{
  "_id": "6a1ef4ccb401979e7341641d",
  "Package": "pammtools",
  "Title": "Piece-Wise Exponential Additive Mixed Modeling Tools for\nSurvival Analysis",
  "Version": "0.7.6",
  "Date": "2026-05-19",
  "Authors@R": "c(\nperson(\"Andreas\", \"Bender\", , \"andreas.bender@stat.uni-muenchen.de\", role = c(\"aut\", \"cre\"), comment=c(ORCID = \"0000-0001-5628-8611\")),\nperson(\"Fabian\", \"Scheipl\", , \"fabian.scheipl@stat.uni-muenchen.de\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-8172-3603\")),\nperson(\"Johannes\", \"Piller\", , \"johannes.piller@lmu.de\", role = c(\"aut\"), comment = c(ORCID = \"0009-0008-3010-9556\")),\nperson(\"Philipp\", \"Kopper\", , \"philipp.kopper@stat.uni-muenchen.de\", role = c(\"aut\"), comment = c(ORCID=\"0000-0002-5037-7135\")),\nperson(\"Lukas\", \"Burk\", , \"burk@leibniz-bips.de\", role = c(\"ctb\"), comment = c(ORCID=\"0000-0001-7528-3795\")))",
  "Description": "The Piece-wise exponential (Additive Mixed) Model (PAMM;\nBender and others (2018) <doi: 10.1177/1471082X17748083>) is a\npowerful model class for the analysis of survival (or\ntime-to-event) data, based on Generalized Additive (Mixed)\nModels (GA(M)Ms). It offers intuitive specification and robust\nestimation of complex survival models with stratified baseline\nhazards, random effects, time-varying effects, time-dependent\ncovariates and cumulative effects (Bender and others (2019)),\nas well as support for left-truncated data as well as competing\nrisks, recurrent events and multi-state settings. pammtools\nprovides tidy workflow for survival analysis with PAMMs,\nincluding data simulation, transformation and other functions\nfor data preprocessing and model post-processing as well as\nvisualization.",
  "Config/Needs/website": "coxme, eha, etm, scam, msm, mvna, rjags, brms,\nTBFmultinomial",
  "License": "MIT + file LICENSE",
  "LazyData": "true",
  "URL": "https://adibender.github.io/pammtools/",
  "BugReports": "https://github.com/adibender/pammtools/issues",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://adibender.r-universe.dev",
  "Date/Publication": "2026-06-02 14:54:43 UTC",
  "RemoteUrl": "https://github.com/adibender/pammtools",
  "RemoteRef": "HEAD",
  "RemoteSha": "1e7f63fbca38ab2bd2b7ab350c096c42725d0cc8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 15:15:38 UTC",
    "User": "root"
  },
  "Author": "Andreas Bender [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5628-8611>),\nFabian Scheipl [aut] (ORCID: <https://orcid.org/0000-0001-8172-3603>),\nJohannes Piller [aut] (ORCID: <https://orcid.org/0009-0008-3010-9556>),\nPhilipp Kopper [aut] (ORCID: <https://orcid.org/0000-0002-5037-7135>),\nLukas Burk [ctb] (ORCID: <https://orcid.org/0000-0001-7528-3795>)",
  "Maintainer": "Andreas Bender <andreas.bender@stat.uni-muenchen.de>",
  "MD5sum": "4ccbef89f3fa1f7f9bacfdfd797b00f4",
  "_user": "adibender",
  "_type": "src",
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  "_created": "2026-06-02T15:15:38.000Z",
  "_published": "2026-06-02T15:20:44.944Z",
  "_distro": "noble",
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  "_tags": [],
  "_topics": [
    "additive-models",
    "pamm",
    "pammtools",
    "piece-wise-exponential",
    "survival-analysis"
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  "_stars": 51,
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/pammtools.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/adibender/pammtools",
  "_realowner": "adibender",
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      "date": "2020-03-12"
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      "date": "2020-05-27"
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      "date": "2025-03-24"
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      "date": "2026-02-16"
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  "_exports": [
    "%>%",
    "add_cif",
    "add_counterfactual_transitions",
    "add_cumu_hazard",
    "add_hazard",
    "add_surv_prob",
