_pkgdown.yml

url: https://r.ubiquity.tools
template:
  #math-rendering: mathjax
  math-rendering: katex
  bootstrap: 5
  params:
    bootswatch: united 
reference:
- title: "System Basics"  
  desc: "Building systems, setting options, access workshop elements etc."
- contents:
  - build_system
  - system_new
  - system_new_list
  - workshop_fetch
  - system_fetch_parameters
  - system_fetch_iiv
  - system_fetch_set
  - system_fetch_template
  - system_fetch_TSsys
  - system_view
  - system_check_requirements
  - system_set_option
  - system_set_parameter
  - system_set_iiv
- title: "Simulation"
  desc: "Individual and population simulations"
- contents:
  - run_simulation_ubiquity
  - simulate_subjects
  - system_load_data
  - system_select_set
  - som_to_df
  - system_check_steady_state
  - system_zero_inputs
  - system_set_parameter
  - system_set_bolus
  - system_set_rate
  - system_set_covariate
  - run_simulation_titrate
  - system_new_tt_rule
  - system_set_tt_cond
  - system_set_tt_rate
- title: "Estimation"
  desc: "Naive-pooled parameters estimation"
- contents:
  - system_estimate_parameters
  - system_fetch_guess
  - system_set_guess
  - system_plot_cohorts
  - system_clear_cohorts
  - system_define_cohort
  - system_define_cohorts_nm
  - system_simulate_estimation_results
  - system_od_general
- title: "Reporting"
  desc: "The following functions are used to create, modify and save Word and PowerPoint reports"
- contents:
  - starts_with("system_rpt_")
  - starts_with("system_fetch_rpt_")
  - starts_with("system_set_rpt_")
- title: "NCA"
  desc: "The following functions are used to run NCA and summarize results"
- contents:
  - system_fetch_nca
  - system_fetch_nca_columns
  - starts_with("system_nca_")
- title: "General Functions"
  desc: ""
- contents:
  - calculate_halflife
  - check_deps
  - gg_axis  
  - gg_log10_xaxis  
  - gg_log10_yaxis  
  - estimate_parameters
  - linspace
  - logspace
  - pad_string
  - prepare_figure
  - vp
  - var2string
  - system_log_debug_save
  - system_log_init
  - tic
  - toc 
- title: "In development"
  desc: "The following are under development"
- contents:
  - system_glp_init
  - system_glp_scenario
navbar:
  left:
  - text: Tutorials
    icon: fas fa-chalkboard-teacher
    menu:
        - text: "--------------------------"
        - text: "Getting Started"
        - text: "Individual and Population Simulations"
          href: articles/Simulation.html
        - text: "ubiquity Modeling Language"
          href: articles/Language.html
        - text: "Naive-Pooled Parameter Estimation"
          href: articles/Estimation.html
        - text: "--------------------------"
        - text: "Other Analysis Options"
        - text: "Deploying Your Models in a Shiny App"
          href: articles/Deployment.html
        - text: "Trial/Rule-Based Simulations"
          href: articles/Titration.html
        - text: "Estimation of In Vitro/Static Systems"
          href: articles/In_Vitro.html
        - text: "Non-Compartmental Analysis"
          href: articles/NCA.html
        - text: "Integrated Word and PowerPoint Reporting"
          href: articles/Reporting.html
        - text: "--------------------------"
        - text: "More Help"
        - text: "Howtos"
          href: articles/Howto.html
  - text: Screencasts  
    icon: fas fa-video
    menu:
        - text: "--------------------------"
        - text: "Modeling"
        - text: "Individual and Population Simulations"
          href: https://vimeo.com/382859445
        - text: "Model Deployment"
          href: https://vimeo.com/382860283
        - text: "Naive-Pooled Parameter Estimation"
          href: https://vimeo.com/manage/videos/382829588 
        - text: "--------------------------"
        - text: "Other Tools"
        - text: "Tabula: Extracting Tabular Data from PDFs"
          href: https://vimeo.com/650643574
  - text: "Functions"
    icon: fas fa-hat-wizard
    href: reference/index.html
  - text: "News"
    icon: fas fa-rss
    href: news/index.html