Wavelet Approaches to Studies of Synchrony in Ecology and Other Fields

Documentation for package ‘wsyn’ version 1.0.4

Help Pages

-- A --

addranks	Adds rank information to a 'coh' or 'wlmtest' object
addwmfs	Adds wavelet mean field information to a 'clust' object
addwpmfs	Adds wavelet phasor mean field information to a 'clust' object

-- B --

bandtest	Aggregate significance across a timescale band
bandtest.coh	Aggregate significance across a timescale band
bandtest.default	Aggregate significance across a timescale band
bandtest.wlmtest	Aggregate significance across a timescale band
bctrans	The one-parameter family of Box-Cox transformations

-- C --

cleandat	Clean (spatio)temporal data matrices to make them ready for analyses using the 'wsyn' package
cluseigen	Community structure detection in networks
clust	Detection and description of clusters of synchronous locations
clust_methods	Basic methods for the 'clust' class
coh	Coherence
coh_methods	Basic methods for the 'coh' class

-- E --

errcheck_stdat	Error check for appropriate spatio-temporal data
errcheck_times	Error check 'times'
errcheck_tsdat	Error check for appropriate temporal data
errcheck_tts	Error check whether inputs are suitable for a tts object
errcheck_wavparam	Error check wavelet transform parameters

-- F --

fastcohtest	Fast algorithm for significance testing coherence using Fourier surrogates
fftsurrog	Surrogate time series using Fourier surrogates