    "add_tdc",
    "add_term",
    "add_trans_prob",
    "arrange",
    "as_ped",
    "as_ped_multistate",
    "combine_df",
    "cumulative",
    "distinct",
    "fcumu",
    "filter",
    "full_join",
    "geom_hazard",
    "geom_stephazard",
    "geom_stepribbon",
    "geom_surv",
    "GeomHazard",
    "GeomStepHazard",
    "GeomStepribbon",
    "GeomSurv",
    "get_cumu_coef",
    "get_cumu_eff",
    "get_intervals",
    "get_laglead",
    "get_partial_ll",
    "get_plotinfo",
    "get_terms",
    "gg_cumu_eff",
    "gg_fixed",
    "gg_laglead",
    "gg_partial",
    "gg_partial_ll",
    "gg_re",
    "gg_slice",
    "gg_smooth",
    "gg_state_occupation",
    "gg_tensor",
    "group_by",
    "inner_join",
    "int_info",
    "is.pamm",
    "is.ped",
    "left_join",
    "make_newdata",
    "mutate",
    "nest_tdc",
    "pamm",
    "ped_info",
    "rename",
    "right_join",
    "sample_frac",
    "sample_info",
    "sample_n",
    "select",
    "seq_range",
    "sim_pexp",
    "slice",
    "split_data",
    "summarise",
    "tidy_fixed",
    "tidy_re",
    "tidy_smooth",
    "tidy_smooth2d",
    "transmute",
    "ungroup"
  ],
  "_datasets": [
    {
      "name": "daily",
      "title": "Time-dependent covariates of the 'patient' data set.",
      "object": "daily",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "CombinedID",
        "Study_Day",
        "caloriesPercentage",
        "proteinGproKG"
      ],
      "rows": 18797,
      "table": true,
      "tojson": true
    },
    {
      "name": "nuclear",
      "title": "Time until nuclear power plant construction in different regions.",
      "object": "nuclear",
      "class": [
        "data.frame"
      ],
      "fields": [
        "construction_time",
        "status",
        "region"
      ],
      "rows": 724,
      "table": true,
      "tojson": true
    },
    {
      "name": "patient",
      "title": "Survival data of critically ill ICU patients",
      "object": "patient",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Year",
        "CombinedicuID",
        "CombinedID",
        "Survdays",
        "PatientDied",
        "survhosp",
        "Gender",
        "Age",
        "AdmCatID",
        "ApacheIIScore",
        "BMI",
        "DiagID2"
      ],
      "rows": 2000,
      "table": true,
      "tojson": true
    },
    {
      "name": "simdf_elra",
      "title": "Simulated data with cumulative effects",
      "object": "simdf_elra",
      "class": [
        "nested_fdf",
        "sim_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id",
        "time",
        "status",
        "x1",
        "x2",
        "tz1",
        "z.tz1",
        "tz2",
        "z.tz2"
      ],
      "rows": 250,
      "table": true,
      "tojson": true
    },
    {
      "name": "staph",
      "title": "Time until staphylococcus aureaus infection in children, with possible recurrence",
      "object": "staph",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id",
        "t.start",
        "t.stop",
        "event",
        "enum",
        "hiv"
      ],
      "rows": 374,
      "table": true,
      "tojson": true
    },
    {
      "name": "tumor",
      "title": "Stomach area tumor data",
      "object": "tumor",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "days",
        "status",
        "charlson_score",
        "age",
        "sex",
        "transfusion",
        "complications",
        "metastases",
        "resection"
      ],
      "rows": 776,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_cif",
      "title": "Add cumulative incidence function to data",
      "topics": [
        "add_cif",
        "add_cif.default"
      ]
    },
    {
      "page": "add_counterfactual_transitions",
      "title": "Add counterfactual observations for possible transitions",
      "topics": [
        "add_counterfactual_transitions"
      ]
    },
    {
      "page": "add_hazard",
      "title": "Add predicted (cumulative) hazard to data set",
      "topics": [
