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gustavdeliusgustavdelius
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Avoid use of \dontrun in examples wherever possible. Use \donttest only for long-running examples.
1 parent ba1b69a commit 106ff44

40 files changed

+50
-96
lines changed

‎R/data.R

+6-22
Original file line numberDiff line numberDiff line change
@@ -21,12 +21,8 @@
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#' @source{Blanchard et al.}
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#' @docType data
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#' @name NS_species_params
24-
#' @examples
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#' \dontrun{
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#' @examples
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#' params <- MizerParams(NS_species_params)
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#' sim = project(params)
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#' plot(sim)
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#' }
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"NS_species_params"
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# NS_species_params_gears ----
@@ -52,13 +48,8 @@
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#' @source{Blanchard et al.}
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#' @docType data
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#' @name NS_species_params_gears
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#' @examples
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#' \dontrun{
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#' @examples
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#' params <- MizerParams(NS_species_params_gears)
58-
#' sim = project(params, effort = c(Industrial = 0, Pelagic = 1,
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#' Beam = 0.5, Otter = 0.5))
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#' plot(sim)
61-
#' }
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"NS_species_params_gears"
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# NS_interaction ----
@@ -70,14 +61,9 @@
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#' @source{Blanchard et al.}
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#' @docType data
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#' @name NS_interaction
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#' @examples
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#' \dontrun{
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#' @examples
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#' params <- MizerParams(NS_species_params_gears,
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#' interaction = NS_inter)
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#' sim = project(params, effort = c(Industrial = 0, Pelagic = 1,
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#' Beam = 0.5, Otter = 0.5))
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#' plot(sim)
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#' }
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#' interaction = NS_interaction)
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"NS_interaction"
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#' Alias for `NS_interaction`
@@ -104,7 +90,7 @@
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#' @name NS_params
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#' @family example parameter objects
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' sim = project(NS_params, effort = c(Industrial = 0, Pelagic = 1,
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#' Beam = 0.5, Otter = 0.5))
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#' plot(sim)
@@ -122,8 +108,6 @@
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#' @docType data
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#' @name NS_sim
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#' @family example parameter objects
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#' @examples
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#' \dontrun{
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#' @examples
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#' plotBiomass(NS_sim)
128-
#' }
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"NS_sim"

‎R/deprecated.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -416,7 +416,7 @@ set_trait_model <- function(no_sp = 10,
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#' Royal Society, 276, 109-114
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#' @concept deprecated
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' params <- set_community_model(f0=0.7, z0=0.2, recruitment=3e7)
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#' # This is now achieved with
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#' params <- newCommunityParams(f0 = 0.7, z0 = 0.2)
@@ -505,7 +505,7 @@ set_community_model <- function(max_w = 1e6,
505505
#' @export
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#' @concept deprecated
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#' @examples
508-
#' \dontrun{
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#' \donttest{
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#' params <- NS_params
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#' sim <- project(params, t_max = 20, effort = 0.5)
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#' n <- sim@n[21,,]

‎R/get_initial_n.R

+1-4
Original file line numberDiff line numberDiff line change
@@ -14,10 +14,7 @@
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#' @concept helper
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#' @return A matrix (species x size) of population abundances.
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#' @examples
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#' \dontrun{
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#' params <- newMultispeciesParams(NS_species_params_gears)
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#' init_n <- get_initial_n(params)
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#' }
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#' init_n <- get_initial_n(NS_params)
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get_initial_n <- function(params, n0_mult = NULL, a = 0.35) {
2219
if (!is(params,"MizerParams"))
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stop("params argument must of type MizerParams")

‎R/project.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -85,7 +85,7 @@ NULL
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#'
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#' @export
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' params <- NS_params
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#' # With constant fishing effort for all gears for 20 time steps
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#' sim <- project(params, t_max = 20, effort = 0.5)

