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  "Title": "Compositional Models to Longitudinal Microbiome Data",
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  "Authors@R": "person(given = \"Irene\",\nfamily = c(\"Creus\", \"Martí\"),\nrole = c(\"aut\", \"cre\"),\nemail = \"ircrmar@mat.upv.es\",\ncomment=c(ORCID = \"0000-0002-7962-4478\"))",
  "Author": "Irene Creus Martí [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7962-4478>)",
  "Maintainer": "Irene Creus Martí <ircrmar@mat.upv.es>",
  "Description": "Implementation of models to analyse compositional\nmicrobiome time series taking into account the interaction\nbetween groups of bacteria. The models implemented are\ndescribed in Creus-Martí et al (2018, ISBN:978-84-09-07541-6),\nCreus-Martí et al (2021) <doi:10.1155/2021/9951817> and\nCreus-Martí et al (2022) <doi:10.1155/2022/4907527>.",
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  "Repository": "https://creus-marti.r-universe.dev",
  "Date/Publication": "2025-06-13 13:01:54 UTC",
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  "_exports": [
    "B1MODImatrizP",
    "B1MODImodel",
    "Balance",
    "BPBM_Matrix",
    "Estimate_Param_EstParmFunc",
    "Estimate_Param_FBM",
    "Estimating_BPBM",
    "EstParmFunc",
    "EstParmFunc_FBM",
    "ExpectedValue_EstParmFunc",
    "ExpectedValues_EstParmFunc_FBM",
    "ExpectedValuess_BPBM",
    "FromVectorToMatrix_BPBM",
    "FVectorPBmodeloPredi",
    "Graphics",
    "GraphicsPrediction",
    "GraphicsPredictionBPBM",
    "GraphicsSPBal",
    "LogVeroFuncBUENA",
    "MaxBacteria",
    "MaxBacteriaPred",
    "ObtainigValuePB",
    "ObtainigValueSPBal",
    "ObtainingDIC",
    "PBalance",
    "PBalancePredi",
    "PBmodel",
    "PCAbiplot",
    "Percen_Variance",
    "PlotDendogram",
    "PredictionBPBM",
    "PredictionEstParmFunc",
    "PredictionFBM",
    "PreparingTheData",
    "QualityControl",
    "ridgeregression",
    "rxnrate",
    "StudyingParam",
    "Table_alr_Dirich_glv",
    "TableBPBM",
    "TableFBM",
    "TauAndParameters_EstParmFunc_FBM",
    "vecttor",
    "ZeroData"
  ],
  "_datasets": [
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      "name": "cockroach",
      "title": "cockroach dataset",
      "object": "cockroach",
      "class": [
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        "array"
      ],
      "fields": [
        "Time",
        "g__Dysgonomonas",
        "g__Fusobacterium",
        "g__Bacteroides",
        "f__Lachnospiraceae",
        "g__Desulfovibrio",
        "g__Candidatus_Soleaferrea",
        "g__Alistipes",
        "f__Ruminococcaceae",
        "g__Blattabacterium",
        "g__Erysipelatoclostridium",
        "f__Enterobacteriaceae",
        "c__Bacteroidia",
        "g__Breznakia",
        "f__Tannerellaceae",
        "g__Christensenellaceae_R-7_group",
        "g__Mucispirillum",
        "o__Rs-K70_termite_group",
        "g__Pseudomonas",
        "g__Paludibacter",
        "g__Lachnospiraceae_UCG-010",
        "f__Dysgonomonadaceae",
        "g__Parabacteroides",
        "g__Ruminiclostridium_5",
        "g__Enterococcus",
        "f__Paludibacteraceae",
        "g__Lachnoclostridium",
        "g__[Eubacterium]_coprostanoligenes_group",
        "f__Acidaminococcaceae",
        "g__Tyzzerella_3",
        "f__Desulfovibrionaceae",
        "g__Hydrogenoanaerobacterium",
        "g__Akkermansia",
        "g__Odoribacter",
        "g__Robinsoniella",
        "f__Rikenellaceae",
        "g__Raoultibacter",
        "c__vadinHA49",
        "f__Christensenellaceae",
        "f__Clostridiales_vadinBB60_group",
        "o__Rhodospirillales",
