{
  "_id": "6a16c3f7acfb0bcc41d882de",
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  "Version": "1.0.4",
  "Type": "Package",
  "Title": "Wavelet Approaches to Studies of Synchrony in Ecology and Other\nFields",
  "Authors@R": "c(\nperson(\"Daniel C.\", \"Reuman\", email = \"reuman@ku.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Thomas L.\", \"Anderson\", email=\"anderstl@gmail.com\", role=c(\"aut\")),\nperson(\"Jonathan A.\", \"Walter\", email = \"jaw3es@virginia.edu\", role=c(\"aut\")),\nperson(\"Lei\", \"Zhao\", email = \"lei.zhao@cau.edu.cn\", role=c(\"aut\")),\nperson(\"Lawrence W.\", \"Sheppard\", email=\"lwsheppard@ku.edu\", role=c(\"aut\"))\n)",
  "Description": "Tools for a wavelet-based approach to analyzing spatial\nsynchrony, principally in ecological data. Some tools will be\nuseful for studying community synchrony. See, for instance,\nSheppard et al (2016) <doi: 10.1038/NCLIMATE2991>, Sheppard et\nal (2017) <doi: 10.1051/epjnbp/2017000>, Sheppard et al (2019)\n<doi: 10.1371/journal.pcbi.1006744>.",
  "License": "GPL-3",
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  "Repository": "https://reumandc.r-universe.dev",
  "Date/Publication": "2022-05-09 19:33:23 UTC",
  "RemoteUrl": "https://github.com/reumandc/wsyn",
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  "Author": "Daniel C. Reuman [aut, cre],\nThomas L. Anderson [aut],\nJonathan A. Walter [aut],\nLei Zhao [aut],\nLawrence W. Sheppard [aut]",
  "Maintainer": "Daniel C. Reuman <reuman@ku.edu>",
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    "message": "typo in vignette that made a difference\n",
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    "description": "Professor, Dpmt of Ecology and Evolutionary Biology; Senior Scientist, Center for Ecological Research; U Kansas. I do data science and quantitative ecology.",
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  "_exports": [
    "addwmfs",
    "addwpmfs",
    "bandtest",
    "cleandat",
    "cluseigen",
    "clust",
    "coh",
    "get_adj",
    "get_bandp",
    "get_clusters",
    "get_coefs",
    "get_coher",
    "get_coords",
    "get_dat",
    "get_dat1",
    "get_dat2",
    "get_drop",
    "get_methodspec",
    "get_mns",
    "get_modres",
    "get_modval",
    "get_norm",
    "get_ranks",
    "get_sigmethod",
    "get_signif",
    "get_times",
    "get_timescales",
    "get_values",
    "get_wlmobj",
    "get_wmfs",
    "get_wpmfs",
    "get_wtopt",
    "get_wts",
    "is.connected",
    "modularity",
    "plotmag",
    "plotmap",
    "plotphase",
    "plotrank",
    "power",
    "predsync",
    "set_adj",
    "set_bandp",
    "set_clusters",
    "set_coefs",
    "set_coher",
    "set_coords",
    "set_dat",
    "set_dat1",
    "set_dat2",
    "set_drop",
    "set_methodspecs",
    "set_mns",
    "set_modres",
    "set_modval",
    "set_norm",
    "set_ranks",
    "set_sigmethod",
    "set_signif",
    "set_times",
    "set_timescales",
    "set_values",
    "set_wlmobj",
    "set_wmfs",
    "set_wpmfs",
    "set_wtopt",
    "set_wts",
    "surrog",
    "syncexpl",
    "synmat",
    "tts",
    "wlm",
    "wlmtest",
    "wmf",
    "wpmf",
    "wt"
  ],
  "_help": [
    {
      "page": "addranks",
      "title": "Adds rank information to a 'coh' or 'wlmtest' object",
      "topics": [
        "addranks"
      ]
    },
    {
      "page": "addwmfs",
      "title": "Adds wavelet mean field information to a 'clust' object",
      "topics": [
        "addwmfs"
      ]
    },
    {
      "page": "addwpmfs",
      "title": "Adds wavelet phasor mean field information to a 'clust' object",
      "topics": [
        "addwpmfs"
      ]
    },
    {
      "page": "bandtest",
      "title": "Aggregate significance across a timescale band",
      "topics": [
        "bandtest",
        "bandtest.coh",
        "bandtest.default",
        "bandtest.wlmtest"
      ]
    },
    {
      "page": "bctrans",
      "title": "The one-parameter family of Box-Cox transformations",
      "topics": [
        "bctrans"
      ]
    },
    {
      "page": "cleandat",
      "title": "Clean (spatio)temporal data matrices to make them ready for analyses using the 'wsyn' package",