‎R/rate_functions.R

+12-12
Original file line numberDiff line numberDiff line change
@@ -103,7 +103,7 @@ getEncounter <- function(params, n = initialN(params),
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#' @export
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#' @family rate functions
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' params <- NS_params
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#' # Get initial feeding level
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#' fl <- getFeedingLevel(params)
@@ -190,7 +190,7 @@ getCriticalFeedingLevel <- function(params) {
190190
#' reproduction is calculated with [getERepro()].
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#' @family rate functions
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' params <- NS_params
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#' # Project with constant fishing effort for all gears for 20 time steps
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#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -231,7 +231,7 @@ getEReproAndGrowth <- function(params, n = initialN(params),
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#' @export
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#' @family rate functions
233233
#' @examples
234-
#' \dontrun{
234+
#' \donttest{
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#' params <- NS_params
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#' # With constant fishing effort for all gears for 20 time steps
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#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -274,7 +274,7 @@ getPredRate <- function(params, n = initialN(params),
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#' @family rate functions
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#' @export
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#' @examples
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#' \dontrun{
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#' \donttest{
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#' params <- NS_params
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#' # With constant fishing effort for all gears for 20 time steps
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#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -347,7 +347,7 @@ getM2 <- getPredMort
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#' @family rate functions
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#' @export
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#' @examples
350-
#' \dontrun{
350+
#' \donttest{
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#' params <- NS_params
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#' # With constant fishing effort for all gears for 20 time steps
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#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -414,7 +414,7 @@ getM2Background <- getResourceMort
414414
#' @export
415415
#' @family rate functions
416416
#' @examples
417-
#' \dontrun{
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#' \donttest{
418418
#' params <-NS_params
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#' # Get the fishing mortality when effort is constant
420420
#' # for all gears and time:
@@ -530,7 +530,7 @@ getFMortGear <- function(object, effort, time_range) {
530530
#' @export
531531
#' @family rate functions
532532
#' @examples
533-
#' \dontrun{
533+
#' \donttest{
534534
#' params <- NS_params
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#' # Get the total fishing mortality when effort is constant for all
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#' # gears and time:
@@ -660,7 +660,7 @@ getFMort <- function(object, effort, time_range, drop = TRUE) {
660660
#' @seealso [getPredMort()], [getFMort()]
661661
#' @family rate functions
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#' @examples
663-
#' \dontrun{
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#' \donttest{
664664
#' params <- NS_params
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#' # Project with constant fishing effort for all gears for 20 time steps
666666
#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -714,7 +714,7 @@ getZ <- getMort
714714
#' @export
715715
#' @family rate functions
716716
#' @examples
717-
#' \dontrun{
717+
#' \donttest{
718718
#' params <- NS_params
719719
#' # Project with constant fishing effort for all gears for 20 time steps
720720
#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -758,7 +758,7 @@ getESpawning <- getERepro
758758
#' @seealso [getERepro()], [getEReproAndGrowth()]
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#' @family rate functions
760760
#' @examples
761-
#' \dontrun{
761+
#' \donttest{
762762
#' params <- NS_params
763763
#' # Project with constant fishing effort for all gears for 20 time steps
764764
#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -794,7 +794,7 @@ getEGrowth <- function(params, n = initialN(params),
794794
#' @seealso [getRDD()]
795795
#' @family rate functions
796796
#' @examples
797-
#' \dontrun{
797+
#' \donttest{
798798
#' params <- NS_params
799799
#' # Project with constant fishing effort for all gears for 20 time steps
800800
#' sim <- project(params, t_max = 20, effort = 0.5)
@@ -838,7 +838,7 @@ getRDI <- function(params, n = initialN(params),
838838
#' @seealso [getRDI()]
839839
#' @family rate functions
840840
#' @examples
841-
#' \dontrun{
841+
#' \donttest{
842842
#' params <- NS_params
843843
#' # Project with constant fishing effort for all gears for 20 time steps
844844
#' sim <- project(params, t_max = 20, effort = 0.5)

‎R/reproduction.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -71,7 +71,7 @@ mizerRDI <- function(params, n, n_pp, n_other, t,
7171
#' @export
7272
#' @family functions calculating density-dependent reproduction rate
7373
#' @examples
74-
#' \dontrun{
74+
#' \donttest{
7575
#' # choose an example params object
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#' params <- NS_params
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#' # We set the reproduction rate functions

‎R/setExtMort.R

-2
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@@ -43,7 +43,6 @@
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#' @export
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#' @family functions for setting parameters
4545
#' @examples
46-
#' \dontrun{
4746
#' params <- newMultispeciesParams(NS_species_params)
4847
#'
4948
#' #### Setting allometric death rate #######################
@@ -57,7 +56,6 @@
5756
#'
5857
#' # Change the external mortality rate in the params object
5958
#' ext_mort(params) <- allo_mort
60-
#' }
6159
setExtMort <- function(params, ext_mort = NULL,
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z0pre = 0.6, z0exp = -1 / 4,
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reset = FALSE, z0 = deprecated(), ...) {

‎R/setInitialValues.R

+1-1
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@@ -40,7 +40,7 @@
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#' @export
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#' @family functions for setting parameters
4242
#' @examples
43-
#' \dontrun{
43+
#' \donttest{
4444
#' params <- NS_params
4545
#' sim <- project(params, t_max = 20, effort = 0.5)
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#' params <- setInitialValues(params, sim)

‎R/setPredKernel.R

-2
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@@ -74,7 +74,6 @@
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#' @export
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#' @family functions for setting parameters
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#' @examples
77-
#' \dontrun{
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#' ## Set up a MizerParams object
7978
#' params <- NS_params
8079
#'
@@ -94,7 +93,6 @@
9493
#' pred_kernel["Herring", , ] <- sweep(pred_kernel["Herring", , ], 2,
9594
#' params@w_full, "*")
9695
#' params<- setPredKernel(params, pred_kernel = pred_kernel)
97-
#' }
9896
setPredKernel <- function(params,
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pred_kernel = NULL,
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reset = FALSE, ...) {

‎R/steady.R

+1-1
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@@ -221,7 +221,7 @@ projectToSteady <- function(params,
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#' @return A MizerParams or a MizerSim object
222222
#' @export
223223
#' @examples
224-
#' \dontrun{
224+
#' \donttest{
225225
#' params <- newTraitParams()
226226
#' species_params(params)$gamma[5] <- 3000
227227
#' params <- steady(params)

‎man/NS_interaction.Rd

+1-6
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‎man/NS_params.Rd

+1-1
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‎man/NS_sim.Rd

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‎man/NS_species_params.Rd

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‎man/NS_species_params_gears.Rd

-5
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‎man/constantEggRDI.Rd

+1-1
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‎man/getEGrowth.Rd

+1-1
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‎man/getERepro.Rd

+1-1
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‎man/getEReproAndGrowth.Rd

+1-1
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‎man/getESpawning.Rd

+1-1
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‎man/getFMort.Rd

+1-1
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‎man/getFMortGear.Rd

+1-1
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‎man/getFeedingLevel.Rd

+1-1
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