Reduce the number of exported functions (#420)

These functions were exported but aren't really used and add clutter Towards #206 #399
traitecoevo · Jun 2, 2024 · b62c59e · b62c59e
1 parent 7bdb299
commit b62c59e
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Showing 56 changed files with 177 additions and 1,003 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -36,5 +36,6 @@
 ^vignettes/package_organisation.Rmd$
 ^vignettes/parameters.Rmd$
 ^vignettes/patch.Rmd$
+^vignettes/profiling_code.Rmd$
 ^vignettes/self_thinning.Rmd$
 ^vignettes/strategy_new.Rmd$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -41,7 +41,6 @@ Suggests:
     here,
     deSolve,
     numDeriv,
-    parallel,
     RcppR6 (>= 0.2.3),
     knitr,
     rmarkdown,
@@ -57,4 +56,4 @@ Remotes:
 VignetteBuilder: knitr
 URL: https://github.com/traitecoevo/plant
 BugReports: https://github.com/traitecoevo/plant/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,107 +1,58 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(resource_compensation_point,Plant)
-S3method(validate,Parameters)
 export("%>%")
 export(Control)
 export(Disturbance_Regime)
 export(FF16_Environment)
 export(FF16_Individual)
-export(FF16_Node)
 export(FF16_Parameters)
-export(FF16_Patch)
-export(FF16_SCM)
-export(FF16_Species)
-export(FF16_StochasticPatch)
-export(FF16_StochasticPatchRunner)
-export(FF16_StochasticSpecies)
 export(FF16_Strategy)
 export(FF16_expand_state)
 export(FF16_fixed_environment)
 export(FF16_generate_stand_report)
 export(FF16_hyperpar)
 export(FF16_make_environment)
-export(FF16_test_environment)
 export(FF16r_Individual)
-export(FF16r_Node)
 export(FF16r_Parameters)
-export(FF16r_Patch)
-export(FF16r_SCM)
-export(FF16r_Species)
-export(FF16r_StochasticPatch)
-export(FF16r_StochasticPatchRunner)
-export(FF16r_StochasticSpecies)
 export(FF16r_Strategy)
 export(FF16r_hyperpar)
 export(FF16r_make_environment)
-export(FF16r_test_environment)
 export(FF16w_Individual)
-export(FF16w_Node)
-export(FF16w_Parameters)
-export(FF16w_Patch)
-export(FF16w_SCM)
-export(FF16w_Species)
-export(FF16w_StochasticPatch)
-export(FF16w_StochasticPatchRunner)
-export(FF16w_StochasticSpecies)
 export(FF16w_Strategy)
 export(FF16w_fixed_environment)
 export(FF16w_hyperpar)
 export(FF16w_make_environment)
-export(FF16w_test_environment)
 export(Individual)
-export(Internals)
 export(Interpolator)
 export(K93_Environment)
 export(K93_Individual)
-export(K93_Node)
 export(K93_Parameters)
-export(K93_Patch)
-export(K93_SCM)
-export(K93_Species)
-export(K93_StochasticPatch)
-export(K93_StochasticPatchRunner)
-export(K93_StochasticSpecies)
 export(K93_Strategy)
 export(K93_fixed_environment)
 export(K93_hyperpar)
 export(K93_make_environment)
 export(K93_test_environment)
 export(No_Disturbance)
 export(NodeSchedule)
-export(OdeControl)
 export(TF24_Environment)
 export(TF24_Individual)
-export(TF24_Node)
 export(TF24_Parameters)
-export(TF24_Patch)
-export(TF24_SCM)
-export(TF24_Species)
-export(TF24_StochasticPatch)
-export(TF24_StochasticPatchRunner)
-export(TF24_StochasticSpecies)
 export(TF24_Strategy)
 export(TF24_fixed_environment)
 export(TF24_generate_stand_report)
 export(TF24_hyperpar)
 export(TF24_make_environment)
 export(TF24_test_environment)
 export(Weibull_Disturbance_Regime)
-export(bounds)
-export(bounds_infinite)
 export(build_schedule)
-export(cbind_list)
-export(check_bounds)
-export(check_point)
-export(clamp_domain)
 export(environment_type)
 export(expand_parameters)
 export(fast_control)
 export(grow_individual_to_height)
 export(grow_individual_to_size)
 export(grow_individual_to_time)
 export(hyperpar)
-export(individual_list)
 export(integrate_over_size_distribution)
 export(interpolate_to_heights)
 export(interpolate_to_times)
@@ -114,16 +65,13 @@ export(make_environment)
 export(make_hyperpar)
 export(make_patch)
 export(make_scm_integrate)
-export(make_transparent)
 export(mutant_parameters)
-export(nlsolve)
 export(node_schedule_times_default)
 export(optimise_individual_rate_at_height_by_trait)
 export(optimise_individual_rate_at_size_by_trait)
 export(param_hyperpar)
 export(plant_log_console)
 export(plot_size_distribution)
-export(rbind_list)
 export(resource_compensation_point)
 export(run_plant_benchmarks)
 export(run_scm)
@@ -136,15 +84,11 @@ export(scm_state)
 export(seq_log)
 export(seq_log_range)
 export(seq_range)
-export(splinefun_log)
-export(splinefun_loglog)
-export(strategy)
-export(strategy_default)
 export(strategy_list)
 export(tidy_individual)
 export(tidy_patch)
 export(trait_matrix)
-export(validate)
+export(util_colour_set_opacity)
 importFrom(R6,R6Class)
 importFrom(Rcpp,evalCpp)
 importFrom(grDevices,col2rgb)

