View source: R/mobr_boxplots.R
calc_div | R Documentation |
Compute various diversity indices from a vector of species abundances (i.e., one row of a community matrix)
calc_div(
x,
index,
effort = NA,
rare_thres = 0.05,
replace = FALSE,
C_target = NULL,
extrapolate = TRUE,
...
)
x |
is a vector of species abundances |
index |
The calculated biodiversity indices. The options are
See Details for additional information on the biodiversity statistics. |
effort |
The standardized number of individuals used for the calculation of rarefied species richness. This can a be single integer or a vector of integers. |
rare_thres |
The threshold that determines how pct_rare is computed. It can range from (0, 1] and defaults to 0.05 which specifies that any species with less than or equal to 5 considered rare. It can also be specified as "N/S" which results in using average abundance as the threshold which McGill (2011) found to have the best small sample behavior. |
replace |
Used for |
C_target |
When computing coverage based richness ( |
extrapolate |
Boolean which specifies if richness should be extrapolated when effort is larger than the number of individuals using the chao1 method. |
... |
additional arguments that can be passed to the function
|
data(inv_tank)
calc_div(tank_comm[1, ], 'S_n', effort = c(5, 10))
calc_div(tank_comm[1, ], 'S_C', C_target = 0.9)
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