# Wavelet Approaches to Studies of Synchrony in Ecology and Other Fields

## Documentation for package ‘wsyn’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C E F G I M N P S T W

## -- 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