StandardiseRawTaxa: Standardise Raw Taxa

In aquaMetrics/aquaMetrics: Freshwater Biotic indices

Description

This function standardise taxa retrieved from NEMS to all available Taxon Levels. Most of the times this function will be run to generate the input data required by the other functions present in this package.

Usage

StandardiseRawTaxa(family.df = NULL, species.df = NULL,
                   infer.lower.levels = FALSE,
                   aggregate = "sample")

Arguments

family.df	An optional data frame containing family-level data from NEMS (Analysis: FW_TAX_ID) with at least six columns and in the specified order. Extra columns can be added, but they must be only related to Sampling Point. See 'Details'.
species.df	An optional data frame containing species-level data from NEMS (Analysis: MIXTAX_TST) with at least six columns and in the specified order. Extra columns can be added, but they must be only related to Sampling Point. See 'Details'.
infer.lower.levels	Flag (TRUE/FALSE) to infer Taxonomic Levels at TL1, TL2 and TL3 from species-level data.
aggregate	Indicates whether the aggregation is either done by "sample" or by "season". Depending on the aggregation, input data frames should be composed of different type of columns.

Details

Both family.df and species.df are data frames containing at least the following six columns, depending on the 'aggregate' parameter:
"season": Site, Season (integer), Year, Maitland Code, Maitland Name, Abundance.
"sample": Site, Sample Number, Sample Date (Date object), Maitland Code, Maitland Name, Abundance.
Actually, the routine performs the same calculations for both types of aggregation, the only change is the name of the output data frame's columns.

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 list containing 3 data frames.

standard.taxa: Dataframe containing the following columns (depending on input data): TL (integer), Sampling Point, Season or Sample, Year or Date, Maitland Code, Name, Abundance, Infered (integer).
The column Infered indicates whether TL1/TL2/TL3 were infered from data in species.df If the user entered extra columns within the input dataframes they will be included here as well.

not.included.families: Dataframe (which can be empty) containing those input families that have not been found in any of the TL lists.

not.included.species: Dataframe (which can be empty) containing those input species that have not been found in any of the TL lists.

Note

More extra columns can be added to aggregate data by different criteria, i.e., other than season/date. For doing so you must fill all season/date fields with a dummy value: 1. Thus, the aggregation would disregard season/date as an aggregation column.

Examples

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