        "g__Incertae_Sedis",
        "g__Intestinimonas",
        "f__Flavobacteriaceae",
        "g__Ruminococcaceae_UCG-009",
        "g__[Eubacterium]_brachy_group",
        "o__Clostridiales",
        "g__Ruminiclostridium_9",
        "f__Peptococcaceae",
        "g__Desulfatiferula",
        "g__Butyricicoccus",
        "g__Tyzzerella",
        "g__Oxalobacter",
        "g__Nitrosomonas",
        "g__Serratia",
        "g__Anaerotruncus",
        "g__Sanguibacteroides",
        "g__GCA-900066225",
        "g__Blattella_germanica_(German_cockroach)",
        "f__Family_XIII",
        "o__Micrococcales",
        "o__Mollicutes_RF39",
        "f__Syntrophomonadaceae",
        "g__Ruminococcus_2",
        "g__Cutibacterium",
        "Unassigned",
        "p__Proteobacteria",
        "p__Firmicutes",
        "p__Bacteroidetes",
        "o__Selenomonadales",
        "o__Saccharimonadales",
        "o__Microtrichales",
        "o__Gastranaerophilales",
        "o__Desulfovibrionales",
        "o__Chloroplast",
        "o__Chitinophagales",
        "o__Betaproteobacteriales",
        "o__Bacteroidales",
        "o__Babeliales",
        "k__Bacteria",
        "g__Wolbachia",
        "g__Williamsia",
        "g__Veillonella",
        "g__Truepera",
        "g__Treponema_2",
        "g__Tannerella",
        "g__Subdoligranulum",
        "g__Streptomyces",
        "g__Streptococcus",
        "g__Steroidobacter",
        "g__Stenotrophomonas",
        "g__Staphylococcus",
        "g__Sphingomonas",
        "g__SP3-e08",
        "g__Skermanella",
        "g__Shinella",
        "g__Shewanella",
        "g__Selenomonas_3",
        "g__Ruminococcaceae_UCG-014",
        "g__Ruminococcaceae_UCG-013",
        "g__Ruminococcaceae_UCG-011",
        "g__Ruminococcaceae_UCG-010",
        "g__Ruminococcaceae_UCG-005",
        "g__Ruminococcaceae_NK4A214_group",
        "g__rumen_bacterium_YS2",
        "g__Rubellimicrobium",
        "g__Rothia",
        "g__Roseomonas",
        "g__Renibacterium",
        "g__Pseudoxanthomonas",
        "g__Pseudopropionibacterium",
        "g__Pseudoglutamicibacter",
        "g__Pseudofulvimonas",
        "g__Prevotellaceae_NK3B31_group",
        "g__Prevotella_9",
        "g__Porphyromonas",
        "g__Pelomonas",
        "g__Paracoccus",
        "g__Papillibacter",
        "g__Oligella",
        "g__Nibribacter",
        "g__Neisseria",
        "g__Mycobacterium",
        "g__Mitsuokella",
        "g__Microvirga",
        "g__Micrococcus",
        "g__Microbacterium",
        "g__Massilia",
        "g__Marinomonas",
        "g__Lysinibacillus",
        "g__Leucobacter",
        "g__Lawsonella",
        "g__Lactobacillus",
        "g__Lachnospiraceae_UCG-004",
        "g__Lachnospiraceae_NK4A136_group",
        "g__Lachnospiraceae_NC2004_group",
        "g__Lachnoclostridium_5",
        "g__Kocuria",
        "g__Jeotgalicoccus",
        "g__Hymenobacter",
        "g__Harryflintia",
        "g__Halomonas",
        "g__Gemella",
        "g__Gardnerella",
        "g__Fournierella",
        "g__Flavisolibacter",
        "g__Finegoldia",
        "g__Escherichia-Shigella",
        "g__Erysipelothrix",
        "g__Enhydrobacter",
        "g__Elusimicrobium",
        "g__Eikenella",
        "g__Dolosigranulum",
        "g__Delftia",
        "g__Curvibacter",
        "g__Corynebacterium_1",
        "g__Corynebacterium",
        "g__Caulobacter",
        "g__Castellaniella",
        "g__Capnocytophaga",
        "g__Candidatus_Tammella",
        "g__Candidatus_Saccharimonas",
        "g__Candidatus_Endomicrobium",
        "g__Candidatus_Adiutrix_intracellularis",
