CalcCC: Climate Change Metric

In aquaMetrics/aquaMetrics: Freshwater Biotic indices

Description

A temperature metric that computes the ratio or porportion of organisms with different temperature tolerances. It can be calculated at Taxonomic Levels 5 and 4

Usage

CalcCC(data, season = NULL, TL = 5L,
       method = 1L)

Arguments

data	A dataframe containing standardised taxa with at least eight columns and in the specified order. Extra columns can be added, but they must be related to Sampling Point. See 'Details'
season	Optional. An integer vector containing up to 7 elements, from 1L to 7L. It is only needed when the input data frame contains Season and Year instead of Sample ID and Date. See 'Details' for more info about input columns.
TL	An integer vector containing up to 2 elements which would represent the taxonomic level to calulate Climate Change at.
method	It can take either take the numeric value 1L, which computes the percentage of indicators, or 2 which calculates the proportion of n thermal indicators (useful when data contain log abundances rather than counts).

Details

The input dataframe data must contain a minimum of eight columns in the specified order: TL (Taxonomic Level), Site, Season or Sample ID, Year or Date (Date object), Maitland Code, Maitland Name, Abundance, Infered (Code returned by the function StandardiseRawTaxa which can be declared as 0 if StandardiseRawTaxa is not used). If the data frame contains Season and Year instead of Sample ID / Date, the season parameter must be a vector of the form c(1L, 3L, 5L), indicating which seasons, and combination of seasons, must be computed. This function works with both current Maitland Codes and new ones, defined as of JUL-2014.

The available codes for Season and a general description of Taxonomic Levels are defined in the main help page of the aquaMetrics package.

Value

A dataframe with the following columns: TL, Site, Season or Sample ID, Year or Date (Date object), Infered, extra columns - if any, and CC metrics which contain CS (Cold Stenotherms), WS (Warm Stenotherms), E (Eurytherms) and TIndicators (Percentage or proportion of thermal indicators in the sample).

Note

The extra columns can be used to aggregate data by different criteria, i.e., other than season or Sample ID. For doing so you must fill all season fields with a dummy value 1. Thus, the aggregation will disregard season/SampleID as an aggregation column.

See Also

StandardiseRawTaxa

Examples

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aquaMetrics/aquaMetrics documentation built on May 6, 2019, 7:26 a.m.