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Calculates ISI, the Indicator Species Index

Source: R/ISI.R
ISI.Rd

ISI() matches a list of species with the Norwegian species list and calculates ISI the Indicator Species Index. (Borgersen et al, 2019)

Usage

ISI(
  df,
  by = NULL,
  var_species = "species",
  df_species = NULL,
  version = "2018"
)

Arguments

df

a dataframe of species observations

by

a vector of column names found in df by which calculations should be grouped e.g. c("station","date")

var_species

name of the column in df containing species names

df_species

optional dataframe with user-specified species list.

version

string, version of the index to be calculated. The default value is "2018". The the only other valid value for version is "2012".

Value

a list of two dataframes:

  • ISI : results of the ISI index calculations. For each unique combination of byvariables the following values are calculated:

    • ISI<version> : the sensitivity index ISI2018 or ISI2012

    • S : the number of species

    • N : the number of individuals

  • match : the original dataframe with columns added from the species list. For a user-specified list provided df_species, all columns will be included. If the user-specified species list contains only a single column with species names, then a new column match will be created, with a value of 1 indicating a match and an NA value where no match was found. One of the following columns will be included, depending on the ISI version:

    • ES100min5_2018 : species sensitivity values used to calculate ISI2018

    • ES100min5_2012 : species sensitivity values used to calculate ISI2012

Details

If the function is called with the argument check_species = TRUE then only species which are successfully matched with the specified species list are included in the calculations. This is the default. If the function is called with check_species = FALSEthen all rows are counted.

References

Borgersen, G., Trannum, H.C., Gundersen, H., Vedal, J. (2019). Oppdatering av bløtbunnsartenes sensitivitetsverdier (Report No. 7366). Norsk institutt for vannforskning (NIVA). https://hdl.handle.net/11250/2600903

Rygg, B., Norling, K. (2013). Norwegian Sensitivity Index (NSI) for marine macroinvertebrates, and an update of Indicator Species Index (ISI). (Report No. 6475). Norsk institutt for vannforskning (NIVA). 46 pp.

See also

NSI() which calculates the Norwegian Sensitivity Index. For more details, see`vignette("other-indices").

Examples


ISI(test_data_NO, by="station", var_species ="species")
#> $ISI
#> # A tibble: 2 × 3
#>   station         ISI2018     S
#>   <chr>             <dbl> <int>
#> 1 Ærøy (U10)         7.31    61
#> 2 Ærøydypet (U12)    6.79    39
#> 
#> $matched
#> # A tibble: 206 × 13
#>    station       sample species count ES100avg_2018 ES100min5_2018 ES100avg_2012
#>    <chr>         <chr>  <chr>   <dbl>         <dbl>          <dbl>         <dbl>
#>  1 Ærøy (U10)    G1     Dipoly…     1            NA             NA          NA  
#>  2 Ærøy (U10)    G2     Zoeala…     1            NA             NA          NA  
#>  3 Ærøydypet (U… G1     Zoeala…     2            NA             NA          NA  
#>  4 Ærøydypet (U… G2     Zoeala…     2            NA             NA          NA  
#>  5 Ærøy (U10)    G1     Zoeala…     5            NA             NA          NA  
#>  6 Ærøy (U10)    G2     Animal…     1            NA             NA          NA  
#>  7 Ærøy (U10)    G1     Tanaid…    13            NA             NA          28.6
#>  8 Ærøy (U10)    G2     Tanaid…     1            NA             NA          28.6
#>  9 Ærøydypet (U… G2     Ophiur…     1            NA             NA          27.8
#> 10 Ærøy (U10)    G1     Bivalv…     1            NA             NA          28.4
#> # ℹ 196 more rows
#> # ℹ 6 more variables: ES100min5_2012 <dbl>, group_AMBI <dbl>, group_NSI <dbl>,
#> #   group_ISI <dbl>, Revidert <chr>, Kommentar <chr>
#>