Updated files for package building

Author: Ovec8hkin

Meta/vignette.rds

@@ -0,0 +1,85 @@
+#' Default Operating Model for Alaska Sablefish
+#' 
+#' Dataset containing demographic matrices, observation
+#' process parameters, and initial numbers-at-age for 
+#' the alaska sablefish population. This data is used as
+#' the base for all operating models used in this 
+#' package.
+#' 
+#' @format list containing OM components
+#' 
+"sable_om"
+
+#' Sablefish assessment
+#'
+#' A dataset containing sablefish assessment results.
+#' This data is used for defining the historical recruitment
+#' timeseries.
+#'
+#' @format A list containing assessment data
+#' 
+"sablefish_assessment_data"
+
+#' Random Recruitment OM Object
+#' 
+#' An operating model object that will generate future
+#' recruitment by randomly resampling from teh historical
+#' recruitment timeseries
+#' 
+#' @format An operating model object
+#' 
+"om_rand_recruit"
+
+#' Cylic Recruitment OM Object
+#' 
+#' An operating model object that will generate future
+#' recruitment via a cyclic pattern of Beverton-Holt SRRs.
+#' The first cycle is a low recruitment phase lasting 20 
+#' years, the second cycle is a high recruitment phase
+#' lasting 5 years.
+#' 
+#' @format An operating model object
+#' 
+"om_bhcyclic_recruit"
+
+#' Crash Recruitment OM Object
+#' 
+#' An operating model object that will generate future
+#' recruitment via a recruitment crash for the first 20
+#' years, and then resort to resampling from the historical
+#' recruitment timeseries.
+#' 
+#' @format An operating model object
+#' 
+"om_crash_recruit"
+
+# F40 Managament Procedure
+#'
+#' An example management procedure that replicates
+#' the NPFMC F40 harvest control rule policy that
+#' is operationally used to manage sablefish in
+#' Alaska.
+#' 
+#' @format A management procedure object.
+#' 
+"mp_f40"
+
+# Harvest Cap Managament Procedure
+#'
+#' An example management procedure that applies
+#' a 25,000 mt cap on annual harvest to the 
+#' operational F40% harvest control rule policy.
+#' 
+#' @format A management procedure object.
+#' 
+"mp_25cap"
+
+# Stability Constraint Managament Procedure
+#'
+#' An example management procedure that applied
+#' a symmetric 5% stability constraint to the
+#' operational F40% harvest control rule policy.
+#' 
+#' @format A management procedure object.
+#' 
+"mp_5perc"

R/data.R

@@ -84,7 +84,7 @@ regime_recruits <- function(mus, cvs, nyears, regime_length, starting_regime, se
 }
 
 #' Beverton-Holt stock recruitment relationship
-#' #'
+#' 
 #' Defines a function factory for yieding recruitment from a Bevrton-Holt
 #' stock recruitment relationship, parameterized using steepeness. Initial
 #' call to this function sets up a new function that takes the current SSB
@@ -116,6 +116,23 @@ beverton_holt <- function(h, R0, S0, sigR, seed){
     }
 }
 
+#' Regime Beverton-Holt stock recruitment relationship
+#'
+#' Defines a two-regime recruitment function where each regime
+#' is defined by a Beverton-Holt stock recruitment relationship 
+#' with differeing levels of R0 or sigR.
+#'
+#' @param h steepness (0.2 <= h <= 1.0)
+#' @param sbpr spawning biomass per recruit at unfished conditions
+#' @param R0s vector of unfished recruitments (one for each regime, max 2)
+#' @param sigRs vector of recruitment variability (one for each regime, max 2)
+#' @param nyears total number of years of recruitments to generate
+#' @param regime_length vector of length of each regime
+#' @param starting_regime regime to start with (0 = first regime, 1 = second regime)
+#' @param seed random seed for reproducability
+#'
+#' @export bevholt_regimes
+#'
 bevholt_regimes <- function(h, sbpr, R0s, sigRs, nyears, regime_length, starting_regime, seed){
     set.seed(seed)
     function(ssb, y){

R/recruitment_utils.R

@@ -2,7 +2,7 @@
 #' 
 #' Set MP object list items to reasonable default values.
 #'
-#' @export setup_mse_options
+#' @export setup_mp_options
 #'
 #' @example
 #'
@@ -45,6 +45,14 @@ setup_hcr_options <- function(){
     )
 }
 
+#' Setup MSE Options Object
+#' 
+#' Set MSE optios list items to reasonable default values.
+#'
+#' @export setup_mse_options
+#'
+#' @example
+#'
 setup_mse_options <- function(){
     return(
         list(