Fixing various issues with rcmdcheck

- unused packages
- function documentation

DESCRIPTION

@@ -25,8 +25,6 @@ Imports:
     R6,
     loggr,
     crayon,
-    nleqslv,
-    BB,
     magrittr,
     tibble,
     rlang,
@@ -46,7 +44,6 @@ Suggests:
     rmarkdown,
     markdown,
     bench,
-    dplyr,
     ggplot2,
     ggridges,
     patchwork,

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(resource_compensation_point,Plant)
+S3method(validate,Parameters)
 export("%>%")
 export(Control)
 export(Disturbance_Regime)
@@ -32,7 +33,6 @@ export(K93_Strategy)
 export(K93_fixed_environment)
 export(K93_hyperpar)
 export(K93_make_environment)
-export(K93_test_environment)
 export(No_Disturbance)
 export(NodeSchedule)
 export(TF24_Environment)
@@ -43,7 +43,6 @@ 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(build_schedule)
 export(environment_type)

R/RcppR6.R

@@ -1,6 +1,6 @@
 ## Generated by RcppR6: do not edit by hand
 ## Version: 0.2.4
-## Hash: 1e61b714fa073aff744206eaac010b91
+## Hash: 1c60048bc1d88826061cc8bb250fbbc8
 
 ##' @importFrom Rcpp evalCpp
 ##' @importFrom R6 R6Class
@@ -5829,9 +5829,10 @@ StochasticPatchRunner <- function(T, E) {
   ret
 }
 
-##' FF16_Environment object
-##' @param  light_availability_spline_rescale_usually whether to rescale intervals when estimating light environment
+##' Create an FF16_Environment object.
 ##' @param  soil_number_of_depths Number of soil layers to include
+##' @param light_availability_spline_rescale_usually whether to rescale intervals when estimating light environment
+##' @rdname FF16_Environment
 ##' @export
 `FF16_Environment` <- function(light_availability_spline_rescale_usually, soil_number_of_depths) {
   FF16_Environment__ctor(light_availability_spline_rescale_usually, soil_number_of_depths)
@@ -5945,7 +5946,7 @@ StochasticPatchRunner <- function(T, E) {
   ret
 }
 
-##' K93_Environment object
+##' @rdname FF16_Environment
 ##' @export
 `K93_Environment` <- function() {
   K93_Environment__ctor()
@@ -6066,9 +6067,7 @@ StochasticPatchRunner <- function(T, E) {
   ret
 }
 
-##' TF24_Environment object
-##' @param  light_availability_spline_rescale_usually whether to rescale intervals when estimating light environment
-##' @param  soil_number_of_depths Number of soil layers to include
+##' @rdname FF16_Environment
 ##' @export
 `TF24_Environment` <- function(light_availability_spline_rescale_usually, soil_number_of_depths) {
   TF24_Environment__ctor(light_availability_spline_rescale_usually, soil_number_of_depths)

R/benchmark.R

@@ -25,7 +25,8 @@ run_plant_benchmarks <- function(strategy_types = list(FF16 = FF16_Strategy,
   }
 
   message("Running benchmarks via `run_plant_benchmarks`")
-  bench::press(strategy = names(strategy_types),
+  strategy <- names(strategy_types)
+  bench::press(strategy = strategy,
                {
                  bench::mark(
                    check = FALSE,
@@ -58,7 +59,8 @@ run_resource_consumption_benchmarks <- function(its = 10) {
   }
 
   message("Running resource consumption benchmarks`")
-  bench::press(soil_layers = c(1, 10, 50, 100),
+  soil_layers <- c(1, 10, 50, 100)
+  bench::press(soil_layers = soil_layers,
                {
                  bench::mark(
                    check = FALSE,

R/ff16.R

@@ -1,30 +1,43 @@
-##' Create a FF16 Plant or Node
-##' @title Create a FF16 Plant or Node
+##' Create a FF16 Individual
+##' @title Create a FF16 Individual
 ##' @param s A \code{\link{FF16_Strategy}} object
 ##' @export
-##' @rdname FF16
+##' @rdname FF16_individual
 ##' @examples
 ##' pl <- FF16_Individual()
 ##' pl$height
 FF16_Individual <- function(s=FF16_Strategy()) {
   Individual("FF16", "FF16_Env")(s)
 }
 