-- G --

get_adj	Set and get methods for classes in the 'wsyn' package
get_adj.clust	Basic methods for the 'clust' class
get_adj.default	Set and get methods for classes in the 'wsyn' package
get_bandp	Set and get methods for classes in the 'wsyn' package
get_bandp.coh	Basic methods for the 'coh' class
get_bandp.default	Set and get methods for classes in the 'wsyn' package
get_bandp.wlmtest	Basic methods for the 'wlmtest' class
get_clusters	Set and get methods for classes in the 'wsyn' package
get_clusters.clust	Basic methods for the 'clust' class
get_clusters.default	Set and get methods for classes in the 'wsyn' package
get_coefs	Set and get methods for classes in the 'wsyn' package
get_coefs.default	Set and get methods for classes in the 'wsyn' package
get_coefs.wlm	Basic methods for the 'wlm' class
get_coher	Set and get methods for classes in the 'wsyn' package
get_coher.coh	Basic methods for the 'coh' class
get_coher.default	Set and get methods for classes in the 'wsyn' package
get_coher.wlm	Basic methods for the 'wlm' class
get_coords	Set and get methods for classes in the 'wsyn' package
get_coords.clust	Basic methods for the 'clust' class
get_coords.default	Set and get methods for classes in the 'wsyn' package
get_dat	Set and get methods for classes in the 'wsyn' package
get_dat.clust	Basic methods for the 'clust' class
get_dat.default	Set and get methods for classes in the 'wsyn' package
get_dat.wlm	Basic methods for the 'wlm' class
get_dat.wmf	Basic methods for the 'wmf' class
get_dat.wpmf	Basic methods for the 'wpmf' class
get_dat.wt	Basic methods for the 'wt' class
get_dat1	Set and get methods for classes in the 'wsyn' package
get_dat1.coh	Basic methods for the 'coh' class
get_dat1.default	Set and get methods for classes in the 'wsyn' package
get_dat2	Set and get methods for classes in the 'wsyn' package
get_dat2.coh	Basic methods for the 'coh' class
get_dat2.default	Set and get methods for classes in the 'wsyn' package
get_drop	Set and get methods for classes in the 'wsyn' package
get_drop.default	Set and get methods for classes in the 'wsyn' package
get_drop.wlmtest	Basic methods for the 'wlmtest' class
get_methodspec	Set and get methods for classes in the 'wsyn' package
get_methodspec.clust	Basic methods for the 'clust' class
get_methodspec.default	Set and get methods for classes in the 'wsyn' package
get_mns	Set and get methods for classes in the 'wsyn' package
get_mns.clust	Basic methods for the 'clust' class
get_mns.default	Set and get methods for classes in the 'wsyn' package
get_modres	Set and get methods for classes in the 'wsyn' package
get_modres.clust	Basic methods for the 'clust' class
get_modres.default	Set and get methods for classes in the 'wsyn' package
get_modval	Set and get methods for classes in the 'wsyn' package
get_modval.default	Set and get methods for classes in the 'wsyn' package
get_modval.wlm	Basic methods for the 'wlm' class
get_norm	Set and get methods for classes in the 'wsyn' package
get_norm.coh	Basic methods for the 'coh' class
get_norm.default	Set and get methods for classes in the 'wsyn' package
get_norm.wlm	Basic methods for the 'wlm' class
get_ranks	Set and get methods for classes in the 'wsyn' package
get_ranks.coh	Basic methods for the 'coh' class
get_ranks.default	Set and get methods for classes in the 'wsyn' package
get_ranks.wlmtest	Basic methods for the 'wlmtest' class
get_sigmethod	Set and get methods for classes in the 'wsyn' package
get_sigmethod.coh	Basic methods for the 'coh' class
get_sigmethod.default	Set and get methods for classes in the 'wsyn' package
get_signif	Set and get methods for classes in the 'wsyn' package
get_signif.coh	Basic methods for the 'coh' class
get_signif.default	Set and get methods for classes in the 'wsyn' package
get_signif.wlmtest	Basic methods for the 'wlmtest' class
get_signif.wpmf	Basic methods for the 'wpmf' class
get_times	Set and get methods for classes in the 'wsyn' package
get_times.clust	Basic methods for the 'clust' class
get_times.coh	Basic methods for the 'coh' class
get_times.default	Set and get methods for classes in the 'wsyn' package
get_times.tts	Basic methods for the 'tts' class
get_times.wlm	Basic methods for the 'wlm' class
get_times.wmf	Basic methods for the 'wmf' class
