CalcSPEAR: SPEcies At Risk

Description Usage Arguments Details Value Note References See Also Examples


Indicator based on biological traits used to detect effects of pesticides on non-target freshwater invertebrate organisms. It can be calculated at Taxonomic Levels 2, 4 and 5.


CalcSPEAR(data, season = NULL, TL = 2L,



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'


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.


An integer vector containing up to 3 elements which would represent the taxonomic level to calulate SPEAR at.

Flag (TRUE / FALSE) to inform the program whether the recovery area information has been added to the input parameters.


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). The presence of Recovery area Information can be included adding a ninth column named Rec whose possible values are NULL, 1 or 0, for unknown, presence and no presence, respectively.

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.

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


A dataframe with the following columns: TL, Site, Season or Sample ID, Year or Date (Date object), Infered, Recovery Area information, SPEAR index, Water quality classes, Calculated Toxic Exposure (see 'Note'), Aggregated SPEAR abundance and Aggregated SPEAR Log(Abundance). The last two columns are merely informative and not required when showing SPEAR results.


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

The computed Calculated Toxicant Exposure is only valid for sampling times during and shortly after the main agricultural insecticide use (first 3 months of the agricultural season).


Liess M. & Von der Ohe P. 2005. Analyzing effects of pesticides on invertebrate communities in streams. Environ Toxicol Chem. 24: 954-965.

Wogram J. & Liess M. 2001. Rank ordering of macroinvertebrate species sensitivity to toxic compounds by comparison with that of Daphnia magna. Bull Environ Contam Toxicol. 67: 360-367

Liess M., Schaefer R., Schriever C. 2008. The footprint of pesticide stress in communities - Species traits reveal community effects of toxicants. Science of the Total Environment. 406: 484-490

See Also



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