+##' @title Setup an a model system with default or specified parameters
+##'
+##' @description Setup an a model system with default or specified parameters. 
+##' This function enables you initialize a model system. Use the model name to start different models. 
+##' @param ... Arguments to be passed to the model constructor. These include
+##' 
+##'   *`patch_area`: Area of idnividfual patch. Only relevant for stochastic model. Default is 1.0m2.
+##'   *`max_patch_lifetime`: The maximum time in years we want to simulate
+##'   *`strategies`: A list of stratgies to simulate. The default is an empty list.
+##'   *`strategy_default`: Values for the default startegy. The default values are those specified in the C++ code for the model.
+##'   *`node_schedule_times_default`: Default vector of times at which to introduce nodes. The default is chosen to have close spacing at the start of the simulation.
+##'   *`node_schedule_times`: A list with each element containing the vector of times we want to introduce nodes for each strategy. The default is an empty list.
+##'   *`ode_times`: A vector of patch ages we want the ode solver to stop at
 ##' @export
-##' @rdname FF16
-FF16_Parameters <- function() {
-  Parameters("FF16","FF16_Env")()
+##' @rdname FF16_Parameters
+##' @examples
+##' p1 <- FF16_Parameters()
+##' p2 <- FF16_Parameters(max_patch_lifetime = 10.0, patch_area = 1.0, strategies = list(FF16_Strategy()), strategy_default = FF16_Strategy(), node_schedule_times_default = node_schedule_times_default(10.0), node_schedule_times = list(node_schedule_times_default(10.0)), ode_times = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10))
+FF16_Parameters <- function(...) {
+  Parameters("FF16","FF16_Env")(...)
 }
 
-
-## Helper to create FF16_environment object. Useful for running individuals
-##' @title create FF16_environment object
-##' @param light_availability_spline_tol 
-##'
-##' @param light_availability_spline_nbase 
-##' @param light_availability_spline_max_depth 
-##' @param light_availability_spline_rescale_usually 
-##'
+## Helper functions to create an XXX_Environment object. Useful for running individuals
+##' @title create a model Environment object
+##' @param light_availability_spline_tol Error tolerance of adpative spline method. Deafult is 1e-4.
+##' @param light_availability_spline_nbase Parameter used in adaptive spline method. Default is 17.
+##' @param light_availability_spline_max_depth Parameter used in adaptive spline method. Default is 16.
+##' @inheritParams FF16_Environment
 ##' @export
 ##' @rdname FF16_make_environment
 FF16_make_environment <- function(light_availability_spline_tol = 1e-4, 
@@ -44,15 +57,16 @@ FF16_make_environment <- function(light_availability_spline_tol = 1e-4,
   return(e)
 }
 
-##' Construct a fixed environment for FF16 strategy
+##' Construct a fixed environment for a model
 ##'
 ##' @param e Value of environment (deafult  = 1.0)
-##' @param height_max = 150.0 maximum possible height in environment
-##' @rdname FF16_Environment
+##' @param height_max maximum possible height in environment
+##' @param ... Additional parameters to be passed to \code{XXXX_make_environment}, where XXXX referes to model name.
+##' @rdname FF16_fixed_environment
 ##'
 ##' @export
-FF16_fixed_environment <- function(e=1.0, height_max = 150.0) {
-  env <- FF16_make_environment()
+FF16_fixed_environment <- function(e=1.0, height_max = 150.0, ...) {
+  env <- FF16_make_environment(...)
   env$set_fixed_environment(e, height_max)
   env
 }
@@ -165,7 +179,7 @@ FF16_generate_stand_report <- function(results,
 ##' @param latitude degrees from equator (0-90), used in solar model [deg]
 ##' @importFrom stats coef nls
 ##' @export
-##' @rdname FF16_hyperpar
+##' @rdname make_FF16_hyperpar
 make_FF16_hyperpar <- function(
                                 lma_0=0.1978791,
                                 B_kl1=0.4565855,
@@ -349,5 +363,6 @@ make_FF16_hyperpar <- function(
 ##' @param s A strategy object
 ##' @param filter A flag indicating whether to filter columns. If TRUE, any numbers
 ##' that are within eps of the default strategy are not replaced.
+##' @rdname FF16_hyperpar
 ##' @export
 FF16_hyperpar <- make_FF16_hyperpar()

