Get seagrass average abundance and occurrence across transects
Source:R/anlz_transectocc.R
anlz_transectocc.RdGet seagrass average abundance and occurrence across transects
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 (attached macroalgae), Dapis (cyanobacteria), and Chaetomorpha (drift green algea), whereas all other attached and drift algae species are aggregated. Drift or attached macroalgae and cyanobacteria (Dapis) estimates may not be accurate prior to 2021.
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) { # \dontrun{
transect <- read_transect()
} # }
anlz_transectocc(transect)
#> # A tibble: 43,596 × 6
#> # Groups: Date, Transect [1,557]
#> 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 "Caulerpa" 41 0 0
#> 3 1997-10-11 S2T3 "Chaetomorpha" 41 0 0
#> 4 1997-10-11 S2T3 "DA" 41 0 0
#> 5 1997-10-11 S2T3 "DB: Dictyota\r\n" 41 0 0
#> 6 1997-10-11 S2T3 "DB: Drift Brown\r\n" 41 0 0
#> 7 1997-10-11 S2T3 "DG: Drift Green" 41 0 0
#> 8 1997-10-11 S2T3 "DG: Ulva" 41 0 0
#> 9 1997-10-11 S2T3 "DG: Ulva fasciata\r\n" 41 0 0
#> 10 1997-10-11 S2T3 "DG: Ulva intestinales\r\n" 41 0 0
#> # ℹ 43,586 more rows