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  "Title": "Diversity-Dependent Diversification",
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  "Description": "Implements maximum likelihood and bootstrap methods based\non the diversity-dependent birth-death process to test whether\nspeciation or extinction are diversity-dependent, under various\nmodels including various types of key innovations. See Etienne\net al. 2012, Proc. Roy. Soc. B 279: 1300-1309,\n<DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat.\n180: E75-E89, <DOI:10.1086/667574>, Etienne et al. 2016. Meth.\nEcol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565> and\nLaudanno et al. 2021. Syst. Biol. 70: 389–407,\n<DOI:10.1093/sysbio/syaa048>. Also contains functions to\nsimulate the diversity-dependent process.",
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      "page": "bd_loglik",
      "title": "Loglikelihood for diversity-independent diversification model",
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        "bd_loglik"
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      "page": "bd_ML",
      "title": "Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model",
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        "bd_ML"
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      "title": "Function to convert a set of branching times into a phylogeny with random topology This code is taken from the package TESS by Sebastian Hoehna, where the function is called tess.create.phylo",
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    {
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      "title": "Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d",
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    },
    {
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      "title": "Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics",
      "topics": [
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    },
    {
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      "title": "Function to simulate a key innovation in macro-evolution with the innovative clade decoupling from the diversity-dependent diversification dynamics of the main clade",
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        "dd_KI_sim"
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    },
    {
      "page": "dd_loglik",
      "title": "Loglikelihood for diversity-dependent diversification models",
      "topics": [
        "dd_loglik"
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    },
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    {
      "page": "dd_ML",
      "title": "Maximization of the loglikelihood under a diversity-dependent diversification model",
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    },
    {
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      "title": "Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_d",
      "topics": [
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    },
    {
      "page": "dd_MS_ML",
      "title": "Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics",
      "topics": [
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    },
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      "title": "Function to simulate the diversity-dependent diversification process",
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