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.
1 2 3
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'.
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'.
Flag (TRUE/FALSE) to infer Taxonomic Levels at TL1, TL2 and TL3 from species-level data.
Indicates whether the aggregation is either done by
species.df are data frames containing at least
the following six columns, depending on the 'aggregate' parameter:
Sample Date (Date object),
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
A list containing 3 data frames.
standard.taxa: Dataframe containing the following columns (depending on input data):
Infered indicates whether TL1/TL2/TL3 were infered from
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.
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.
1 2 3 4
## Not run: #No examples yet ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.