get_times.wpmf	Basic methods for the 'wpmf' class
get_times.wt	Basic methods for the 'wt' class
get_timescales	Set and get methods for classes in the 'wsyn' package
get_timescales.coh	Basic methods for the 'coh' class
get_timescales.default	Set and get methods for classes in the 'wsyn' package
get_timescales.tts	Basic methods for the 'tts' class
get_timescales.wlm	Basic methods for the 'wlm' class
get_timescales.wmf	Basic methods for the 'wmf' class
get_timescales.wpmf	Basic methods for the 'wpmf' class
get_timescales.wt	Basic methods for the 'wt' class
get_values	Set and get methods for classes in the 'wsyn' package
get_values.default	Set and get methods for classes in the 'wsyn' package
get_values.tts	Basic methods for the 'tts' class
get_values.wmf	Basic methods for the 'wmf' class
get_values.wpmf	Basic methods for the 'wpmf' class
get_values.wt	Basic methods for the 'wt' class
get_wlmobj	Set and get methods for classes in the 'wsyn' package
get_wlmobj.default	Set and get methods for classes in the 'wsyn' package
get_wlmobj.wlmtest	Basic methods for the 'wlmtest' class
get_wmfs	Set and get methods for classes in the 'wsyn' package
get_wmfs.clust	Basic methods for the 'clust' class
get_wmfs.default	Set and get methods for classes in the 'wsyn' package
get_wpmfs	Set and get methods for classes in the 'wsyn' package
get_wpmfs.clust	Basic methods for the 'clust' class
get_wpmfs.default	Set and get methods for classes in the 'wsyn' package
get_wtopt	Set and get methods for classes in the 'wsyn' package
get_wtopt.coh	Basic methods for the 'coh' class
get_wtopt.default	Set and get methods for classes in the 'wsyn' package
get_wtopt.wlm	Basic methods for the 'wlm' class
get_wtopt.wmf	Basic methods for the 'wmf' class
get_wtopt.wpmf	Basic methods for the 'wpmf' class
get_wtopt.wt	Basic methods for the 'wt' class
get_wts	Set and get methods for classes in the 'wsyn' package
get_wts.default	Set and get methods for classes in the 'wsyn' package
get_wts.wlm	Basic methods for the 'wlm' class

-- I --

is.connected

Tests if a graph is connected

-- M --

makeunweighted	For converting certain synchrony matrices to unweighted versions
mnphase	Mean phase of coherence
modularity	Modularity of a community structure of a graph

-- N --

normforcoh

Normalization for the 'coh' function

-- P --

plotmag	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.coh	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.default	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.tts	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.wlmtest	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.wmf	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.wpmf	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmag.wt	For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects
plotmap	Map clusters from a 'clust' object
plotphase	For plotting the phases of values in 'tts' and 'coh' objects
plotphase.coh	For plotting the phases of values in 'tts' and 'coh' objects
plotphase.default	For plotting the phases of values in 'tts' and 'coh' objects
plotphase.tts	For plotting the phases of values in 'tts' and 'coh' objects
plotphase.wmf	For plotting the phases of values in 'tts' and 'coh' objects
plotphase.wpmf	For plotting the phases of values in 'tts' and 'coh' objects
plotphase.wt	For plotting the phases of values in 'tts' and 'coh' objects
plotrank	Plots 'ranks' slot for 'coh' and 'wlmtest' objects
plotrank.coh	Plots 'ranks' slot for 'coh' and 'wlmtest' objects
plotrank.default	Plots 'ranks' slot for 'coh' and 'wlmtest' objects
plotrank.wlmtest	Plots 'ranks' slot for 'coh' and 'wlmtest' objects
power	Power of a 'tts' object
power.tts	Power of a 'tts' object
predsync	Predicted synchrony of a wavelet linear model
predsync.wlm	Predicted synchrony of a wavelet linear model
print.clust	Basic methods for the 'clust' class
print.coh	Basic methods for the 'coh' class
print.summary_wsyn	Print method for 'summary_wsyn' class
print.tts	Basic methods for the 'tts' class
print.wlm	Basic methods for the 'wlm' class
print.wlmtest	Basic methods for the 'wlmtest' class
print.wmf	Basic methods for the 'wmf' class
print.wpmf	Basic methods for the 'wpmf' class
print.wt	Basic methods for the 'wt' class

