_pkgdown.yaml

url: https://darth-git.github.io/darthpack

reference:
- title: "01 Model inputs"
  desc: >
    In this component, all model input variables are declared and values are set.
    The point of this component is to group input variables together and organize 
    them in a logical fashion that can be easily communicated to a user.
  contents:
  - '`load_mort_data`'  
  - '`load_all_params`'
  - '`update_param_list`'  
- title: "02 Decision model"
  desc: >
    This component is the heart of the decision analysis: the implementation of 
    the decision model. In this section of the framework, a function is created 
    that maps model inputs to outputs, via the dynamic and/or stochastic 
    processes that the decision model represents. The model itself could be a 
    decision tree, Markov model, stochastic simulation, and so on. The output 
    stored from the model at this stage should be sufficiently general and 
    comprehensive to accommodate calibration, validation, and the main policy 
    analysis. Constructing the model as a function at this stage facilitates 
    subsequent components of model development and analysis, as these processes 
    will all call the same model function but pass different parameter values 
    and/or calculate different final outcomes from the model outputs. The model 
    function also facilitates the use of parallel computing efforts for 
    computationally intensive tasks, such as calibration and probabilistic 
    sensitivity analysis (PSA).
  contents:
  - '`decision_model`'
  - '`check_sum_of_transition_array`'
  - '`check_transition_probability`'
- title: "03 Calibration"
  desc: >
    In this component, the unknown parameters of the decision model are 
    calibrated by matching model outputs to specified calibration targets using
    a Bayesian approach. The function `calibration_out` produces model outputs 
    corresponding to the calibration targets. This function takes a vector of 
    parameters that need to be calibrated and a list with all parameters of 
    decision model and computes model outputs to be used for calibration routines.
    We use the `IMIS` function from the `IMIS` package that calls the functions 
    `likelihood`, `sample.prior` and `prior`, to draw samples from the posterior 
    distribution. The functions are specified in the *03_calibration_functions.R* 
    file in the `R` folder.
  contents:
  - '`calibration_out`'  
  - '`likelihood`'
  - '`log_lik`'
  - '`log_post`'
  - '`log_prior`'
  - '`posterior`'
  - '`prior`'
  - '`sample.prior`'
- title: "04 Validation"
  desc: >
    In this component, the calibrated model is internally validated by 
    comparing the predicted outputs from the model evaluated at the calibrated 
    parameters against the calibration targets. The computation of the 
    model-predicted outputs using the MAP estimate is done by inserting the 
    `v_calib_post_map` data into the `calibration_out` function previously 
    described in component *03 Calibration*. The function `data_summary` 
    summarizes the model-predicted posterior outputs into different summary 
    statistics, including the estimated values for survival, prevalence and the 
    proportion of sicker individuals at cycles 10, 20 and 30. 
  contents:
  - '`data_summary`'
- title: "05a Probabilistic analysis"
  desc: >
    In this subcomponent, decision uncertainty is evaluated by propagating the 
    uncertainty through the CEA using probabilistic sensitivity analysis (PSA).
    The function `generate_psa_params` generates a PSA dataset for all the CEA 
    input parameters.
  contents:
  - '`generate_psa_params`'
- title: "05b Deterministic analysis"
  desc: >
    This subcomponent performs a deterministic CEA, followed by some 
    deterministic sensitivity analysis, including one-way, two-way and tornado 
    sensitivity analyses. The function `calculate_ce_out` calculates costs and 
    effects for a given vector of parameters using a simulation model.
  contents:
  - '`calculate_ce_out`'
  - '`owsa_det`'
  - '`twsa_det`'
- title: "General"
  desc: ~
  contents:
  - '`open_guide`'
- title: "Data"
  desc: ~
  contents:
  - '`all_cause_mortality`'
  - '`df_params_init`'  
  - '`SickSicker_targets`'
  - '`m_calib_post`'
  - '`v_calib_post_map`'
  - '`l_psa`'  

news:
- one_page: false

navbar:
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      text: "github"
      href: https://github.com/DARTH-git/darthpack

authors:
  DARTH workgroup:
    href: https://darthworkgroup.com