R/ff16r.R

@@ -4,7 +4,7 @@
 ##' @title Create a FF16r Plant or Node
 ##' @param s A \code{\link{FF16r_Strategy}} object
 ##' @export
-##' @rdname FF16r
+##' @rdname FF16r_Individual
 ##' @examples
 ##' pl <- FF16r_Individual()
 ##' pl$height
@@ -13,50 +13,17 @@ FF16r_Individual <- function(s=FF16r_Strategy()) {
 }
 
 ##' @export
-##' @rdname FF16r
+##' @rdname FF16_Parameters
 FF16r_Parameters <- function() {
   Parameters("FF16r","FF16_Env")()
 }
 
-## Helper:
 ##' @export
-##' @rdname FF16_Environment
-##' @param light_availability_spline_rescale_usually turns on environment rescaling (default = TRUE)
-FF16r_make_environment <- function(light_availability_spline_rescale_usually = TRUE) {
-
-  FF16_make_environment(light_availability_spline_rescale_usually)
-}
-
-
-##' This makes a pretend light environment over the plant height,
-##' slightly concave up, whatever.
-##' @title Create a test environment for FF16r startegy
-##' @param height top height of environment object
-##' @param n number of points
-##' @param light_env function for light environment in test object
-##' @param n_strategies number of strategies for test environment
-##' @rdname FF16r_test_environment
-##' @examples
-##' environment <- plant:::FF16r_test_environment(10)
-FF16r_test_environment <- function(height, n=101, light_env=NULL,
-                             n_strategies=1) {
-  hh <- seq(0, height, length.out=n)
-  if (is.null(light_env)) {
-    light_env <- function(x) {
-      exp(x/(height*2)) - 1 + (1 - (exp(.5) - 1))/2
-    }
-  }
-  ee <- light_env(hh)
-  interpolator <- Interpolator()
-  interpolator$init(hh, ee)
-
-  ret <- FF16r_make_environment()
-  ret$light_availability$spline <- interpolator
-  attr(ret, "light_env") <- light_env
-  ret
-}
-
+##' @rdname FF16_make_environment
+FF16r_make_environment <- FF16_make_environment
 
+##' @rdname FF16_test_environment
+FF16r_test_environment <- FF16_test_environment
 
 ##' Hyperparameters for FF16r physiological model
 ##' @title Hyperparameters for FF16r physiological model
@@ -82,7 +49,6 @@ FF16r_test_environment <- function(height, n=101, light_env=NULL,
 ##' @param latitude degrees from equator (0-90), used in solar model [deg]
 ##' @importFrom stats coef nls
 ##' @export
-##' @rdname FF16r_hyperpar
 make_FF16r_hyperpar <- function(
                                 lma_0=0.1978791,
                                 B_kl1=0.4565855,
@@ -256,9 +222,6 @@ make_FF16r_hyperpar <- function(
 
 ##' Hyperparameter function for FF16r physiological model
 ##' @title Hyperparameter function for FF16r physiological model
-##' @param m A matrix of trait values, as returned by \code{trait_matrix}
-##' @param s A strategy object
-##' @param filter A flag indicating whether to filter columns. If TRUE, any numbers
-##' that are within eps of the default strategy are not replaced.
+##' @inheritParams FF16_hyperpar
 ##' @export
 FF16r_hyperpar <- make_FF16r_hyperpar()

