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  "Title": "A Network Tool to Dissect Spatial Community Ecology",
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  "Description": "Most existing approaches for network reconstruction can\nonly infer an overall network and, also, fail to capture a\ncomplete set of network properties. To address these issues, a\nnew model has been developed, which converts static data into\ntheir 'dynamic' form. 'idopNetwork' is an 'R' interface to this\nmodel, it can inferring informative, dynamic, omnidirectional\nand personalized networks. For more information on functional\nclustering part, see Kim et al. (2008)\n<doi:10.1534/genetics.108.093690>, Wang et al. (2011)\n<doi:10.1093/bib/bbr032>. For more information on our model,\nsee Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao\net al. (2022) <doi:10.1080/19490976.2022.2106103>.",
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      "page": "get_par_int",
      "title": "acquire initial parameters for functional clustering",
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      "topics": [
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      "title": "least-square fit for qdODE model",
      "topics": [
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      "title": "wrapper for qdODE_all in parallel version",
      "topics": [
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      "page": "qdODE_plot_all",
      "title": "plot all decompose plot",
      "topics": [
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      "page": "qdODE_plot_base",
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      "topics": [
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  "_rundeps": [
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      "source": "idopNetwork_vignette.Rmd",
      "filename": "idopNetwork_vignette.html",
      "title": "idopNetwork_vignette",
      "author": "Ang Dong",
      "engine": "knitr::rmarkdown",
      "headings": [
        "About",
        "1. Input data",
        "1.1 gut microbe OTUs data",
        "1.2 mustard microbe OTUs data",
        "2. power curve fitting",
        "3. Functional clustering",
        "3.1 mean curve",
        "3.2 covariance matrix",
        "3.3 initial parameters",
        "3.4 functional clustering (power-equation,SAD1)",
        "3.5 bi-functional clustering (power-equation,biSAD1)",
        "3.6 sub-clustering",
        "4. LASSO-based variable selection",
        "4.1 For Modules",
        "4.2 For Microbes",
        "5 qdODE solving",
        "5.1 solving qdODE between modules",
        "5.2 solving qdODE within a module",
        "6 idopNetwork reconstruction",
        "6.1 network between modules",
        "6.2 network within a module",
        "6.3 network comparison",
        "",
        "Troubleshooting",
        "Session info"
      ],
      "created": "2022-11-23 12:42:42",
      "modified": "2022-11-23 12:42:42",
      "commits": 1
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