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  "Title": "C++ Implementations of Phylogenetic Cladogenesis Calculations",
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  "Date": "2018-11-21",
  "Authors@R": "c(person(\"Nicholas J.\", \"Matzke\", email=\"nickmatzke.ncse@gmail.com\", role=\nc(\"aut\", \"cre\", \"cph\")))",
  "Author": "Nicholas J. Matzke [aut, cre, cph]",
  "Maintainer": "Nicholas J. Matzke <nickmatzke.ncse@gmail.com>",
  "Description": "Various cladogenesis-related calculations that are slow in\npure R are implemented in C++ with Rcpp. These include the\ncalculation of the probability of various scenarios for the\ninheritance of geographic range at the divergence events on a\nphylogenetic tree, and other calculations necessary for models\nwhich are not continuous-time markov chains (CTMC), but where\nchange instead occurs instantaneously at speciation events.\nTypically these models must assess the probability of every\npossible combination of (ancestor state, left descendent state,\nright descendent state).  This means that there are up to (# of\nstates)^3 combinations to investigate, and in biogeographical\nmodels, there can easily be hundreds of states, so calculation\ntime becomes an issue.  C++ implementation plus clever tricks\n(many combinations can be eliminated a priori) can greatly\nspeed the computation time over naive R implementations.\nCITATION INFO: This package is the result of my Ph.D. research,\nplease cite the package if you use it!  Type:\ncitation(package=\"cladoRcpp\") to get the citation information.",
  "URL": "http://phylo.wikidot.com/biogeobears",
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    "message": "perm remove DS_Store: https://brandoncaples.com/martech/2022/git-remove-ds-store\n",
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    "numstates_from_numareas",
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    "rcpp_calc_anclikes_sp_COOprobs",
    "rcpp_calc_anclikes_sp_COOweights_faster",
    "rcpp_calc_anclikes_sp_prebyte",
    "rcpp_calc_anclikes_sp_rowsums",
    "rcpp_calc_anclikes_sp_using_COOprobs",
    "rcpp_calc_rowsums_for_COOweights_columnar",
    "rcpp_calc_splitlikes_using_COOweights_columnar",
    "Rcpp_combn_zerostart",
    "rcpp_convolve",
    "rcpp_mult2probvect",
    "rcpp_states_list_to_DEmat",
    "strsplit3"
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      "page": "00-cladoRcpp-package",
      "title": "Phylogenetic probability calculations using Rcpp",
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        "cladorcpp-package",
        "cladoRcpp",
        "cladorcpp"
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    },
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      "topics": [
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    },
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    },
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