Ensure that all functions include a description of the values returned

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.1.6
-Date: 2023-09-15 18:15:02 UTC
-SHA: 03782485a4ec155145da49da0476c498a1b019e2
+Date: 2023-09-18 14:42:04 UTC
+SHA: 28daf1f7c21db3a333d9752661e1771ca4d259bb

R/helper.R

@@ -6,6 +6,8 @@
 #'
 #' @export
 #'
+#' @return Returns a Fibonacci sequence as a vector.
+#'
 #' @examples
 #'
 #' fibonacci(2, 200)
@@ -44,6 +46,8 @@ fibonacci <- function(from, to) {
 #' @param x      an \code{R} object
 #' @param units  the units to be used in printing the size
 #'
+#' @return Returns a character with the object size followed by the unit.
+#'
 #' @export
 #'
 

R/icc.R

@@ -9,6 +9,8 @@
 #' @param x      Response variable
 #' @param group  Group
 #'
+#' @return Returns estimate of intraclass correlation.
+#'
 #' @export
 #'
 

R/plot_sim.R

@@ -29,6 +29,8 @@
 #' @import plotly
 #' @importFrom rlang .data
 #'
+#' @return Returns a plot of class \code{plotly}.
+#'
 #' @export
 #' @rdname plot_trend
 plot_trend <- function(sim, sum_ages = sim$ages, col = viridis::viridis(1), ...) {

R/run_strat.R

@@ -30,6 +30,9 @@ error_stats <- function(error) {
 #' @param alk_scale     Spatial scale at which to construct and apply age-length-keys:
 #'                      "division", "strat" or "set".
 #'
+#' @return Returns a list including set details (\code{setdet}), length-frequencies (\code{lf}),
+#' and age-frequencies (\code{af}).
+#'
 #' @export
 #'
 
@@ -124,6 +127,8 @@ strat_data <- function(sim, length_group = 3, alk_scale = "division") {
 #' @param survey_groups   Grouping variables for large-scale summary calculations. e.g. ("year","species")
 #' @param confidence      Percent for confidence limits
 #'
+#' @return Returns a data.table including stratified estimates of abundance.
+#'
 #' @export
 #'
 

R/sim_dist.R

@@ -41,6 +41,8 @@
 #' @param group_years Make space-age-year noise equal across these years
 #' @param model       String indicating either "exponential" or "matern" as the correlation function
 #'
+#' @return Returns a function for use inside \code{\link{sim_distribution}}.
+#'
 #' @export
 
 sim_ays_covar <- function(sd = 2.8, range = 300, lambda = 1, model = "matern",
@@ -169,6 +171,8 @@ sim_ays_covar <- function(sd = 2.8, range = 300, lambda = 1, model = "matern",
 #'                        forces very low values near zero.
 #' @param plot            Produce a simple plot of the simulated values?
 #'
+#' @return Returns a function for use inside \code{\link{sim_distribution}}.
+#'
 #' @examples
 #'
 #' parabola_fun <- sim_parabola(mu = 50, sigma = 5, plot = TRUE)
@@ -242,6 +246,8 @@ sim_parabola <- function(alpha = 0, mu = 200, sigma = 70, sigma_right = NULL,
 #'                 included in argument \code{coeff} as a named list.
 #' @param coeff    Named list of coefficient values used in \code{formula}.
 #'
+#' @return Returns a function for use inside \code{\link{sim_distribution}}.
+#'
 #' @export
 #'
 #' @examples

R/sim_dist_spde.R

@@ -227,6 +227,8 @@ sim_ays_covar_spde <- function(sd = 2.8,
 #' @param cutoff Minimum distance allowed between points
 #' @param ... Other options to pass to inla.mesh.2d
 #'
+#' @return Returns an object of class \code{inla.mesh}.
+#'
 #' @examples
 #'
 #' \donttest{

