_pkgdown.yml

url: https://uupharmacometrics.github.io/xpose/

template:
  params:
    bootswatch: paper

reference:
  - title: Automatic import of run output
    desc:  Import tables and output files from a NLME run to R.
    contents:
    - xpose_data
  - title: Manual import of run output
    desc:  Manually import tables and output files from a NLME run to R.
    contents:
    - read_nm_files
    - read_nm_model
    - manual_nm_import
    - list_nm_tables
    - read_nm_tables
  - title: xpdb examples
    desc: Example of xpose_data
    contents:
    - xpdb_ex_pk
  - title: Data summary
    desc:  Summarize the xpdb content or the run
    contents:
    - print.xpose_data
    - summary.xpose_data
    - prm_table
    - list_vars
    - list_data
    - list_files
    - list_special
  - title: Edit xpdb content
    desc:  Edit data, index or files within an xpdb
    contents:
    - filter.xpose_data
    - slice.xpose_data
    - distinct.xpose_data
    - mutate.xpose_data
    - select.xpose_data
    - rename.xpose_data
    - group_by.xpose_data
    - ungroup.xpose_data
    - summarize.xpose_data
    - irep
    - set_var_types
    - set_var_labels
    - set_var_units
  - title: Access data from an xpdb
    desc:  Access code, data, files or summary from an xpdb object
    contents:
    - get_code
    - get_data
    - get_file
    - get_prm
    - get_special
    - get_summary
  - title: Basic gof
    desc:  Basic goodness-of-fit plots.
    contents:
    - absval_res_vs_idv
    - absval_res_vs_pred
    - res_vs_idv
    - res_vs_pred
    - dv_vs_ipred
    - dv_vs_pred
    - dv_vs_idv
    - ipred_vs_idv
    - pred_vs_idv
    - dv_preds_vs_idv
  - title: Indiviudal plots
    desc:  Indiviudal observations and model predictions profiles by the independent variable
    contents:
    - ind_plots
  - title: Visual predictive checks
    desc:  Visual predictive checks data and plot generation
    contents:
    - vpc_data
    - vpc_opt
    - vpc
  - title: Distribution plots
    desc:  Covariate, parameters, etas and residuals distribution plots
    contents:
    - cov_distrib
    - eta_distrib
    - prm_distrib
    - res_distrib
  - title: QQ plots
    desc:  Covariate, parameters, etas and residuals QQ plots
    contents:
    - cov_qq
    - eta_qq
    - prm_qq
    - res_qq
  - title: Kinetic plots
    desc:  Plots of compartments' amount
    contents:
    - amt_vs_idv
  - title: Minimization diagnostics
    desc: Graphics to evaluate the estimation step
    contents:
    - prm_vs_iteration
    - grd_vs_iteration
  - title: General plotting functions
    desc:  Functions to manually create customized plots from an xpose_data object.
    contents:
    - xplot_distrib
    - xplot_qq
    - xplot_scatter
    - data_opt
  - title: Customize plots
    desc:  Add, customize themes or template titles.
    contents:
    - template_titles
    - update_themes
    - theme_bw2
    - theme_readable
    - theme_xp_default
    - theme_xp_xpose4
  - title: Print and save plots
    desc:  Print plots to the console or save them into a file.
    contents:
    - print.xpose_plot
    - xpose_save
    
authors:
  Benjamin Guiastrennec:
    href: https://github.com/guiastrennec
  Sebastian Ueckert:
    href: https://github.com/sebastianueckert
  Mike K. Smith:
    href: https://github.com/MikeKSmith
  Mats O. Karlsson:
    href: https://katalog.uu.se/profile/?id=XX3384
  Andrew C. Hooker:
    href: https://github.com/andrewhooker

navbar:
  left:
  - text: Articles
    menu:
        - text: "--------------------------"
        - text: "Getting started"
        - text: Cheat sheet (pdf)
          href: reference/figures/cheatsheet.pdf
        - text: Introduction
          href: articles/introduction.html
        - text: Import model outputs
          href: articles/import_model_outputs.html
        - text: Access xpdb data
          href: articles/access_xpdb_data.html
        - text: "--------------------------"
        - text: "Going further"
        - text: Customize plots
          href: articles/customize_plots.html
        - text: Multiple pages
          href: articles/multiple_pages.html
        - text: Visual Predictive Checks (VPC)
          href: articles/vpc.html
        - text: Create interactive plots (beta)
          href: articles/interactive_plots.html
  - text: Functions
    href: reference/index.html
  - text: Plots
    href: articles/plot_list.html
  - text: FAQ
    href: articles/faq.html
  right:
  - text: About
    href: articles/about.html
  - text: News
    href: news/index.html
  - icon: fa-github fa-lg
    href: https://github.com/UUPharmacometrics/xpose
  - icon: fa-download
    href: https://github.com/UUPharmacometrics/xpose/releases