

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

• parent_child_pairs For instance in Spanish bmwp both Ferrissia and Planorbidae receive a score. Abundances of the higher taxonomic level need therefore to be adjusted by subtracting the abundances of the lower taxonomic level.

Acknowledgements

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

References

Extence CA, Balbi DM, Chadd RP. 1999. River flow indexing using British benthic macroinvertebrates: a framework for setting hydroecological objectives. Regulated Rivers: Research and Management 15: 543-574.

See Also

as_biomonitor

Examples

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

# change abundance classes
life(data_agr, abucl = c(1, 9, 99, 999))

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

life_fg <- data.frame(
  Taxon = c("Ephemerellidae", "Leuctridae", "Chironomidae"),
  FG_Score = c(1, 2, 3)
)

life_acc <- data.frame(Taxon = "Ephemerellidae", Correct_Taxon = "Chironomidae")

fs_scores <- data.frame(
  FS = rep(1:3, each = 3), ABUCLASS = rep(1:3, 3),
  SCORE = c(9, 10, 11, 8, 9, 10, 7, 7, 7)
)

# without aggregation rules
life(data_agr, method = life_fg, fs_scores = fs_scores, traceB = TRUE)

# with aggregation

life(data_agr, method = life_fg, agg = life_acc, fs_scores = fs_scores, traceB = TRUE)

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