conservation_value_seq: Sequentially removes occasional species according to...

In fsfrazao/SharedS: Assessing the influence of occasional species on shared-species metrics

Description

This function sequenctially removes occasional species according to increasing abundance and/or occupancy classes and calculates conservation value metrics in order to produce a curve. m1-> the proportion of all species that is shared between two communities m2-> the proportion of all species that is unique to one of the two communities m3-> the proportion of the species that occur in one of the communities that is unique to that community Each metric will be calulated once for each of the removal classes (1 to 'seq').

Usage

conservation_value_seq(x, y, seq, removal_rule = 2,
  removal_routine = "a")

Arguments

x	A community matrix, with species in columns and samples in rows
y	A community matrix, with species in columns and samples in rows
seq	The maximum removal class to be removed. The sequence will wil go from zero to this class (inclusive)
removal_rule	The removal_rule to be used.If 1, applies the removal routine to x and y. If 2, applies on to y.
removal_routine	The removal_routine to be used. If "a", removes by abundance class using the 'occasional_abundance' function. If "o", removes by occupancy class using the 'occasional_occupancy' function. If "b", removes by abundance and then occupancy, using the same occasional class for both.

Value

A list with $m1, $m2 and $m3 vectors, each with seq elements

Examples

data(community_data)

#Select all samples in Evironment 'A'
comm.A<-community_data[which(community_data$environment == "A"),]

# Select only the abundance matrix (columns 1 and 2 contain the 'environment' and 'sample' data)
comm.A <- comm.A[, 3:ncol(comm.A)]

#Select all samples in Evironment 'B'
comm.B<-community_data[which(community_data$environment == "B"),]

# Select only the abundance matrix (columns 1 and 2 contain the 'environment' and 'sample' data)
comm.B <- comm.B[, 3:ncol(comm.B)]

 # Sequentially remove abundance classes from both communities and and calculate the conservation metrics.
 conservation_value_seq(comm.A, comm.B, 5, removal_rule=2, removal_routine="a")
$m1
[1] 0.9666667 0.9333333 0.9333333 0.9000000 0.9000000 0.8333333

$m2
[1] 0.00000000 0.03333333 0.03333333 0.03333333 0.03333333 0.10000000

$m3
[1] 0.00000000 0.03448276 0.03448276 0.03571429 0.03571429 0.10714286

fsfrazao/SharedS documentation built on July 1, 2019, 6:24 p.m.