R/sim_pop.R

@@ -19,6 +19,8 @@
 #' sim_Z does the same as sim_R when phi_age and phi_year are both 0, otherwise values are correlated
 #' in the age and/or year dimension. The covariance structure follows that described in Cadigan (2015).
 #'
+#' @return Returns a function for use inside \code{\link{sim_abundance}}.
+#'
 #' @references Cadigan, Noel G. 2015. A State-Space Stock Assessment Model for Northern Cod,
 #' Including Under-Reported Catches and Variable Natural Mortality Rates. Canadian Journal of
 #' Fisheries and Aquatic Sciences 73 (2): 296-308.
@@ -138,6 +140,8 @@ sim_N0 <- function(N0 = "exp", plot = FALSE) {
 #' @param length       Interval from \code{\link[base]{findInterval}}
 #' @param group        Length group used to cut the length data
 #'
+#' @return Returns a vector indicating the mid-point of the length group.
+#'
 #' @export
 #'
 
@@ -168,6 +172,8 @@ group_lengths <- function(length, group) {
 #' @param digits        Integer indicating the number of decimal places to round the values to
 #' @param plot          Produce a simple plot of the simulated values?
 #'
+#' @return Returns a function for use inside \code{\link{sim_abundance}}.
+#'
 #' @examples
 #' growth_fun <- sim_vonB(Linf = 100, L0 = 5, K = 0.2, log_sd = 0.05, length_group = 1, plot = TRUE)
 #' growth_fun(age = rep(1:15, each = 100))
@@ -223,7 +229,7 @@ sim_vonB <- function(Linf = 120, L0 = 5, K = 0.1, log_sd = 0.1,
 #' @param   N_at_age    Abundance-at-age matrix
 #' @param   lak         Length-age-key (i.e. probability of being in a specific length group given age)
 #'
-#' @return  Returns abundance-at-length matrix
+#' @return  Returns abundance-at-length matrix.
 #'
 #' @export
 #'

R/sim_survey.R

@@ -8,6 +8,8 @@
 #' @param x0     The x-value of the sigmoid's midpoint
 #' @param plot   Plot relationship
 #'
+#' @return Returns a function for use in \code{\link{sim_survey}}.
+#'
 #' @examples
 #' logistic_fun <- sim_logistic(k = 2, x0 = 3, plot = TRUE)
 #' logistic_fun(x = 1:10)
@@ -28,6 +30,8 @@ sim_logistic <- function(k = 2, x0 = 3, plot = FALSE) {
 #'
 #' @param sim Simulation from \code{\link{sim_distribution}}
 #'
+#' @return Returns a rounded simulation object. Largely used as a helper in \code{\link{sim_survey}}.
+#'
 #' @export
 #'
 
@@ -60,6 +64,8 @@ round_sim <- function(sim) {
 #'                        (Note: allowing resampling may create bias because
 #'                        depletion is imposed at the cell level)
 #'
+#' @return Returns a data.table including details of each set location.
+#'
 #' @export
 #'
 #' @examples
@@ -317,6 +323,8 @@ sim_survey <- function(sim, n_sims = 1, q = sim_logistic(), trawl_dim = c(1.5, 0
 #'
 #' @details \code{\link{sim_survey}} is hard-wired here to be "light" to minimize object size.
 #'
+#' @return Returns an object of the same structure as \code{\link{sim_survey}}.
+#'
 #' @examples
 #'
 #' \donttest{

R/test_surveys.R

@@ -10,6 +10,8 @@
 #' @param ages_cap          Vector of maximum number of otoliths to collect per length group
 #'                          per division per year
 #'
+#' @return Returns a data.frame including all combinations of the supplied vectors.
+#'
 #' @export
 #'
 

R/vis_sim.R

@@ -6,6 +6,8 @@
 #'                       \code{\link{sim_survey}} or \code{\link{test_surveys}}.
 #' @param ...            Additional arguments to send to \link[rmarkdown]{run}
 #'
+#' @return No value returned; function produces an interactive dashboard.
+#'
 #' @examples
 #'
 #' \donttest{