doc edits

Author: stevencarlislewalker

R/formula_list_generators.R

@@ -328,7 +328,7 @@ MockChangeModel = function() {
 }
 
 
-##' State Updates
+##' Change How State Variables are Updated
 ##' 
 ##' These functions return a modified version of a model specification, such 
 ##' that the state variables are updated each time step according to different 
@@ -803,7 +803,7 @@ HazardUpdateMethod = function(change_model) {
 
 # Change Components
 
-#' Flow
+#' Specify Flow Between Compartments.
 #' 
 #' Specify different kinds of flows between compartments.
 #' 
@@ -1045,6 +1045,8 @@ to_change_component.formula = function(x) Formula(x)
 #' 
 #' @param model A model object.
 #'
+#' @describeIn mp_expand Synonym of `mp_expand` present only for 
+#' back-compatibility. Please use `mp_expand` in new projects.
 #' @export
 mp_reduce = function(model) UseMethod("mp_reduce")
 

R/make_model_index.R

@@ -54,10 +54,10 @@ get_mod_info <- function(f) {
     return(data.frame(dir=f_base, res))
 }
 
-#' Print a table of contents of available models
+#' Print a Table of Existing Models
 #'
-#' Collects information from the headers of the README files in the model directories
-#' and returns the results as a data frame
+#' Collects information from the headers of the README files in
+#' model directories and returns the results as a data frame
 #'
 #' @param dir directory to list
 #' @param show_missing (logical) include entries for models with no README information?

R/mp_library.R

@@ -3,7 +3,7 @@ mp_library = function(...) {
   stop("under construction")
 }
 
-#' TMB Library
+#' Read Item from a Model Library
 #' 
 #' Get a TMB model specification from a model library.
 #' 
@@ -62,7 +62,7 @@ mp_tmb_library = function(..., package = NULL, alternative_specs = FALSE) {
   stop("Malformed model library entry.")
 }
 
-#' Model Starter
+#' Copy Existing Model as a Starting Point
 #'
 #' Create a directory with a template model definition.
 #'

R/mp_tmb_model_spec.R

@@ -256,7 +256,7 @@ must_save_time_args = function(formulas) {
   return(time_args)
 }
 
-#' Specify a TMB Model
+#' Create TMB Model Specification
 #' 
 #' Specify a simulation model in the TMB engine.
 #' 

_pkgdown.yml

@@ -18,10 +18,16 @@ reference:
 
 - subtitle: Create Model Specifications
   desc: >
-    Functions for creating, finding, and reading model specification objects.
+    Functions for creating new model specification objects.
   contents:
   - mp_tmb_model_spec
   - mp_per_capita_flow
+  
+- subtitle: Find Model Specifications
+  desc: >
+    Functions for finding, copying, and loading existing model
+    specification objects.
+  contents:
   - show_models
   - mp_tmb_library
   - mp_model_starter
@@ -35,7 +41,6 @@ reference:
   - mp_tmb_insert_reports
   - mp_euler
   - mp_expand
-  - mp_reduce
 
 - subtitle: Explore Model Specifications
   desc: > 
@@ -80,7 +85,7 @@ reference:
   - mp_par
   - mp_traj
   - mp_rbf
-  - mp_identity
+  - transform_distr_param
 
 - subtitle: Specify Distributional Assumptions
   desc: >