_pkgdown.yml

url: https://rdinnager.github.io/slimr

destination: docs
reference:
  - title: Install and setup SLiM software for use with slimr
  - contents:
    - slim_setup
  - title: slimr verbs
    desc: Functions that can be inserted in slimr code blocks for metaprogramming.
  - subtitle: Main slimr verbs
    desc: The three main functions that can be called inside `slim_block` calls for metaprogramming
  - contents:
    - r_output
    - r_inline
    - r_template
  - subtitle: r_output_ special variants
  - contents:
    - starts_with("r_output_")
  - subtitle: r_template_ special variants
  - contents:
    - starts_with("r_template_")
  - subtitle: slimr_block_ verbs
    desc: These function generate full code blocks and can be used inside `slim_script` calls.
  - contents:
    - starts_with("slim_block_")
  - title: Creating slimr_script objects
    desc: These functions help you create and manipulate `slimr_script` objects, which contain SLiM simulation instructions
  - contents:
      - slim_script
      - slim_block
      - slim_function
      - slim_script_render
      - slim_load_globals
      - slim_unload_globals
  - title: Run a slimr_script object and return results to R
  - contents:
    - slim_run
  - title: Extract Output from slimr_results Objects
  - contents:
    - starts_with("slim_extract_")
  - title: Work with SLiM recipes from SLiM manual
  - contents:
    - slim_get_recipe
    - slim_get_recipes
  - title: Operators
  - contents:
    - "`%.%`"
    - "`%?%`"
    - "`%else%`"
  - title: SLiM Callbacks
    desc: Function stubs for SLiM callback Functions
  - contents:
      - slim_callbacks
      - initialize
      - late
      - early
      - fitness
      - fitnessEffect
      - mateChoice
      - modifyChild
      - mutation
      - mutationEffect
      - recombination
      - interaction
      - reproduction
      - survival
  - title: SLiM Class Objects
    desc: >
      Objects representing the different classes used in SLiM. These can be used to look up and
      autocomplete what methods or properties are available for a class
  - contents:
    - Chromosome
    - Ch
    - Eidos
    - E
    - Genome
    - G
    - GenomicElement
    - GE
    - GenomicElementType
    - GET
    - Individual
    - In
    - Initialize
    - Init
    - InteractionType
    - IT
    - LogFile
    - LF
    - Mutation
    - M
    - MutationType
    - MT
    - SLiMBuiltin
    - SB
    - SLiMEidosBlock
    - SEB
    - SLiMgui
    - SG
    - SpatialMap
    - SM
    - SS
    - Subpopulation
    - P
    - Substitution
    - S
    - slim_classes
  - title: SLiM Class Methods
    desc: >
      SLiM methods by SLiM class. Note that if a function appears multiple times within a class,
      that is because a method with the same name exists in other classes. Each links to the same
      documentation which combines documentation for all classes in one place. This is a bug created
      by limitation in the R documentation system, but shouldn't cause the user any issues.
  - subtitle: Chromosome
  - contents:
    - has_concept("Chromosome")
  - subtitle: Community
  - contents:
    - has_concept("Community")
  - subtitle: Eidos
  - contents:
    - has_concept("Eidos")
  - subtitle: Genome
  - contents:
    - has_concept("Genome")
  - subtitle: GenomicElement
  - contents:
    - has_concept("GenomicElement")
  - subtitle: GenomicElementType
  - contents:
    - has_concept("GenomicElementType")
  - subtitle: Individual
  - contents:
    - has_concept("Individual")
  - subtitle: Initialize
  - contents:
    - has_concept("Initialize")
  - subtitle: InteractionType
  - contents:
    - has_concept("InteractionType")
  - subtitle: LogFile
  - contents:
    - has_concept("LogFile")
  - subtitle: Mutation
  - contents:
    - has_concept("Mutation")
  - subtitle: MutationType
  - contents:
    - has_concept("MutationType")
  - subtitle: SLiMBuiltin
  - contents:
    - has_concept("SLiMBuiltin")
  - subtitle: SLiMEidosBlock
  - contents:
    - has_concept("SLiMEidosBlock")
  - subtitle: SLiMSim
  - contents:
    - has_concept("SLiMSim")
  - subtitle: SLiMgui
  - contents:
    - has_concept("SLiMgui")
  - subtitle: SpatialMap
  - contents:
    - has_concept("SpatialMap")
  - subtitle: Species
  - contents:
    - has_concept("Species")
  - subtitle: Subpopulation
  - contents:
    - has_concept("Subpopulation")
  - subtitle: Substitution
  - contents:
    - has_concept("Substitution")
  - title: Convert between R-like and SLiM-like code
  - contents:
    - slim_code_Rify
    - slim_code_SLiMify
    - as_slimr_script
    - as_slimr_code
    - as_slim_text
    - as_slim_text.slimr_script
  - title: Datasets
  - contents:
    - slim_recipes
    - load_herm
  - title: Uncategorized
  - contents:
    - code
    - end_gen
    - first
    - get_block
    - get_slim_call
    - minimal_slim_sim
    - minimal_slimr_script
    - new_slimr_script_coll
    - reconstruct
    - reconstruct.slimr_script
    - slimr_clip_original
    - slimr_code
    - slimr_name
    - slimr_open_original
    - slimr_script_coll
    - slim_template_info
    - slimr_write
    - slim_file
    - slim_install_path
    - slim_is_avail
    - slim_make_pop_input
    - slim_open
    - slim_results_to_data
    - slim_script_duration