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Get seagrass average abundance and occurrence across transects

Usage

anlz_transectocc(transect)

Arguments

transect

data frame returned by read_transect

Value

A data frame with abundance and frequency occurrence estimates aggregated by species, transect, and date. The nsites column is the total number of placements that were sampled along a transect for a particular date.

Details

Abundance and frequency occurrence are estimated as in Sherwood et al. 2017, equations 1 and 2. In short, frequency occurrence is estimated as the number of instances a species was observed along a transect divided by the number of placements along a transect and average abundance was estimated as the sum of species-specific Braun-Blanquet scores divided by the number of placements along a transect. The estimates are obtained for all seagrass species including Caulerpa, whereas all attached and drift algae species are aggregated.

References

Sherwood, E.T., Greening, H.S., Johansson, J.O.R., Kaufman, K., Raulerson, G.E. 2017. Tampa Bay (Florida, USA): Documenting seagrass recovery since the 1980's and reviewing the benefits. Southeastern Geographer. 57(3):294-319.

Examples

if (FALSE) {
transect <- read_transect()
}
anlz_transectocc(transect)
#> # A tibble: 30,282 × 6
#> # Groups:   Date, Transect [1,442]
#>    Date       Transect Savspecies              nsites foest bbest
#>    <date>     <chr>    <chr>                    <int> <dbl> <dbl>
#>  1 1997-10-11 S2T3     "AA"                        41     0     0
#>  2 1997-10-11 S2T3     "CYAN: Lyngbya/Dapis"       41     0     0
#>  3 1997-10-11 S2T3     "Caulerpa"                  41     0     0
#>  4 1997-10-11 S2T3     "DA"                        41     0     0
#>  5 1997-10-11 S2T3     "DG: Chaetomorpha\r\n"      41     0     0
#>  6 1997-10-11 S2T3     "DG: Drift Green"           41     0     0
#>  7 1997-10-11 S2T3     "DG: Ulva"                  41     0     0
#>  8 1997-10-11 S2T3     "DG: Ulva fasciata\r\n"     41     0     0
#>  9 1997-10-11 S2T3     "DR: Acanthophora"          41     0     0
#> 10 1997-10-11 S2T3     "DR: Drift Red"             41     0     0
#> # … with 30,272 more rows