diff --git a/R/RcppR6.R b/R/RcppR6.R
@@ -1,6 +1,6 @@
 ## Generated by RcppR6: do not edit by hand
 ## Version: 0.2.4
-## Hash: 86d2dab10f9081823f16a63c8035a2ae
+## Hash: 1e61b714fa073aff744206eaac010b91
 
 ##' @importFrom Rcpp evalCpp
 ##' @importFrom R6 R6Class
@@ -700,7 +700,6 @@ OdeRunner <- function(T) {
 ##' @title ODE Control parameters
 ##' @param ...,values Values to initialise the struct with (either as
 ##' variadic arguments, or as a list, but not both).
-##' @export
 `OdeControl` <- function(..., values=list(...)) {
   ret <- OdeControl__ctor()
   if (length(values) > 0L) {
@@ -1620,7 +1619,6 @@ IndividualRunner <- function(T, E) {
 ##' @title Extract Internals from plant object
 ##' @param s_size ???
 ##' @param a_size ???
-##' @export
 `Internals` <- function(s_size, a_size) {
   Internals__ctor(s_size, a_size)
 }

diff --git a/R/bounds.R b/R/bounds.R
diff --git a/R/ff16.R b/R/ff16.R
@@ -10,55 +10,12 @@ FF16_Individual <- function(s=FF16_Strategy()) {
   Individual("FF16", "FF16_Env")(s)
 }
 
-##' @export
-##' @rdname FF16
-FF16_Node <- function(s=FF16_Strategy()) {
-  Node("FF16", "FF16_Env")(s)
-}
-
-##' @export
-##' @rdname FF16
-FF16_Species <- function(s=FF16_Strategy()) {
-  Species("FF16", "FF16_Env")(s)
-}
-
 ##' @export
 ##' @rdname FF16
 FF16_Parameters <- function() {
   Parameters("FF16","FF16_Env")()
 }
 
-##' @export
-##' @rdname FF16
-##' @param p A \code{Parameters<FF16,FF16_Env>} object
-FF16_Patch <- function(p) {
-  Patch("FF16", "FF16_Env")(p)
-}
-
-##' @export
-##' @rdname FF16
-FF16_SCM <- function(p) {
-  SCM("FF16", "FF16_Env")(p)
-}
-
-##' @export
-##' @rdname FF16
-FF16_StochasticSpecies <- function(s=FF16_Strategy()) {
-  StochasticSpecies("FF16", "FF16_Env")(s)
-}
-
-##' @export
-##' @rdname FF16
-FF16_StochasticPatch <- function(p) {
-  StochasticPatch("FF16", "FF16_Env")(p)
-}
-
-##' @export
-##' @rdname FF16
-FF16_StochasticPatchRunner <- function(p) {
-  StochasticPatchRunner("FF16", "FF16_Env")(p)
-}
-
 
 ## Helper to create FF16_environment object. Useful for running individuals
 ##' @title create FF16_environment object
@@ -108,10 +65,9 @@ FF16_fixed_environment <- function(e=1.0, height_max = 150.0) {
 ##' @param n number of points
 ##' @param light_env function for light environment in test object
 ##' @param n_strategies number of strategies for test environment
-##' @export
 ##' @rdname FF16_test_environment
 ##' @examples
-##' environment <- FF16_test_environment(10)
+##' environment <- plant:::FF16_test_environment(10)
 FF16_test_environment <- function(height, n=101, light_env=NULL,
                                   n_strategies=1) {