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  "Title": "R Wrappers for EXPOKIT; Other Matrix Functions",
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  "Date": "2026-04-01",
  "Authors@R": "c(person(\"Nicholas J.\", \"Matzke\", email=\"nickmatzke.ncse@gmail.com\", role=\nc(\"aut\", \"cre\", \"cph\")), person(\"Roger B.\", \"Sidje\", email =\n\"roger.b.sidje@ua.edu\", role = c(\"aut\", \"cph\")),\nperson(\"Drew\", \"Schmidt\", email=\"schmidt@math.utk.edu\", role=\"aut\"))",
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  "Maintainer": "Nicholas J. Matzke <nickmatzke.ncse@gmail.com>",
  "Copyright": "See /inst/LAPACK_LICENSE.txt for code in /src.",
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      "date": "2017-08-15"
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      "date": "2018-01-31"
    },
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      "date": "2018-05-06"
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    "maxent",
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    "SparseM_coo_to_REXPOKIT_coo"
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      "page": "00_rexpokit-package",
      "title": "Matrix exponentiation with EXPOKIT in R",
      "concept": [
        "exponentiation",
        "matrix",
        "phylogenetics",
        "transition"
      ],
      "topics": [
        "rexpokit-package",
        "rexpokit"
      ]
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      "page": "zzz_coo2mat",
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      "topics": [
        "coo2mat"
      ]
    },
    {
      "page": "expokit_dgexpv_Qmat",
      "title": "EXPOKIT dgexpv matrix exponentiation on Q matrix",
      "topics": [
        "expokit_dgexpv_Qmat"
      ]
    },
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      "topics": [
        "expokit_dgpadm_Qmat"
      ]
    },
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      "topics": [
        "expokit_dmexpv_Qmat"
      ]
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