      "topics": [
        "cleandat"
      ]
    },
    {
      "page": "cluseigen",
      "title": "Community structure detection in networks",
      "topics": [
        "cluseigen"
      ]
    },
    {
      "page": "clust",
      "title": "Detection and description of clusters of synchronous locations",
      "topics": [
        "clust"
      ]
    },
    {
      "page": "clust_methods",
      "title": "Basic methods for the 'clust' class",
      "topics": [
        "clust_methods",
        "get_adj.clust",
        "get_clusters.clust",
        "get_coords.clust",
        "get_dat.clust",
        "get_methodspec.clust",
        "get_mns.clust",
        "get_modres.clust",
        "get_times.clust",
        "get_wmfs.clust",
        "get_wpmfs.clust",
        "print.clust",
        "set_adj.clust",
        "set_clusters.clust",
        "set_coords.clust",
        "set_dat.clust",
        "set_methodspecs.clust",
        "set_mns.clust",
        "set_modres.clust",
        "set_times.clust",
        "set_wmfs.clust",
        "set_wpmfs.clust",
        "summary.clust"
      ]
    },
    {
      "page": "coh",
      "title": "Coherence",
      "topics": [
        "coh"
      ]
    },
    {
      "page": "coh_methods",
      "title": "Basic methods for the 'coh' class",
      "topics": [
        "coh_methods",
        "get_bandp.coh",
        "get_coher.coh",
        "get_dat1.coh",
        "get_dat2.coh",
        "get_norm.coh",
        "get_ranks.coh",
        "get_sigmethod.coh",
        "get_signif.coh",
        "get_times.coh",
        "get_timescales.coh",
        "get_wtopt.coh",
        "print.coh",
        "set_bandp.coh",
        "set_coher.coh",
        "set_dat1.coh",
        "set_dat2.coh",
        "set_norm.coh",
        "set_ranks.coh",
        "set_sigmethod.coh",
        "set_signif.coh",
        "set_times.coh",
        "set_timescales.coh",
        "set_wtopt.coh",
        "summary.coh"
      ]
    },
    {
      "page": "errcheck_stdat",
      "title": "Error check for appropriate spatio-temporal data",
      "topics": [
        "errcheck_stdat"
      ]
    },
    {
      "page": "errcheck_times",
      "title": "Error check 'times'",
      "topics": [
        "errcheck_times"
      ]
    },
    {
      "page": "errcheck_tsdat",
      "title": "Error check for appropriate temporal data",
      "topics": [
        "errcheck_tsdat"
      ]
    },
    {
      "page": "errcheck_tts",
      "title": "Error check whether inputs are suitable for a tts object",
      "topics": [
        "errcheck_tts"
      ]
    },
    {
      "page": "errcheck_wavparam",
      "title": "Error check wavelet transform parameters",
      "topics": [
        "errcheck_wavparam"
      ]
    },
    {
      "page": "fastcohtest",
      "title": "Fast algorithm for significance testing coherence using Fourier surrogates",
      "topics": [
        "fastcohtest"
      ]
    },
    {
      "page": "fftsurrog",
      "title": "Surrogate time series using Fourier surrogates",
      "topics": [
        "fftsurrog"
      ]
    },
    {
      "page": "is.connected",
      "title": "Tests if a graph is connected",
      "topics": [
        "is.connected"
      ]
    },
    {
      "page": "makeunweighted",
      "title": "For converting certain synchrony matrices to unweighted versions",
      "topics": [
        "makeunweighted"
      ]
    },
    {
      "page": "mnphase",
      "title": "Mean phase of coherence",
      "topics": [
        "mnphase"
      ]
    },
    {
      "page": "modularity",
      "title": "Modularity of a community structure of a graph",
      "topics": [
        "modularity"
      ]
    },
    {
      "page": "normforcoh",
      "title": "Normalization for the 'coh' function",
      "topics": [
        "normforcoh"
      ]
    },
    {
      "page": "plotmag",
      "title": "For plotting the magnitude of values in 'tts', 'coh' and 'wlmtest' objects",
      "topics": [
        "plotmag",
        "plotmag.coh",
        "plotmag.default",
        "plotmag.tts",
        "plotmag.wlmtest",
        "plotmag.wmf",
        "plotmag.wpmf",
        "plotmag.wt"
      ]
    },
    {
      "page": "plotmap",
      "title": "Map clusters from a 'clust' object",
