_pkgdown.yml

url: https://adibender.github.io/pammtools
template:
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    ganalytics: UA-44545040-3
    docsearch:
      api_key: c3726dcbf089f0b26f496305ed030c22
      index_name: pammtools
reference:
  - title: "Transform data to Piece-wise Exponential Data (PED) format"
    desc: "Functions to transform data sets in different formats to PED format,
    suitable to be fit as PAMMs."
    contents:
      - as_ped
  - title: "PED helper functions"
    desc: "Functions that help extract (interval-specific) summary information
    from PED and create newdata, e.g., for prediction and plotting."
    contents:
      - int_info
      - ped_info
      - make_newdata
      - get_intervals
  - title: "Extract information from PAMMs"
    desc: "Functions that help extract information from fitted model objects,
    e.g., smooth effects for plotting"
    contents:
      - tidy_fixed
      - tidy_smooth
      - tidy_smooth2d
      - tidy_re
      - get_cumu_coef
      - as.data.frame.crps
      - predictSurvProb.pamm
  - title: "Augment functions"
    desc: "Functions that augment a data set by different quantaties like the
    hazard rate."
    contents:
      - add_term
      - add_hazard
      - add_surv_prob
      - add_cif
  - title: "Convenience functions for visualization of model outputs."
    desc: "Functions that facilitate effect plots (smooth effects, etc.)"
    contents:
      - gg_fixed
      - gg_smooth
      - gg_tensor
      - gg_re
      - gg_slice
      - gg_partial
      - gg_partial_ll
      - gg_laglead
      - gg_cumu_eff
      - geom_hazard
      - geom_stepribbon
      - get_plotinfo
  - title: "Data sets"
    desc: "Data sets contained in **`pammtools`**"
    contents:
      - tumor
      - patient
      - daily
      - staph
      - simdf_elra
  - title: "Utilities"
    desc: "Utility functions"
    contents:
      - seq_range
      - sim_pexp
      - get_laglead
      - add_tdc
      - pammtools
      - get_terms
articles:
  - title: "Articles"
    desc: "Several articles/vignettes that describe the usage of PAMMs"
    contents:
    - data-transformation
    - baseline
    - basics
    - strata
    - splines
    - tveffects
    - frailty
    - tdcovar
    - left-truncation
    - model-evaluation
    - cumulative-effects
    - convenience
    - competing-risks
    - recurrent-events
    - smj-tutorial

navbar:
  type: default
  left:
  - text: Reference
    href: reference/index.html
  - text: Articles
    menu:
    - text: Data transformation
      href: articles/data-transformation.html
    - text: Estimating the baseline hazard
      href: articles/baseline.html
    - text: Basic modeling
      href: articles/basics.html
    - text: Non-linear effects (penalized splines)
      href: articles/splines.html
    - text: Workflow and convenience functions
      href: articles/convenience.html
    - text: Stratified models
      href: articles/strata.html
    - text: Time-varying effects (TVEs)
      href: articles/tveffects.html
    - text: Frailties (random effects)
      href: articles/frailty.html
    - text: Time-dependent covariates (TDCs)
      href: articles/tdcovar.html
    - text: Left-truncated data
      href: articles/left-truncation.html
    - text: Model evaluation
      href: articles/model-evaluation.html
    - text: Cumulative effects/Exposure-Lag-Response Associations
      href: articles/cumulative-effects.html
    - text: Competing Risks
      href: articles/competing-risks.html
    - text: Recurrent Events
      href: articles/recurrent-events.html
    - text: 'Paper: A generalized additive model approach to time-to-event analysis'
      href: articles/smj-tutorial.html
  - text: News
    href: news/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/adibender/pammtools

development:
  mode: auto
  version_label: default
  version_tooltip: "Version"