_pkgdown.yml

development:
  mode: release
url: https://levisc8.github.io/ipmr
authors:
  Sam Levin:
    href: https://github.com/levisc8
template:
  params:
    bootswatch: yeti
navbar:
  title: "ipmr"
  left:
    - icon: fa-home fa-lg
      href: index.html
    - text: "Functions"
      href: reference/index.html
    - text: "Vignettes"
      menu:
        - text: "Introduction to ipmr"
          href: articles/ipmr-introduction.html
        - text: "General IPMs"
          href: articles/general-ipms.html
        - text: "Index Notation in ipmr"
          href: articles/index-notation.html
        - text: "Age X Size IPMs"
          href: articles/age_x_size.html
        - text: "Density/Frequency Dependent IPMs"
          href: articles/density-dependence.html
        - text: "proto_ipm Data Structure"
          href: articles/proto-ipms.html
    - text: "News"
      href: news/index.html

reference:
  - title: "IPM Construction and Reporting"
    desc: >
      Functions for initializing an IPM, constructing sub-kernels, defining
      numerical integration, defining initial conditions, defining the
      environmental state, handling eviction, and generating automated reports
      describing the IPM.
  - contents:
      - init_ipm
      - starts_with("define")
      - truncated_distributions
      - use_vr_model
      - starts_with("make_ipm")
  - title: "Projection Diagnostics"
    desc: >
      Evaluate the behavior of the population projection.
  - contents:
      - conv_plot
  - title: "Access parts of a proto_ipm and IPM objects"
    desc: >
      Extract and set various pieces of information from `proto_ipm` and IPM
      objects.
  - contents:
      - domains
      - collapse_pop_state
  - title: "Further Analyses"
    desc: >
      Functions to for analysis of asymptotic dynamics, and helpers to extract
      information needed for analysis of stochastic dynamcis.
  - contents:
      - lambda
      - right_ev
      - make_iter_kernel
      - mean_kernel
      - mat_power
      - right_mult
      - starts_with("as.matrix")
  - title: "Printing and Plotting"
    desc: >
      Functions to print and plot `proto_ipm` and IPM objects.
  - contents:
      - ipm_to_df
      - starts_with("print")
      - starts_with("plot")
  - title: "Exported Data"
    desc: >
      Pre-built `proto_ipm`s and a set of raw demographic data for an [Israeli
      Carpobrotus population](https://doi.org/10.1371/journal.pone.0250879).
  - contents:
      - sim_di_det_ex
      - gen_di_det_ex
      - iceplant_ex
      - monocarp_proto