In dhope/BASSr: Benefit Applied Strategic Sampling

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(DiagrammeR)

yellow are helper functions
dark blue are main runner functions
light blue are exported, user-facing functions
white are un-exported, internal functions
grey are deprecated functions

grViz("digraph boxes_and_circles {

  compound=true;

  # a 'graph' statement
  graph [overlap = true, fontsize = 10]

  # several 'node' statements
  node [shape = rectangle, fontname = 'Courier New', 
        fixedsize = false, style=filled, fillcolor=white]

  no_grts [label = 'noGRTS_BASS_run()' fillcolor = 'cadetblue3']

  prepare_hab_long [label = 'prepare_hab_long()']
  quick_ben [label = 'quick_ben()']
  allhexes [label = 'allhexes()' fillcolor = 'pink']
  draw_rand [label = 'draw_random_samples()' fillcolor = 'lightblue1']

  # Helpers
  costs [label = 'estimate_cost_study_area()' fillcolor = 'khaki1']
  study_area [label = 'create_study_area()' fillcolor = 'khaki1']
  clean [label = 'clean_land_cover()' fillcolor = 'khaki1']
  prepare_cost [label = 'prepare_cost()' fillcolor = 'khaki1']
  get_road [label = 'getroaddensity()']

  #  
  calc_inc_prob [label = 'calculate_inclusion_probs()' fillcolor = 'lightblue1']

  # Selection?
  grts [label = 'run_grts_on_BASS()' fillcolor = 'cadetblue3']
  subsample_benefit [label = 'subsample_grts_and_calc_benefit()']
  select_sites [label = 'select_sites()' fillcolor = 'lightblue1']
  down [label = 'downweight_selection_pr()' fillcolor = 'lightblue1']
  gen_dist_mat [label = 'gen_dist_mat()']
  create_sites [label = 'create_sites()' fillcolor = 'lightblue1']

  # Deprecated?
  full_sel [label = 'run_full_BASS_w_selection()' fillcolor = 'grey70']
  extract_habitat_cost [label = 'extract_habitat_cost()' fillcolor = 'grey70']
  genraster [label = 'genraster()' fillcolor = 'grey70']


  opposite [label = 'oppositeSigns()' fillcolor = 'pink']
  sumH [label = 'sumH()' fillcolor = 'pink']
  sumC [label = 'sumC()' fillcolor = 'pink']
  speedbass [label = 'speedbass()' fillcolor = 'pink']

  getresults [label = 'getresults_BASS()']
  genpoints [label = 'generate_Points_around_centroid()']

  subgraph cluster_1 {
    style=filled;
    fillcolor = 'cadetblue3';
    label = 'full_BASS_run()';
        fontname = 'Courier New';
        fontsize = 14;
        node[];
    draw_rand->prepare_hab_long [lhead=cluster_0];
    allhexes->calc_inc_prob

    subgraph cluster_0 {
      style=filled;
          fillcolor = 'lightblue1'
          node [style=filled,color=white];
          prepare_hab_long -> quick_ben -> allhexes;
          label = 'calculate_benefit()';
          fontname = 'Courier New';
          fontsize = 14;
    }
  }


  # several 'edge' statements
  edge []

  clean->draw_rand [style=dashed,lhead=cluster_1];
  costs->draw_rand [lhead=cluster_1, style=dashed]
  costs->calc_inc_prob [style=dashed]
  costs->no_grts [style=dashed]

  prepare_cost->get_road
  down->gen_dist_mat

  subsample_benefit->prepare_hab_long[lhead=cluster_0];

  no_grts->prepare_hab_long[lhead=cluster_0];

  select_sites->grts

  # C++
  speedbass->sumC
  opposite->sumH [style=invis]

  # Dep
  extract_habitat_cost->genraster

  # Random
  genSSU->getresults->genpoints [style=invis]


}", )