Description Usage Arguments Details Value Author(s) Examples
A set of simple functions to obtain components, summary tables or indexlike
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.
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x 

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.
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
Roland Kaiser
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50  # 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)

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