_pkgdown.yml

destination: docs

url: https://merck.github.io/gsDesign2/

template:
  bootstrap: 5
  bslib:
    preset: "bootstrap"
    primary: "#00857c"
    navbar-light-brand-color: "#fff"
    navbar-light-brand-hover-color: "#fff"
    navbar-light-color: "#fff"
    navbar-light-hover-color: "#fff"
    navbar-light-active-color: "#fff"
    dropdown-link-hover-color: "#fff"
    dropdown-link-hover-bg: "#00857c"
  math-rendering: "katex"

footer:
  structure:
    left: [developed_by, built_with, legal]
    right: [blank]
  components:
    legal: "<br>Copyright &copy; 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
    blank: "<span></span>"

reference:
- title: "Fixed design"
  desc: >
    Functions to calculate power/sample size in fixed designs.
  contents:
    - fixed_design_ahr
    - fixed_design_fh
    - fixed_design_mb
    - fixed_design_lf
    - fixed_design_maxcombo
    - fixed_design_milestone
    - fixed_design_rmst
    - fixed_design_rd
- title: "Average hazard ratio"
  desc: >
    Functions for the average hazard ratio (AHR) method.
  contents:
    - ahr
    - expected_time
    - expected_event
    - gs_info_ahr
    - gs_power_ahr
    - gs_design_ahr
    - gs_update_ahr
    - ahr_blinded
- title: "Weighted logrank"
  desc: >
    Functions for the weighted logrank test (WLR) method.
  contents:
    - wlr_weight_fh
    - wlr_weight_1
    - gs_info_wlr
    - gs_power_wlr
    - gs_design_wlr
- title: "MaxCombo"
  desc: >
    Functions for the MaxCombo method.
  contents:
    - gs_info_combo
    - gs_spending_combo
    - gs_power_combo
    - gs_design_combo
- title: "Risk difference"
  desc: >
    Functions for risk differences.
  contents:
    - gs_info_rd
    - gs_power_rd
    - gs_design_rd
- title: "Input definition"
  desc: >
    Helper functions to define inputs for study design.
  contents:
    - define_enroll_rate
    - define_fail_rate
- title: "Summary and display tables"
  desc: >
    Functions to summarize fixed / group sequential design results.
  contents:
    - summary.fixed_design
    - summary.gs_design
    - as_gt
    - as_gt.fixed_design
    - as_gt.gs_design
    - as_rtf
    - as_rtf.fixed_design
    - as_rtf.gs_design
    - to_integer
    - to_integer.fixed_design
    - to_integer.gs_design
- title: "Boundary functions"
  desc: >
    Functions to specify the upper and lower bound in group sequential designs.
    They are not recommended to use alone.
    Instead, they should be used companied with gs_design_npe, gs_power_npe, ect..
  contents:
    - gs_b
    - gs_spending_bound
- title: "Expected ..."
  desc: >
    Functions for computing trial events.
  contents:
    - expected_event
    - expected_time
    - expected_accrual
- title: "Piecewise exponential"
  desc: >
    Functions for computing piecewise exponential distributions.
  contents:
    - ppwe
    - s2pwe
- title: "Low-level helpers"
  desc: >
    Functions to calculate sample size or number of events under non-constant treatment effect over time.
  contents:
    - gs_power_npe
    - gs_design_npe
    - gs_create_arm
    - pw_info

articles:

- title: "Quick start"
  desc: >
    A quick start guide for gsDesign2.
  contents:
  - gsDesign2

- title: "NPH technical background"
  desc: >
    Some technical background introduction to non-proportional hazards, such as Z-score, B-values, and canonical form.
  contents:
  - articles/story-npe-background
  - articles/story-canonical-h0-h1
  - articles/story-compute-npe-bound
  - articles/story-npe-integration
  - articles/story-arbitrary-distribution
  - articles/story-power-evaluation-with-spending-bound
  - articles/story-compute-expected-events
  - articles/story-info-formula

- title: "Comparision of multiple NPH tests"
  desc: >
    Comparison of power among different tests, such as regular logrank test, weighted logrank test with different weights (i.e., Fleming-Harrington, Magirr-Burman, etc.), and MaxCombo.
  contents:
  - articles/story-compare-power-delay-effect


- title: "Designs with futility bounds"
  desc: >
    Designs with both efficacy and binding/unbinding futility bounds.
  contents:
  - articles/story-nph-futility
  - articles/story-seven-test-types

- title: "Designs by AHR"
  desc: >
    Develop designs for time-to-event endpoints by average hazard ratio.
  contents:
  - articles/story-design-with-spending
  - articles/story-design-with-ahr
  - articles/story-ahr-under-nph
  - articles/story-integer-design
  - articles/story-spending-time-example
  - articles/story-update-boundary

- title: "Designs with binary endpoints"
  desc: >
    Develop designs for binary endpoints.
  contents:
  - articles/story-risk-difference