        "g__Brevundimonas",
        "g__Brachybacterium",
        "g__Blastococcus",
        "g__Bifidobacterium",
        "g__Bdellovibrio",
        "g__bacterium_PM5-3",
        "g__Bacillus",
        "g__Aquabacterium",
        "g__Anaerovorax",
        "g__Anaerosporobacter",
        "g__Anaerofustis",
        "g__Anaerofilum",
        "g__Anaerococcus",
        "g__Anaerobacillus",
        "g__Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium",
        "g__Aggregatibacter",
        "g__Agathobacter",
        "g__Aeromonas",
        "g__Acinetobacter",
        "g__Acidovorax",
        "g__[Eubacterium]_oxidoreducens_group",
        "g__[Eubacterium]_nodatum_group",
        "f__Synergistaceae",
        "f__Saprospiraceae",
        "f__Rhodobacteraceae",
        "f__Rhizobiaceae",
        "f__Nocardioidaceae",
        "f__Neisseriaceae",
        "f__Microscillaceae",
        "f__Micromonosporaceae",
        "f__M2PB4-65_termite_group",
        "f__JG30-KF-CM45",
        "f__Gemmataceae",
        "f__Erysipelotrichaceae",
        "f__Desulfobacteraceae",
        "f__CR-115",
        "f__Caldilineaceae",
        "f__Burkholderiaceae",
        "f__Beutenbergiaceae",
        "f__Bacillaceae",
        "f__Acetobacteraceae",
        "c__KD4-96",
        "c__Gammaproteobacteria",
        "c__Elusimicrobia",
        "c__Deltaproteobacteria",
        "c__Clostridia",
        "c__Alphaproteobacteria"
      ],
      "rows": 105,
      "table": true,
      "tojson": true
    },
    {
      "name": "Simulated",
      "title": "Gut microbiome simulated dataset",
      "object": "Simulated",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "t",
        "sp1",
        "sp2",
        "sp3",
        "sp4",
        "sp5"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "CoDaLoMic-package",
      "title": "CoDaLoMic",
      "topics": [
        "CoDaLoMic-package",
        "CoDaLoMic"
      ]
    },
    {
      "page": "B1MODImatrizP",
      "title": "Ridge regression matrix",
      "topics": [
        "B1MODImatrizP"
      ]
    },
    {
      "page": "B1MODImodel",
      "title": "Obtaining the regression value of the FBM",
      "topics": [
        "B1MODImodel"
      ]
    },
    {
      "page": "Balance",
      "title": "Calculating the balance of the FBM model",
      "topics": [
        "Balance"
      ]
    },
    {
      "page": "BPBM_Matrix",
      "title": "Obtains the matrix of covariates of the BPBM",
      "topics": [
        "BPBM_Matrix"
      ]
    },
    {
      "page": "cockroach",
      "title": "cockroach dataset",
      "topics": [
        "cockroach"
      ]
    },
    {
      "page": "Estimate_Param_EstParmFunc",
      "title": "Estimating Parameters of EstParmFunc",
      "topics": [
        "Estimate_Param_EstParmFunc"
      ]
    },
    {
      "page": "Estimate_Param_FBM",
      "title": "Estimating Parameters of EstParmFunc_FBM",
      "topics": [
        "Estimate_Param_FBM"
      ]
    },
    {
      "page": "Estimating_BPBM",
      "title": "Estimating BPBM",
      "topics": [
        "Estimating_BPBM"
      ]
    },
    {
      "page": "EstParmFunc",
      "title": "Writting the loglikelihood of the dirichlet",
      "topics": [
        "EstParmFunc"
      ]
    },
    {
      "page": "EstParmFunc_FBM",
      "title": "Writting the loglikelihood of the dirichlet",
      "topics": [
        "EstParmFunc_FBM"
      ]
    },
    {
      "page": "ExpectedValue_EstParmFunc",
      "title": "Obtaining the value of the Dirichlet parameters, the expected value and the variance.",
      "topics": [
        "ExpectedValue_EstParmFunc"
      ]