-- S --

setget_methods	Set and get methods for classes in the 'wsyn' package
setmints	Shifts a vector according to the argument mints
set_adj	Set and get methods for classes in the 'wsyn' package
set_adj.clust	Basic methods for the 'clust' class
set_adj.default	Set and get methods for classes in the 'wsyn' package
set_bandp	Set and get methods for classes in the 'wsyn' package
set_bandp.coh	Basic methods for the 'coh' class
set_bandp.default	Set and get methods for classes in the 'wsyn' package
set_bandp.wlmtest	Basic methods for the 'wlmtest' class
set_clusters	Set and get methods for classes in the 'wsyn' package
set_clusters.clust	Basic methods for the 'clust' class
set_clusters.default	Set and get methods for classes in the 'wsyn' package
set_coefs	Set and get methods for classes in the 'wsyn' package
set_coefs.default	Set and get methods for classes in the 'wsyn' package
set_coefs.wlm	Basic methods for the 'wlm' class
set_coher	Set and get methods for classes in the 'wsyn' package
set_coher.coh	Basic methods for the 'coh' class
set_coher.default	Set and get methods for classes in the 'wsyn' package
set_coher.wlm	Basic methods for the 'wlm' class
set_coords	Set and get methods for classes in the 'wsyn' package
set_coords.clust	Basic methods for the 'clust' class
set_coords.default	Set and get methods for classes in the 'wsyn' package
set_dat	Set and get methods for classes in the 'wsyn' package
set_dat.clust	Basic methods for the 'clust' class
set_dat.default	Set and get methods for classes in the 'wsyn' package
set_dat.wlm	Basic methods for the 'wlm' class
set_dat.wmf	Basic methods for the 'wmf' class
set_dat.wpmf	Basic methods for the 'wpmf' class
set_dat.wt	Basic methods for the 'wt' class
set_dat1	Set and get methods for classes in the 'wsyn' package
set_dat1.coh	Basic methods for the 'coh' class
set_dat1.default	Set and get methods for classes in the 'wsyn' package
set_dat2	Set and get methods for classes in the 'wsyn' package
set_dat2.coh	Basic methods for the 'coh' class
set_dat2.default	Set and get methods for classes in the 'wsyn' package
set_drop	Set and get methods for classes in the 'wsyn' package
set_drop.default	Set and get methods for classes in the 'wsyn' package
set_drop.wlmtest	Basic methods for the 'wlmtest' class
set_methodspecs	Set and get methods for classes in the 'wsyn' package
set_methodspecs.clust	Basic methods for the 'clust' class
set_methodspecs.default	Set and get methods for classes in the 'wsyn' package
set_mns	Set and get methods for classes in the 'wsyn' package
set_mns.clust	Basic methods for the 'clust' class
set_mns.default	Set and get methods for classes in the 'wsyn' package
set_modres	Set and get methods for classes in the 'wsyn' package
set_modres.clust	Basic methods for the 'clust' class
set_modres.default	Set and get methods for classes in the 'wsyn' package
set_modval	Set and get methods for classes in the 'wsyn' package
set_modval.default	Set and get methods for classes in the 'wsyn' package
set_modval.wlm	Basic methods for the 'wlm' class
set_norm	Set and get methods for classes in the 'wsyn' package
set_norm.coh	Basic methods for the 'coh' class
set_norm.default	Set and get methods for classes in the 'wsyn' package
set_norm.wlm	Basic methods for the 'wlm' class
set_ranks	Set and get methods for classes in the 'wsyn' package
set_ranks.coh	Basic methods for the 'coh' class
set_ranks.default	Set and get methods for classes in the 'wsyn' package
set_ranks.wlmtest	Basic methods for the 'wlmtest' class
set_sigmethod	Set and get methods for classes in the 'wsyn' package
set_sigmethod.coh	Basic methods for the 'coh' class
set_sigmethod.default	Set and get methods for classes in the 'wsyn' package
set_signif	Set and get methods for classes in the 'wsyn' package
set_signif.coh	Basic methods for the 'coh' class
set_signif.default	Set and get methods for classes in the 'wsyn' package
set_signif.wlmtest	Basic methods for the 'wlmtest' class
set_signif.wpmf	Basic methods for the 'wpmf' class
set_times	Set and get methods for classes in the 'wsyn' package
set_times.clust	Basic methods for the 'clust' class
set_times.coh	Basic methods for the 'coh' class
set_times.default	Set and get methods for classes in the 'wsyn' package
set_times.tts	Basic methods for the 'tts' class
set_times.wlm	Basic methods for the 'wlm' class
set_times.wmf	Basic methods for the 'wmf' class
set_times.wpmf	Basic methods for the 'wpmf' class
set_times.wt	Basic methods for the 'wt' class
set_timescales	Set and get methods for classes in the 'wsyn' package
set_timescales.coh	Basic methods for the 'coh' class
set_timescales.default	Set and get methods for classes in the 'wsyn' package
set_timescales.tts	Basic methods for the 'tts' class
set_timescales.wlm	Basic methods for the 'wlm' class
set_timescales.wmf	Basic methods for the 'wmf' class
set_timescales.wpmf	Basic methods for the 'wpmf' class
set_timescales.wt	Basic methods for the 'wt' class
set_values	Set and get methods for classes in the 'wsyn' package
set_values.default	Set and get methods for classes in the 'wsyn' package
set_values.tts	Basic methods for the 'tts' class
set_values.wmf	Basic methods for the 'wmf' class
set_values.wpmf	Basic methods for the 'wpmf' class
set_values.wt	Basic methods for the 'wt' class
set_wlmobj	Set and get methods for classes in the 'wsyn' package
set_wlmobj.default	Set and get methods for classes in the 'wsyn' package
set_wlmobj.wlmtest	Basic methods for the 'wlmtest' class
set_wmfs	Set and get methods for classes in the 'wsyn' package
set_wmfs.clust	Basic methods for the 'clust' class
set_wmfs.default	Set and get methods for classes in the 'wsyn' package
set_wpmfs	Set and get methods for classes in the 'wsyn' package
set_wpmfs.clust	Basic methods for the 'clust' class
set_wpmfs.default	Set and get methods for classes in the 'wsyn' package
set_wtopt	Set and get methods for classes in the 'wsyn' package
set_wtopt.coh	Basic methods for the 'coh' class
set_wtopt.default	Set and get methods for classes in the 'wsyn' package
set_wtopt.wlm	Basic methods for the 'wlm' class
set_wtopt.wmf	Basic methods for the 'wmf' class
set_wtopt.wpmf	Basic methods for the 'wpmf' class
set_wtopt.wt	Basic methods for the 'wt' class
set_wts	Set and get methods for classes in the 'wsyn' package
set_wts.default	Set and get methods for classes in the 'wsyn' package
set_wts.wlm	Basic methods for the 'wlm' class
summary.clust	Basic methods for the 'clust' class
summary.coh	Basic methods for the 'coh' class
summary.tts	Basic methods for the 'tts' class
summary.wlm	Basic methods for the 'wlm' class
summary.wlmtest	Basic methods for the 'wlmtest' class
summary.wmf	Basic methods for the 'wmf' class
summary.wpmf	Basic methods for the 'wpmf' class
summary.wt	Basic methods for the 'wt' class
surrog	Creates surrogate time series, either Fourier surrogates or amplitude adjusted Fourier surrogates
syncexpl	Amount of synchrony explained, and related quantities
syncexpl.wlm	Amount of synchrony explained, and related quantities
synmat	Synchrony matrices

-- T --

tts	Creator function for the 'tts' class
tts_methods	Basic methods for the 'tts' class

-- W --

warray	Creates an array of wavelet transforms from input timeseries
wavmatwork	Facilitates the computations in synmat for coherence and ReXWT methods
wlm	Wavelet linear models
wlmfit	Fits a wavelet linear model
wlmtest	Statistical comparison of wavelet linear models
wlmtest_methods	Basic methods for the 'wlmtest' class
wlm_methods	Basic methods for the 'wlm' class
wmf	Computes the wavelet mean field from a matrix of spatiotemporal data. Also the creator function for the 'wmf' class.
wmf_methods	Basic methods for the 'wmf' class
wpmf	Wavelet phasor mean field
wpmf_methods	Basic methods for the 'wpmf' class
wt	Computes the wavelet transform of a timeseries. Also the creator function for the 'wt' class.
wt_methods	Basic methods for the 'wt' class