      "topics": [
        "plotmap"
      ]
    },
    {
      "page": "plotphase",
      "title": "For plotting the phases of values in 'tts' and 'coh' objects",
      "topics": [
        "plotphase",
        "plotphase.coh",
        "plotphase.default",
        "plotphase.tts",
        "plotphase.wmf",
        "plotphase.wpmf",
        "plotphase.wt"
      ]
    },
    {
      "page": "plotrank",
      "title": "Plots 'ranks' slot for 'coh' and 'wlmtest' objects",
      "topics": [
        "plotrank",
        "plotrank.coh",
        "plotrank.default",
        "plotrank.wlmtest"
      ]
    },
    {
      "page": "power",
      "title": "Power of a 'tts' object",
      "topics": [
        "power",
        "power.tts"
      ]
    },
    {
      "page": "predsync",
      "title": "Predicted synchrony of a wavelet linear model",
      "topics": [
        "predsync",
        "predsync.wlm"
      ]
    },
    {
      "page": "print.summary_wsyn",
      "title": "Print method for 'summary_wsyn' class",
      "topics": [
        "print.summary_wsyn"
      ]
    },
    {
      "page": "setget_methods",
      "title": "Set and get methods for classes in the 'wsyn' package",
      "topics": [
        "get_adj",
        "get_adj.default",
        "get_bandp",
        "get_bandp.default",
        "get_clusters",
        "get_clusters.default",
        "get_coefs",
        "get_coefs.default",
        "get_coher",
        "get_coher.default",
        "get_coords",
        "get_coords.default",
        "get_dat",
        "get_dat.default",
        "get_dat1",
        "get_dat1.default",
        "get_dat2",
        "get_dat2.default",
        "get_drop",
        "get_drop.default",
        "get_methodspec",
        "get_methodspec.default",
        "get_mns",
        "get_mns.default",
        "get_modres",
        "get_modres.default",
        "get_modval",
        "get_modval.default",
        "get_norm",
        "get_norm.default",
        "get_ranks",
        "get_ranks.default",
        "get_sigmethod",
        "get_sigmethod.default",
        "get_signif",
        "get_signif.default",
        "get_times",
        "get_times.default",
        "get_timescales",
        "get_timescales.default",
        "get_values",
        "get_values.default",
        "get_wlmobj",
        "get_wlmobj.default",
        "get_wmfs",
        "get_wmfs.default",
        "get_wpmfs",
        "get_wpmfs.default",
        "get_wtopt",
        "get_wtopt.default",
        "get_wts",
        "get_wts.default",
        "setget_methods",
        "set_adj",
        "set_adj.default",
        "set_bandp",
        "set_bandp.default",
        "set_clusters",
        "set_clusters.default",
        "set_coefs",
        "set_coefs.default",
        "set_coher",
        "set_coher.default",
        "set_coords",
        "set_coords.default",
        "set_dat",
        "set_dat.default",
        "set_dat1",
        "set_dat1.default",
        "set_dat2",
        "set_dat2.default",
        "set_drop",
        "set_drop.default",
        "set_methodspecs",
        "set_methodspecs.default",
        "set_mns",
        "set_mns.default",
        "set_modres",
        "set_modres.default",
        "set_modval",
        "set_modval.default",
        "set_norm",
        "set_norm.default",
        "set_ranks",
        "set_ranks.default",
        "set_sigmethod",
        "set_sigmethod.default",
        "set_signif",
        "set_signif.default",
        "set_times",
        "set_times.default",
        "set_timescales",
        "set_timescales.default",
        "set_values",
        "set_values.default",
        "set_wlmobj",
        "set_wlmobj.default",
        "set_wmfs",
        "set_wmfs.default",
        "set_wpmfs",
        "set_wpmfs.default",
        "set_wtopt",
        "set_wtopt.default",
        "set_wts",
        "set_wts.default"
      ]
    },
    {
      "page": "setmints",
      "title": "Shifts a vector according to the argument mints",
      "topics": [
        "setmints"
      ]
    },
    {
      "page": "surrog",
      "title": "Creates surrogate time series, either Fourier surrogates or amplitude adjusted Fourier surrogates",
      "topics": [
