docs: pkgdown site articles

R/recruitment.R

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+#' Resample from historical recruitment timeseries
+#'
+#' Draw `n` random samples, with replacement, from the 
+#' historical recruitment timeseries.
+#'
+#' @param n number of samples to draw
+#' @param hist.rec historical recruitment vector
+#' @param seed a random seed (optional)
+#'
+#' @return `n` random samples from the historical
+#' recruitment timeseries.
+#' 
+#' @export resample_recruitment
+#'
+#' @example
+#' set.seed(1120)
+#' n <- 100
+#' hist.rec <- c(100, 200, 50, 100, 120)
+#' resample.recruitment(n, hist.rec)
+#'
+resample_recruitment <- function(n, hist_rec, seed=NA){
+    if(!is.na(seed)){
+        set.seed(seed)
+    }
+    return(sample(hist_rec, n, replace=TRUE))
+}
+
+mean_recruitment <- function(n, log.mu, sd, seed=NA){
+    if(!is.na(seed)){
+        set.seed(seed)
+    }
+    return(exp(log.mu + rnorm(n, 0, sd) - sd^2/2))
+}
+
+#' Generate log-recruitment from two defined regimes of a specified length
+#'
+#' Description
+#'
+#' @param n number of recruitment events
+#' @param mu.rec vector of mean log-recruitment levels, one for each regime
+#' @param sd.rec vector of recruitment variation, one for each regime
+#' @param dur duration of regimes
+#' @param start which regime to start in
+#' @param seed a random seed (optional)
+#'
+#' @return `n` log-recruitment levels from two different regimes of
+#' length `dur`.
+#' @export cyclic.recruitment
+#' 
+#' @example
+cyclic.recruitment <- function(n, mu_rec, sd_rec, dur, start=1, seed=NA){
+
+    if(!is.na(seed)){
+        set.seed(seed)
+    }
+
+    curr_regime <- start
+    duration <- dur[curr_regime]
+    recs <- rep(NA, n)
+    for(i in 0:n){
+        recs[i] <- exp(mu_rec[curr_regime+1] + rnorm(1, 0, sd_rec[curr_regime+1]) - (sd_rec[curr_regime+1]^2)/2)
+        if(i %% duration == 0){
+            curr_regime <- as.numeric(!curr_regime)
+            duration <- dur[curr_regime+1]
+        }
+    }
+    return(recs)
+
+}
+
+beverton_holt <- function(h, R0, S0){
+    function(ssb){
+        return(
+            (4*R0*h*ssb)/((1-h)*R0*(S0/R0) + (5*h - 1)*ssb)
+        )
+    }
+}
+
+bh <- beverton_holt(0.7, 25, 300)
+
+bh
+is.function(bh)
+
+bh <- 1