package documentation

Author: stevencarlislewalker

R/formula_list_generators.R

@@ -803,7 +803,7 @@ HazardUpdateMethod = function(change_model) {
 
 # Change Components
 
-#' Specify Flow Between Compartments.
+#' Specify Flow Between Compartments
 #' 
 #' Specify different kinds of flows between compartments.
 #' 

_pkgdown.yml

@@ -11,15 +11,17 @@ home:
   links:
   - text: Roadmap
     href: https://github.com/orgs/canmod/projects/2
-  - text: Project history and trajectory
+  - 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 models.
+    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
@@ -28,10 +30,11 @@ reference:
 - subtitle: Find Model Specifications
   desc: >
     Functions for finding, copying, and loading existing model
-    specification objects from model libraries.
+    specification objects from model libraries. The `vignette("example_models")`
+    article describes how these functions are used in context.
   contents:
-  - mp_show_models
   - mp_tmb_library
+  - mp_show_models
   - mp_model_starter
 
 - subtitle: Transform Model Specifications
@@ -44,7 +47,7 @@ reference:
   - mp_euler
   - mp_expand
 
-- subtitle: Explore Model Specifications
+- subtitle: Unpack Model Specifications
   desc: > 
     Functions that extract or print information contained within 
     model specifications.
@@ -65,13 +68,14 @@ reference:
   - mp_simulator
 
 - subtitle: Generate Simulations
-  desc: Functions that generate simulations from a simulator object.
+  desc: >
+    Functions that generate simulations from a simulator object.
   contents:
   - mp_trajectory
   - mp_initial
   - mp_final
 
-- subtitle: Explore Model Simulators
+- subtitle: Unpack Model Simulators
   desc: > 
     Functions that extract or print information contained within 
     model simulators.
@@ -106,26 +110,34 @@ reference:
     version of that specification.
   contents:
   - mp_optimize
+  - mp_optimizer_output
 
-- subtitle: Explore Model Calibrators and Calibrations
-  desc: > 
-    Functions that extract or print information contained within 
-    model calibrators.
+- subtitle: Generate Calibrated Simulations and Parameters
+  desc: >
+    Functions that generate simulations and tables of fitted parameters
+    from a calibator object.
   contents:
   - mp_trajectory
   - mp_tmb_coef
-  - mp_tmb
-  - mp_optimizer_output
   - mp_effects_descr
   - mp_tmb_fixef_cov
   - mp_tmbstan_coef
 
+- subtitle: Generate Fitted Parameter Tables
+
+- subtitle: Unpack Model Calibrators and Calibrations
+  desc: > 
+    Functions that extract or print information contained within 
+    model calibrators.
+  contents:
+  - mp_tmb
+
 - title: Utilities
 
 - subtitle: Lightweight Simulation
   desc: >
-    Simple functions for simulation without simulators, so that the 
-    `?engine_functions` can be explored.
+    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
@@ -135,9 +147,9 @@ reference:
     Utilities for constructing matrices, vectors, and lists for 
     use with `macpan2`.
   contents:
+  - nlist
   - empty_matrix
   - mp_zero_vector
-  - nlist
   - rbf
   - mp_binary_operator