_pkgdown.yml

url: https://dd-harp.github.io/ramp.micro/
template:
  bootstrap: 5
navbar:
  left:
  - text: Setup
    menu:
    - text: Point Sets
      href: articles/point_sets.html
    - text: Kernels
      href: articles/kernels.html
    - text: Models
      href: articles/models.html
    - text: Simulation
      href: articles/simulation.html
    - text: Visualization
      href: articles/visualization.html
    - text: Modularity
      href: articles/modularity.html
    - text: Traps
      href: articles/models.html
  - text: Adults
    menu:
    - text: Adult Mosquitoes - BQ
      href: articles/BQ.html
    - text: Adult Mosquitoes - BQS
      href: articles/BQS.html
  - text: Immature
    menu:
    - text: Immature Mosquitoes - L
      href: articles/L.html
  - text: Articles
    menu:
    - text: Mosquito Dispersal
      href: articles/dispersal.html
    - text: Communitites
      href: articles/community.html
  - text: Functions
    href: reference/index.html
  right:
  - icon: fa-github
    href: https://github.com/dd-harp/motrap.micro/
home:
  sidebar:
    structure:
    - links
    - license
    - community
    - citation
    - authors
    - dev
    - custom_news
    components:
      custom_news:
        title: Changelog
        text: <a href="news/index.html">News</a>
reference:
- title: Point Sets
  desc: |
    Functions that generate and visualize resource point sets
- subtitle: Generate Point Sets
  desc: |
    Utilities to generate point sets
  contents:
  - unif_xy
  - lattice
  - clusters_xy
  - clusters_nm
- title: Search & Dispersal
  desc: |
    Utilities for dispersal and demographic matrices
- subtitle: Kernels
  desc: |
     Functions to compute search weights by distance
  contents:
  - make_kF_exp
  - make_kF_pwr
  - make_kF_mix
- subtitle: Make Psi
  desc: |
     Generate the single bout dispersal matrices
  contents:
  - make_Psi_xy
  - make_Psi_xx
- title: Simulation
  desc: |
    Utilities for setting up Models
  contents:
  - SIM
  - steady_state
  - setup_model
  - make_movie
  - make_movie.BQ
  - make_movie.BQS
  - basic_analysis
  - makeKGV
  - make_model_squareLattice
  - make_model_unif
- title: Analyzing Dispersal
  desc: |
    Utilities for analyzing movement
- subtitle: Make K
  desc: |
     Generate matrices describing feeding or egg laying within a single feeding cycle
  contents:
  - make_Kqb
  - make_Kqb.BQ
  - make_Kqb.BQS
  - make_Kbq
  - make_Kbq.BQ
  - make_Kbq.BQS
  - make_Kbb
  - make_Kqq
- subtitle: Plot K
  desc: |
     Plot matrices describing feeding or egg laying within a single feeding cycle
  contents:
  - plot_Kbq
  - plot_Kqb
  - plot_Kbb
  - plot_Kqq
- subtitle: Egg Laying
  desc: |
     Methods to compute and visualize egg dispersal across a mosquito generation
  contents:
  - compute_G
  - compute_G.BQ
  - compute_G.BQS
  - compute_GG
  - plot_dispersal_G
  - plot_dispersal_GG
- subtitle: Parasite transmission potential
  desc: |
     Methods to compute and visualize parasite transmission potential
  contents:
  - compute_V
  - compute_V.BQ
  - compute_V.BQS
  - compute_VC
  - plot_dispersal_V
  - plot_dispersal_VV
- subtitle: Utilites for matrices
  desc: |
     Methods to help streamline matrix visualization
  contents:
  - decompM
  - cutoffValue
  - edgeSubset_fracMass
  - edgeSubset
  - getM_i
  - getNet_i
- subtitle: Compute distances dispersed
  desc: |
     Methods to compute the PMF and CMF for distances dispersed
  contents:
  - dispersal_PMF
  - plotDDpmf
  - plotDDcmf
- title: Adult Mosquito Models
  desc: |
    Methods to set up and compute adult mosquito models
  contents:
  - adult_dynamics
  - save_states_M
  - init_states_M
  - init_adult_model
  - compute_diffs_M
  - setup_adult_model
- subtitle: BQ
  desc: |
     Methods to setup and compute the BQ model
  contents:
  - adult_dynamics.BQ
  - save_states_M.BQ
  - init_states_M.BQ
  - init_adult_model.BQ
  - init_adult_model_BQ
  - compute_diffs_M.BQ
  - setup_dispersal_BQ
  - make_Psi_BQ
  - setup_bionomics_BQ
  - make_demography_BQ
  - setup_adult_model.BQ
- subtitle: BQS
  desc: |
     Methods to setup and compute the BQS model
  contents:
  - adult_dynamics.BQS
  - save_states_M.BQS
  - init_states_M.BQS
  - init_adult_model.BQS
  - init_adult_model_BQS
  - compute_diffs_M.BQS
  - setup_dispersal_BQS
  - make_Psi_BQS
  - setup_bionomics_BQS
  - make_demography_BQS
  - setup_adult_model.BQS
- title: Aquatic Mosquito Models
  desc: |
    Methods to set up and compute aquatic mosquito models
  contents:
  - aquatic_dynamics
  - save_states_L
  - init_states_L
  - init_aquatic_model
  - compute_diffs_L
  - setup_aquatic_model
- subtitle: the basicL model
  desc: |
     Methods to setup and compute basicL
  contents:
  - aquatic_dynamics.basicL
  - save_states_L.basicL
  - init_states_L.basicL
  - init_aquatic_model.basicL
  - init_aquatic_model_basicL
  - compute_diffs_L.basicL
  - setup_aquatic_model.basicL
  - setup_aquatic_model_basicL
- title: Network Analysis
  desc: |
    Methods to set up and analyze communities
- subtitle: Convex Hulls
  desc: |
    Methods to compute and visualize convex hulls around communities
  contents:
  - make_convex_hulls
  - make_convex_hull_i
  - plot_convex_hulls
  - stretch_convex_hull
- subtitle: Tesselate
  desc: |
    Methods to compute and visualize using Delauney / Dirichlet methods
  contents:
  - make_tiles
  - make_tiles.BQ
  - make_tiles.BQS
- title: Visualization
  desc: |
    Methods to visualize objects
- subtitle: Visualize Point Sets
  desc: |
    Utilities to visualize point sets
  contents:
  - plot_points
  - plot_points.BQ
  - plot_points.BQS
  - plot_points_bq
  - plot_points_bqs
  - frame_bq
  - frame_bqs
  - add_points_b
  - add_points_bb
  - add_points_q
  - add_points_qq
  - add_points_s
  - add_points_ss
- subtitle: Plot Dispersal Matrices
  desc: |
     Visualize a generic dispersal matrix
  contents:
  - plot_matrix_xy
  - plot_matrix_xx
  - add_arrows_xy
  - add_arrows_xx
  - add_one_arrow
  - add_nth_arrow_xy
  - add_nth_arrow_xx
  - add_nth_segment
  - add_bent_arrows_xy
  - add_bent_arrows_xx
- subtitle: Plot Psi
  desc: |
     Plot the single bout dispersal matrices
  contents:
  - plot_Psi_bb
  - plot_Psi_bq
  - plot_Psi_bs
  - plot_Psi_qb
  - plot_Psi_qq
  - plot_Psi_qs
  - plot_Psi_sb
  - plot_Psi_sq
  - plot_Psi_ss
  - plot_Psi
  - plot_Psi.BQ
  - plot_Psi_BQmod
  - plot_Psi.BQS
  - plot_Psi_BQSmod