tol_index: Compute Tolerance Indices

Description Usage Arguments Value


Compute Tolerance Indices


tol_index(long.df, master.df, tolerance.value = "BIBI_TV",
  taxa.rank = "FAMILY", remove_na = TRUE)



Taxonomic counts arrange in a long data format (i.e., each row represents a unique sample and taxon).


A master taxa list including taxonomic ranks Phylum through the specified taxonomic rank (Family or Genus) and the an associated list of tolerance values. The default is set to the master taxa list included in the BIBI package. The master taxa list can be viewed with the following script: master.df <- data(master)


The name of the column in the master taxon list (specified using the master variable) that contains tolerance values on a scale of 0-10.


The taxonomic rank used to perform the analysis. You must sepecify either "FAMILY" or "GENUS" (Defualt = "FAMILY").


If taxa are missing tolerance assigned tolerance values (tolerance.value == NA) then the scores could be skewed downward. Setting this parameter to TRUE will exclude these taxa and provide a better estimate of the tolerance measure being calculated.


The average tolerance score per individual for each unique sampling event. This metric is calculated at the family or genus level. If taxon does not have an assigned tolerance value it will not contribute to the final score. The count representing each taxon is multiplied by the taxon's tolerance value. If the tolerance value is missing it would be treated effectively as a zero, which would reduce the average tolerance score; to avoid this issue, it is more effective to remove the taxa without any tolerance values. However, if a large portion of the sample is composed of a taxon or taxa without assigned tolerance values the final value may be a poor representation of the sample. Every effort should be made to assign each taxon a tolerance value. If you have tolerance values that you would like to contribute and share through the BIBI package please email Zachary M. Smith (

zsmith27/Benthos documentation built on May 5, 2019, 2:38 a.m.