R/ff16w.R

@@ -17,11 +17,12 @@ FF16w_Parameters <- function() {
 }
 
 
-## Helper:
 ##' @export
-##' @rdname FF16_Environment
+##' @inheritParams FF16_Environment
 ##' @param soil_number_of_depths the number of soil layers
+##' @param soil_initial_state the initial state of the soil layers
 ##' @param rainfall constant function value for rainfall driver, y = rainfall
+##' @rdname FF16_make_environment
 FF16w_make_environment <- function(light_availability_spline_tol = 1e-4, 
                                    light_availability_spline_nbase = 17,
                                    light_availability_spline_max_depth = 16, 
@@ -70,7 +71,7 @@ FF16w_make_environment <- function(light_availability_spline_tol = 1e-4,
 ##'
 ##' @param e Value of environment (deafult  = 1.0)
 ##' @param height_max = 150.0 maximum possible height in environment
-##' @rdname FF16_Environment
+##' @rdname FF16_fixed_environment
 ##'
 ##' @export
 FF16w_fixed_environment <- function(e=1.0, height_max = 150.0) {
@@ -79,15 +80,7 @@ FF16w_fixed_environment <- function(e=1.0, height_max = 150.0) {
   env
 }
 
-
-##' This makes a pretend light environment over the plant height,
-##' slightly concave up, whatever.
-##' @title Create a test environment for FF16w startegy
-##' @param height top height of environment object
-##' @param n number of points
-##' @param light_env function for light environment in test object
-##' @param n_strategies number of strategies for test environment
-##' @rdname FF16w_test_environment
+##' @rdname FF16_test_environment
 ##' @examples
 ##' environment <- plant:::FF16w_test_environment(10)
 FF16w_test_environment <- function(height,

R/individual.R

@@ -240,17 +240,17 @@ resource_compensation_point.Plant <- function(p, ...) {
 #' The function `optimise_individual_rate_at_height_by_trait` and `optimise_individual_rate_at_size_by_trait` solve for the maximum of
 #' some rate (e.g. growth rate) at a specified height within
 #' the interval of the bounds of a given trait
-#' @param type
-#' @param bounds
-#' @param log_scale
-#' @param tol
-#' @param size
-#' @param size_name
-#' @param rate
-#' @param params
-#' @param env
-#' @param hyperpars
-#'
+#' @param type The type of model to use (e.g. "FF16"). Defaults to "FF16"
+#' @param bounds A vector giving the lower and upper bounds of the trait
+#' @param log_scale Should the trait be optimised on a log scale? Defaults to TRUE
+#' @param tol The tolerance for the optimisation
+#' @param size  The size of the individual to optimise the rate at
+#' @param size_name The name of the size variable specified by \code{size}
+#' @param rate The name of the rate to optimise. Defaults to \code{size_name}
+#' @param params The parameters of the model
+#' @param env The environment of the model
+#' @param hyperpars The hyperparameter function of the model
+#' @param set_state_directly If TRUE, set the state directly to the size, otherwise grows the plant to that size. Defaults to FALSE
 #' @export
 #' @rdname optimise_individual_rate_at_size_by_trait
 #' @author Isaac Towers, Daniel Falster and Andrew O'Reilly-Nugent
@@ -332,6 +332,8 @@ optimise_individual_rate_at_size_by_trait <- function(
   return(ret)
 }
 
+##' @param height Heigh at which grow is optimsied. Defaults to 1
+##' @param ... Additional parameters passed to \code{optimise_individual_rate_at_size_by_trait}
 #' @export
 #' @rdname optimise_individual_rate_at_size_by_trait
 optimise_individual_rate_at_height_by_trait <- function(..., height = 1) {
@@ -350,13 +352,13 @@ solve_max_worker <- function(bounds, f, tol = 1e-3, outcome) {
     ##   NA/Inf replaced by maximum positive value
     ##
     ## which is probably the desired behaviour here.
-    out <- suppressWarnings(optimise(f, interval = bounds, maximum = TRUE, tol = tol))
+    out <- suppressWarnings(stats::optimise(f, interval = bounds, maximum = TRUE, tol = tol))
     # browser()
     ret <- out$maximum
     attr(ret, outcome) <- out$objective
   } else {
     ## This is not very well tested, and the tolerance is not useful:
-    out <- optim(rowMeans(bounds), f,
+    out <- stats::optim(rowMeans(bounds), f,
       method = "L-BFGS-B",
       lower = bounds[, "lower"], upper = bounds[, "upper"],
       control = list(fnscale = -1, factr = 1e10)