        "surrog"
      ]
    },
    {
      "page": "syncexpl",
      "title": "Amount of synchrony explained, and related quantities",
      "topics": [
        "syncexpl",
        "syncexpl.wlm"
      ]
    },
    {
      "page": "synmat",
      "title": "Synchrony matrices",
      "topics": [
        "synmat"
      ]
    },
    {
      "page": "tts",
      "title": "Creator function for the 'tts' class",
      "topics": [
        "tts"
      ]
    },
    {
      "page": "tts_methods",
      "title": "Basic methods for the 'tts' class",
      "topics": [
        "get_times.tts",
        "get_timescales.tts",
        "get_values.tts",
        "print.tts",
        "set_times.tts",
        "set_timescales.tts",
        "set_values.tts",
        "summary.tts",
        "tts_methods"
      ]
    },
    {
      "page": "warray",
      "title": "Creates an array of wavelet transforms from input timeseries",
      "topics": [
        "warray"
      ]
    },
    {
      "page": "wavmatwork",
      "title": "Facilitates the computations in synmat for coherence and ReXWT methods",
      "topics": [
        "wavmatwork"
      ]
    },
    {
      "page": "wlm",
      "title": "Wavelet linear models",
      "topics": [
        "wlm"
      ]
    },
    {
      "page": "wlm_methods",
      "title": "Basic methods for the 'wlm' class",
      "topics": [
        "get_coefs.wlm",
        "get_coher.wlm",
        "get_dat.wlm",
        "get_modval.wlm",
        "get_norm.wlm",
        "get_times.wlm",
        "get_timescales.wlm",
        "get_wtopt.wlm",
        "get_wts.wlm",
        "print.wlm",
        "set_coefs.wlm",
        "set_coher.wlm",
        "set_dat.wlm",
        "set_modval.wlm",
        "set_norm.wlm",
        "set_times.wlm",
        "set_timescales.wlm",
        "set_wtopt.wlm",
        "set_wts.wlm",
        "summary.wlm",
        "wlm_methods"
      ]
    },
    {
      "page": "wlmfit",
      "title": "Fits a wavelet linear model",
      "topics": [
        "wlmfit"
      ]
    },
    {
      "page": "wlmtest",
      "title": "Statistical comparison of wavelet linear models",
      "topics": [
        "wlmtest"
      ]
    },
    {
      "page": "wlmtest_methods",
      "title": "Basic methods for the 'wlmtest' class",
      "topics": [
        "get_bandp.wlmtest",
        "get_drop.wlmtest",
        "get_ranks.wlmtest",
        "get_signif.wlmtest",
        "get_wlmobj.wlmtest",
        "print.wlmtest",
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      "page": "wmf_methods",
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        "get_timescales.wmf",
        "get_values.wmf",
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        "get_timescales.wpmf",
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    "MASS",
    "RColorBrewer",
    "Rcpp",
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    {
      "source": "wsynvignette.Rmd",
      "filename": "wsynvignette.html",
      "title": "Wavelet approaches to synchrony (wsyn) package vignette",
      "author": "Lawrence Sheppard, Jonathan Walter, Thomas Anderson, Lei Zhao, Daniel Reuman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Preparing the data",
        "Missing data",
        "De-meaning, detrending, standardizing variance, and normalizing",
        "The wavelet transform \\label",
        "Time- and timescale-specific measures of synchrony",
        "The wavelet phasor mean field",
        "The wavelet mean field \\label",
        "Coherence",
        "Surrogates \\label",
        "Fourier surrogates",
        "Amplitude-adjusted Fourier surrogates",
        "Fast coherence",
        "Alternatives to the \"quick\" method of assessing significance of wavelet phasor mean field values \\label",
        "Wavelet linear models and their uses for understanding synchrony",
        "Model construction tools",
        "Amounts of synchrony explained",
        "Clustering",
        "The synchrony matrix",
        "The clustering algorithm",
        "Acknowlegements",
        "References"
      ],
      "created": "2018-06-26 11:58:56",
      "modified": "2022-05-09 19:33:23",
      "commits": 29
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