synoptic-methods: Get components of synoptic objects.
In kardinal-eros/synoptic: Synoptic Tables for Vegsoup Objects

synoptic-methods

R Documentation

Get components of synoptic objects.

Description

A set of simple functions to obtain components, summary tables or index-like vectors and matrices of ⁠synoptic⁠ and/or ⁠monoptic⁠ objects. The function names are held as short as possible, reoccurring acronyms include the following: ft stands for Fisher test and fm for fidelity measure.

Usage

nc(x)
nc.n(x)

stat.min(x)
p.max(x)

fm(x)
fm.m(x)

cs(x)
ct(x)
oc(x)
fq(x)

ll(x)
ll.o(x)
tt(x)

d(x)
dc(x)

ft.t(x)
ft.s(x)
ft.n(x)
ft.c(x)
ft.any(x)

ff(x)

q0(x)
q0.25(x)
q0.5(x)
q0.75(x)
q1(x)
qs(x)

pr(x)

Arguments

`x`	`synoptic` object.

Details

The methods have the following meaning for ⁠synoptic⁠ objects.

nc: Returns number of clusters.
nc.n: Returns number of plots per cluster.
stat.min: Reports the applied threshold value for fidelity statistic.
p.max: Reports the applied threshold value of Fisher test.
fm: Returns fidelity values.
fm.m: Returns the cluster with highest fidelity value for each species.
cs: Returns a constancy table.
ct: Returns a contingency table.
oc: Returns a logical matrix of species occurrences in clusters.
fq: Returns species frequencies.
ll: Returns layer assignments.
ll.o: Returns layer assignments as ordered integer (see layernumber).
tt: Returns scientific species names.
d: Returns ⁠TRUE⁠ for faithful species, those with fidelity values and Fisher test above threshold (⁠stat.min⁠ and ⁠p.max⁠) in at least in one cluster.
dc: Returns ⁠TRUE⁠ for faithful species, as above, but only in a particular partition, hence only applicable for class ⁠monoptic⁠.
ft.t: Reports if Fisher test is within threshold ⁠p.max⁠.
ft.s: Returns Fisher test significance symbols.
ft.n: Reports the number of clusters with significant Fisher test (see ⁠p.max⁠).
ft.c: Returns the clusters for which a Fisher test is significant.
ff: Reports if fidelity measure is above threshold ⁠stat.min⁠ and at least one Fisher test is significant (⁠p.max⁠).
ft.any: Reports if at least one cluster is significant for a Fisher test and a given species.
q0, q0.25, q0.5, q0.75, q1: Get abundance quantiles (min, lower, median, upper, max).
qs: Reports if cover is back transformed. If TRUE abundance quantiles are available in original abundance scale, otherwise class midpoints are returned.
pr: Reports the private species, those occurring in a particular cluster only.

Value

The functions are grouped by their returned class and/or mode. Except otherwise mentioned the function return objects equal to ⁠length(x)⁠.

nc, nc.n, stat.min, p.max, fm.m, fq, ll.o, ft.n: Return ⁠numeric⁠ vectors. stat.min and p.max return vectors of length 1, the remaining functions vectors of length(x), the number of species and species layer replicates, respectively.
ll, tt: Return a ⁠character⁠ vector.
d, ff, ft.any pr: Return ⁠logical⁠ vectors.
fm, cs, ct,: Return a ⁠matrix⁠ of mode ⁠numeric⁠ with as many columns as there are clusters (nc(x)).
oc: Return a ⁠matrix⁠ of mode ⁠logical⁠ with as many columns as there are clusters (nc(x)).
ft.t: Returns a ⁠logical⁠ vector sigifing if Fisher test threshold (⁠p.max⁠) is achieved.
ft.s: Returns a ⁠matrix⁠ of mode ⁠character⁠
ft.c: Returns a ⁠list⁠ of ⁠numeric⁠ vectors

Author(s)

Roland Kaiser

Examples

# a dummy example using simulated data
library(vegsoup)
xx <- fidelity(VegsoupPartition(coenoflex(), k = 3))
x <- synoptic(xx)

# show object
x

# number of clusters
nc(x)
# number of samples per cluster
nc.n(x)
# threshold value fidelity statistic
stat.min(x)
# threshold value Fisher test
p.max(x)
# fidelity values
fm(x)
# cluster with highest fidelity
fm.m(x)
# constancy table
cs(x)
# contingency table
ct(x)
# matrix of species occurences
oc(x)
# species frequencies
fq(x)
# layer assigment
ll(x)
# layer assignments as ordered integer
ll.o(x)
# scientific species name
tt(x)

# TRUE if faithful species
d(x)
# Fisher test is within threshold
ft.t(x)
# Fisher test significance symbols
ft.s(x)
# number of clusters with significant Fisher test
ft.n(x)
# clusters for which Fisher test is significant
ft.c(x)
# fidelity measure above threshold and
# at least one significant Fisher test
ff(x)
# at least one species is significant for a Fisher test
ft.any(x)

kardinal-eros/synoptic documentation built on Jan. 13, 2024, 9:16 p.m.