Package index • macpan2

Specifications

Create Model Specifications

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.

mp_tmb_model_spec(): Create TMB Model Specification

mp_per_capita_flow() mp_per_capita_inflow() mp_per_capita_outflow() mp_absolute_flow(): Specify Flow Between Compartments

engine_functions `+` `-` `*` `/` `^` exp log `(` c matrix `%*%` sum rep row_sums col_sums group_sums `[` block t rbind_time rbind_lag cbind_time cbind_lag `:` seq convolution cbind rbind time_step assign unpack recycle clamp dpois dnbinom dnorm rpois rnbinom rnorm `%x%` to_diag from_diag time_group cos print time_var rbinom reulermultinom round pgamma mean sd proportions: Functions Available in the Simulation Engine

Find Model Specifications

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.

mp_tmb_library(): Read Item from a Model Library

mp_show_models() show_models(): Print a Table of Existing Models

mp_model_starter(): Copy Existing Model as a Starting Point

Transform Model Specifications

Functions that take a model specification as input and return a modified version of that specification.

mp_tmb_insert() mp_tmb_update() mp_tmb_delete(): Transform a TMB Model Spec

mp_tmb_insert_reports(): Insert Reports

mp_euler() mp_rk4() mp_rk4_old() mp_euler_multinomial() mp_hazard(): Change How State Variables are Updated

mp_expand() mp_reduce(): Expand Model

Unpack Model Specifications

Functions that extract or print information contained within model specifications.

mp_print_spec() mp_print_before() mp_print_during() mp_print_after(): Print Model Specification

mp_initial() mp_initial_list(): Initial Values

mp_default() mp_default_list(): Default Values

mp_flow_frame(): Flow Frame (experimental)

mp_change_frame(): Change Frame

mp_state_vars(): State Variables

mp_state_dependence_frame(): State Dependence Frame

Simulators

Create New Model Simulators

Functions for creating a model simulator object.

mp_simulator(): Create a Simulator

Generate Simulations

Functions that generate simulations from a simulator object.

mp_trajectory() mp_trajectory_sd() mp_trajectory_ensemble() mp_trajectory_sim() mp_trajectory_replicate(): Trajectory

mp_initial() mp_initial_list(): Initial Values

mp_final() mp_final_list(): Final Values

Unpack Model Simulators

Functions that extract or print information contained within model simulators.

mp_default() mp_default_list(): Default Values

mp_tmb(): Get Underlying TMB Object

Calibrators

Create Model Calibrator

Create a simulator that can be calibrated to data

mp_tmb_calibrator(): Make TMB Calibrator

mp_par(): Fit Parameters

mp_traj(): Trajectory Specification

mp_rbf(): Fit a Time-Varying Parameter with Radial Basis Functions

mp_identity mp_log mp_logit mp_sqrt: Distributional Parameter Transformation

mp_sim_bounds(): Simulation Bounds (Experimental)

mp_time_scale(): Time Scale

Specify Distributional Assumptions

Functions for specifying distributional assumptions for priors and likelihoods.

mp_uniform() mp_normal() mp_log_normal() mp_logit_normal() mp_poisson() mp_neg_bin(): Distributions

mp_fit() mp_nofit(): Fitting Distributional Parameters

Optimize Calibrator Model

Functions that take a model specification as input and return a modified version of that specification.

mp_optimize(): Optimize

mp_optimizer_output(): Optimizer Output

Generate Calibrated Simulations and Parameters

Functions that generate simulations and tables of fitted parameters from a calibator object.

mp_trajectory() mp_trajectory_sd() mp_trajectory_ensemble() mp_trajectory_sim() mp_trajectory_replicate(): Trajectory

mp_tmb_coef(): TMB Model Coefficient Table

mp_effects_descr() mp_add_effects_descr(): Describe Statistical Effects

mp_tmb_fixef_cov(): Covariance of Fixed Effect Estimates

mp_tmbstan_coef(): Model Coefficient Table with stan

Generate Fitted Parameter Tables

Unpack Model Calibrators and Calibrations

Functions that extract or print information contained within model calibrators.

mp_tmb(): Get Underlying TMB Object

Utilities

Lightweight Simulation

Simple functions for simulation without simulator objects, so that the ?engine_functions can be explored in isolation from compartmental models.

engine_eval(): Engine Evaluation

simple_sims(): Simple Iterated Simulation

Creating Matrices, Vectors, and Lists

Utilities for constructing matrices, vectors, and lists for use with macpan2.

nlist(): Self Naming List

empty_matrix: Empty Matrix

mp_zero_vector(): Zero Vector

rbf(): Radial Basis Functions

BinaryOperator() mp_binary_operator(): Binary Operator

Developer Utilities

Utilities for macpan2 developers. TODO: Justify why these are exposed to users or do not expose.

finalizer_char() finalizer_index(): Finalizers

initial_valid_vars(): Initial Valid Variables

make_expr_parser(): Generate an Arithmetic Expression Parser

mp_tmb_expr_list(): Expression List

Reader() CSVReader() JSONReader() TXTReader() RReader() NULLReader(): Reader

Transform() Identity() Log() Logit(): Transform

Not Ready

Box Diagram Layouts (Not Ready)

Functions for semi-automatically laying out compartments in model specifications as boxes on a plot.

mp_layout_grid(): Flow Diagram Grid Layout (experimental)

mp_layout_paths(): Flow Diagram Grid Layout (experimental)

find_all_paths(): Find all Paths Through Compartments

Structured Populations (Not Ready)

Functions for specifying population structure (e.g., age, space, immunity status).

mp_dynamic_model(): Dynamic Model

mp_dynamic_simulator(): TMB Simulator from Dynamic Model

LedgerDefinition: Ledgers

mp_cartesian(): Cartesian Product of Index Tables

mp_extract(): Extract Index

mp_index() print(<Index>) names(<Index>) labelling_column_names(<Index>) labels(<Index>): Model Quantity Index Table

mp_join(): Join Indexes

mp_linear(): Linear Chain Product

mp_positions(): Position Vectors

mp_reference(): Reference Index

mp_rename(): Rename Index Columns

mp_square(): Self Cartesian Product

mp_symmetric(): Symmetric Self Cartesian Product

mp_triangle(): Self Cartesian Product Excluding One Off-Diagonal Side

mp_factors(): Factor an Index

mp_group(): Group an Index

mp_labels(): Index Labels

mp_ledgers(): Bundle up Ledgers

mp_lookup(): Lookup

mp_slices(): Slice an index

mp_structured_vector() mp_set_numbers(): Structured Vectors

mp_subset() mp_setdiff(): Subset of Indexes

mp_union(): Union of Indexes

to_labels() to_names() to_name() to_name_pairs() to_values(): Names and Labels

to_positions(): To Positions

to_string(): To String

mp_aggregate(): Aggregate an Index

StringDataFromFrame() StringDataFromDotted() print(<StringData>): String Data

all_equal() all_consistent() not_all_equal() all_not_equal(): Comparison Functions