        "add_cumu_hazard",
        "add_hazard",
        "add_hazard.default"
      ]
    },
    {
      "page": "add_surv_prob",
      "title": "Add survival probability estimates",
      "topics": [
        "add_surv_prob"
      ]
    },
    {
      "page": "add_tdc",
      "title": "Add time-dependent covariate to a data set",
      "topics": [
        "add_tdc"
      ]
    },
    {
      "page": "add_term",
      "title": "Embeds the data set with the specified (relative) term contribution",
      "topics": [
        "add_term"
      ]
    },
    {
      "page": "add_trans_prob",
      "title": "Add transition probabilities",
      "topics": [
        "add_trans_prob"
      ]
    },
    {
      "page": "as.data.frame.crps",
      "title": "Transform crps object to data.frame",
      "topics": [
        "as.data.frame.crps"
      ]
    },
    {
      "page": "daily",
      "title": "Time-dependent covariates of the 'patient' data set.",
      "topics": [
        "daily"
      ]
    },
    {
      "page": "geom_hazard",
      "title": "(Cumulative) (Step-) Hazard Plots.",
      "topics": [
        "GeomHazard",
        "GeomStepHazard",
        "GeomSurv",
        "geom_hazard",
        "geom_stephazard",
        "geom_surv"
      ]
    },
    {
      "page": "geom_stepribbon",
      "title": "Step ribbon plots.",
      "topics": [
        "GeomStepribbon",
        "geom_stepribbon"
      ]
    },
    {
      "page": "cumulative_coefficient",
      "title": "Extract cumulative coefficients (cumulative hazard differences)",
      "topics": [
        "get_cumu_coef",
        "get_cumu_coef.aalen",
        "get_cumu_coef.cox.aalen",
        "get_cumu_coef.gam"
      ]
    },
    {
      "page": "get_cumu_eff",
      "title": "Calculate (or plot) cumulative effect for all time-points of the follow-up",
      "topics": [
        "get_cumu_eff",
        "gg_cumu_eff"
      ]
    },
    {
      "page": "get_intervals",
      "title": "Information on intervals in which times fall",
      "topics": [
        "get_intervals",
        "get_intervals.default"
      ]
    },
    {
      "page": "get_laglead",
      "title": "Construct or extract data that represents a lag-lead window",
      "topics": [
        "get_laglead",
        "get_laglead.data.frame",
        "get_laglead.default"
      ]
    },
    {
      "page": "get_plotinfo",
      "title": "Extract plot information for all special model terms",
      "topics": [
        "get_plotinfo"
      ]
    },
    {
      "page": "get_terms",
      "title": "Extract the partial effects of non-linear model terms",
      "topics": [
        "get_terms"
      ]
    },
    {
      "page": "gg_fixed",
      "title": "Forrest plot of fixed coefficients",
      "topics": [
        "gg_fixed"
      ]
    },
    {
      "page": "gg_laglead",
      "title": "Plot Lag-Lead windows",
      "topics": [
        "gg_laglead",
        "gg_laglead.default",
        "gg_laglead.LL_df",
        "gg_laglead.nested_fdf"
      ]
    },
    {
      "page": "gg_partial",
      "title": "Visualize effect estimates for specific covariate combinations",
      "topics": [
        "get_partial_ll",
        "gg_partial",
        "gg_partial_ll"
      ]
    },
    {
      "page": "gg_re",
      "title": "Plot Normal QQ plots for random effects",
      "topics": [
        "gg_re"
      ]
    },
    {
      "page": "gg_slice",
      "title": "Plot 1D (smooth) effects",
      "topics": [
        "gg_slice"
      ]
    },
    {
      "page": "gg_smooth",
      "title": "Plot smooth 1d terms of gam objects",
      "topics": [
        "gg_smooth",
        "gg_smooth.default"
      ]
    },
    {
      "page": "gg_state_occupation",
      "title": "Plot State Occupation Probabilities",
      "topics": [
        "gg_state_occupation"
      ]
    },
    {
      "page": "gg_tensor",
      "title": "Plot tensor product effects",
      "topics": [
        "gg_tensor"
      ]
    },
    {
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