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(): Specify Flow Between Compartments

mp_absolute_flow(): Specify Absolute Flow Between Compartments (Experimental)

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 last check_finite: Functions Available in the Simulation Engine

mp_optimized_spec(): Optimized Model Specification

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() mp_tmb_entire_library(): Read Item from a Model Library

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

mp_model_starter(): Copy Existing Model as a Starting Point

mp_model_docs(): Browse Model Docs

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 Specification

mp_tmb_insert_reports(): Transform a TMB Model Specification to Account for Reporting Bias

mp_tmb_insert_log_linear(): Insert Log Linear Model of Time Variation (Experimental)

mp_tmb_insert_trans(): Insert Basic Transformations of Model Variables

mp_tmb_insert_backtrans(): Insert Back Transformations of Model Parameters

mp_euler() mp_rk4() mp_rk4_old() mp_euler_multinomial() mp_discrete_stoch() 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 of Variables Immediately Before the Simulation Loop

mp_default() mp_default_list(): Default Values

mp_flow_frame(): Data Frame Describing Compartmental Model Flows

mp_change_frame(): Data Frame Describing Each Change to Each State Variable

mp_state_vars() mp_flow_vars() mp_state_flow_vars(): State and Flow Variable Names

mp_state_dependence_frame(): Data Frame Describing State Dependent Per-Capita Flow Rates

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_par() mp_trajectory_sd() mp_trajectory_ensemble() mp_trajectory_sim() mp_trajectory_replicate(): Simulate Dynamical Model Trajectories

mp_initial() mp_initial_list(): Initial Values of Variables Immediately Before the Simulation Loop

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 a 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: Link Functions and Transformation

mp_sim_bounds(): Simulation Bounds

mp_sim_offset(): Simulation Offsets

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 calibrator as input and calibrate model parameters, as well as functions that extract underlying objects used during the opimization/calibration process.