_pkgdown.yml

url: https://canmod.github.io/macpan2/
template:
  bootstrap: 5
  package: macpan2
  includes:
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# is not rendering on pkgdown. this magic seems to work for now.
# https://github.com/r-lib/pkgdown/issues/2704#issuecomment-2307055568
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navbar:
  structure:
    left:  [intro, reference, articles, tutorials, news]
    right: [search, github]
home:
  sidebar:
    structure: [toc, links, license, community, citation, authors, dev]
  links:
  - text: Maintainer
    href: https://github.com/stevencarlislewalker
  - text: Roadmap
    href: https://github.com/orgs/canmod/projects/2/views/6
  - text: Presentation slides
    href: https://canmod.net/misc/pyRC
reference:
- title: Specifications

- subtitle: Create Model Specifications
  desc: >
    Functions for creating new model specification objects, which describe
    dynamical models with special support for compartmental modelling. The 
    `vignette("quickstart")` article describes how these functions are used
    in context.
  contents:
  - mp_tmb_model_spec
  - mp_per_capita_flow
  - mp_absolute_flow
  - engine_functions
  - mp_optimized_spec
  
- subtitle: Find Model Specifications
  desc: >
    Functions for finding, copying, and loading existing model
    specification objects from model libraries. The `vignette("example_models")`
    article describes how these functions are used in context.
  contents:
  - mp_tmb_library
  - mp_official_library
  - mp_show_models
  - mp_model_starter
  - mp_model_docs
  - mp_read_rds

- subtitle: Transform Model Specifications
  desc: > 
    Functions that take a model specification as input and return a modified 
    version of that specification.
  contents:
  - mp_tmb_insert
  - mp_tmb_insert_reports
  - mp_tmb_insert_log_linear
  - mp_tmb_insert_glm_timevar
  - mp_tmb_insert_trans
  - mp_tmb_insert_backtrans
  - mp_euler
  - mp_expand
  - mp_version_update

- subtitle: Unpack Model Specifications
  desc: > 
    Functions that extract, print, and/or plot information 
    contained within model specifications.
  contents:
  - mp_print_spec
  - mp_initial
  - mp_default
  - mp_flow_frame
  - mp_change_frame
  - mp_vars
  - mp_state_dependence_frame
  - mp_version
  - mp_dot_layout
  - mp_adjacency
  - find_all_paths

- title: Simulators

- subtitle: Create New Model Simulators
  desc: Functions for creating a model simulator object.
  contents:
  - mp_simulator

- subtitle: Generate Simulations
  desc: >
    Functions that generate simulations from a simulator object.
  contents:
  - mp_trajectory
  - mp_initial
  - mp_final
  
- subtitle: Unpack Model Simulators
  desc: > 
    Functions that extract or print information contained within 
    model simulators.
  contents:
  - mp_default
  - mp_tmb
  - mp_version

- title: Calibrators

- subtitle: Create Model Calibrator
  desc: Create a simulator that can be calibrated to data
  contents:
  - mp_tmb_calibrator
  - mp_par
  - mp_traj
  - mp_rbf
  - transform_distr_param
  - mp_sim_bounds
  - mp_sim_offset
  - mp_time_scale

- subtitle: Specify Distributional Assumptions
  desc: > 
    Functions for specifying distributional assumptions for priors 
    and likelihoods.
  contents:
  - mp_unif
  - mp_fit

- subtitle: Optimize Calibrator Model
  desc: > 
    Functions that take a model calibrator as input and calibrate model
    parameters, as well as functions that extract underlying objects
    used during the opimization/calibration process.
  contents:
  - mp_optimize
  - mp_optimizer_output
  - mp_optimized_spec
  - mp_tmb_objective

- subtitle: Generate Calibrated Simulations, Parameters, and Forecasts
  desc: >
    Functions that generate simulations and tables of fitted parameters
    from a calibator object.
  contents:
  - mp_trajectory
  - mp_tmb_coef
  - mp_effects_descr
  - mp_tmb_fixef_cov
  - mp_tmbstan_coef
  - mp_tmb_profile
  - mp_forecaster

- subtitle: Unpack Model Calibrators and Calibrations
  desc: > 
    Functions that extract or print information contained within 
    model calibrators.
  contents:
  - mp_tmb
  - mp_parameterization
  - mp_version
  - mp_opt_attempted
  - mp_uncertainty_estimated
  - mp_print_obj_fn

- title: Utilities

- subtitle: Lightweight Simulation Utilities
  desc: >
    Simple functions for simulation without simulator objects, so that the 
    `?engine_functions` can be explored in isolation from compartmental models.
  contents:
  - engine_eval
  - simple_sims

- subtitle: Creating Matrices, Vectors, and Lists
  desc: >
    Utilities for constructing matrices, vectors, and lists for 
    use with `macpan2`.
  contents:
  - nlist
  - empty_matrix
  - empty_trajectory
  - mp_zero_vector
  - rbf
  - sparse_matrix_notation
  - mp_binary_operator
  - mp_kronecker_operator

- subtitle: Developer and Power-User Utilities
  desc: >
    Utilities for `macpan2` developers and power-users.
  contents:
  - si_example_object
  - si_example_code
  - mp_tmb_expr_list
  - mp_functions_used
  - Reader
  - Transform

- title: Not Ready

- subtitle: Box Diagrams
  desc: >
    Functions for semi-automatically laying out compartments in model
    specifications as boxes on a plot.
  contents:
  - mp_layout_grid
  - mp_layout_paths

- subtitle: Structured Populations (Not Ready)
  desc: > 
    Functions for specifying population structure 
    (e.g., age, space, immunity status).
  contents:
  - mp_dynamic_model
  - mp_dynamic_simulator
  - LedgerDefinition
  - mp_cartesian
  - mp_extract
  - mp_index
  - mp_join
  - mp_linear
  - mp_positions
  - mp_reference
  - mp_rename
  - mp_square
  - mp_symmetric
  - mp_triangle
  - mp_factors
  - mp_group
  - mp_labels
  - mp_ledgers
  - mp_lookup
  - mp_slices
  - mp_structured_vector
  - mp_subset
  - mp_union
  - to_labels
  - to_positions
  - to_string
  - mp_aggregate
  - StringDataFromFrame
  - all_equal


articles:
- title: User Guides
  navbar: ~
  contents:
  - quickstart
  - example_models
  - calibration
  - real_data
  - options
  - FAQs
- title: Specs
  desc: Specification Documents
  contents:
  - cpp_side
  - vignette_status
- title: Superuser Guides
  desc: Articles aimed at advanced users
  contents:
  - matrix_multiplication
  - kronecker
  - time_varying_parameters_advanced
  - calibration_advanced
  - engine_agnostic_grammar
- title: Developer Guides
  desc: Articles aimed at package developers
  contents:
  - design_concepts
  - development_patterns
  - debugging
  - composing_simulation_models
  - elementwise_binary_operators
  - state_dependent_rates
- title: Not Ready
  desc: Articles that are not ready for users or developers
  contents:
  - time_varying_parameters
  - likelihood_prior_specs
  - state_updaters