    },
    {
      "page": "ExpectedValues_EstParmFunc_FBM",
      "title": "Obtainig the value of the dirichlet parameters, the expected value and the variance.",
      "topics": [
        "ExpectedValues_EstParmFunc_FBM"
      ]
    },
    {
      "page": "ExpectedValuess_BPBM",
      "title": "Obtainig the value of the dirichlet parameters, the expected value and the variance.",
      "topics": [
        "ExpectedValuess_BPBM"
      ]
    },
    {
      "page": "FromVectorToMatrix_BPBM",
      "title": "Writting the parameters in the matrix form required in BPBM model",
      "topics": [
        "FromVectorToMatrix_BPBM"
      ]
    },
    {
      "page": "FVectorPBmodeloPredi",
      "title": "Obtaining a vector with the covariates of the prediction",
      "topics": [
        "FVectorPBmodeloPredi"
      ]
    },
    {
      "page": "Graphics",
      "title": "Plots the time series",
      "topics": [
        "Graphics"
      ]
    },
    {
      "page": "GraphicsPrediction",
      "title": "Plots the time series",
      "topics": [
        "GraphicsPrediction"
      ]
    },
    {
      "page": "GraphicsPredictionBPBM",
      "title": "Plots the time series",
      "topics": [
        "GraphicsPredictionBPBM"
      ]
    },
    {
      "page": "GraphicsSPBal",
      "title": "Obtaining the graphic of the SPBal at all time points",
      "topics": [
        "GraphicsSPBal"
      ]
    },
    {
      "page": "LogVeroFuncBUENA",
      "title": "Writting the loglikelihood of the dirichlet",
      "topics": [
        "LogVeroFuncBUENA"
      ]
    },
    {
      "page": "MaxBacteria",
      "title": "Putting the reference bacteria at the last row",
      "topics": [
        "MaxBacteria"
      ]
    },
    {
      "page": "MaxBacteriaPred",
      "title": "Putting the reference bacteria at the last row",
      "topics": [
        "MaxBacteriaPred"
      ]
    },
    {
      "page": "ObtainigValuePB",
      "title": "Obtaining the principal balances values",
      "topics": [
        "ObtainigValuePB"
      ]
    },
    {
      "page": "ObtainigValueSPBal",
      "title": "Obtaining the selected principal balances values",
      "topics": [
        "ObtainigValueSPBal"
      ]
    },
    {
      "page": "ObtainingDIC",
      "title": "Writting the loglikelihood of the dirichlet",
      "topics": [
        "ObtainingDIC"
      ]
    },
    {
      "page": "PBalance",
      "title": "Calculating balances",
      "topics": [
        "PBalance"
      ]
    },
    {
      "page": "PBalancePredi",
      "title": "Calculating balances for a composition",
      "topics": [
        "PBalancePredi"
      ]
    },
    {
      "page": "PBmodel",
      "title": "Obtaining the regression value of the BPBM",
      "topics": [
        "PBmodel"
      ]
    },
    {
      "page": "PCAbiplot",
      "title": "PCA of the estimated parameters",
      "topics": [
        "PCAbiplot"
      ]
    },
    {
      "page": "Percen_Variance",
      "title": "Percentage of variance",
      "topics": [
        "Percen_Variance"
      ]
    },
    {
      "page": "PlotDendogram",
      "title": "Plotting a dendogram",
      "topics": [
        "PlotDendogram"
      ]
    },
    {
      "page": "PredictionBPBM",
      "title": "Predicting using BPBM",
      "topics": [
        "PredictionBPBM"
      ]
    },
    {
      "page": "PredictionEstParmFunc",
      "title": "Predicting using dirichl-gLV",
      "topics": [
        "PredictionEstParmFunc"
      ]
    },
    {
      "page": "PredictionFBM",
      "title": "Predicting using FBM",
      "topics": [
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