CRAN 1.2.2

DESCRIPTION

@@ -5,7 +5,7 @@ Version: 1.2.2
 Authors@R: c(person("Quang", "Huynh", email = "quang@bluematterscience.com", role = c("aut", "cre")), 
   person("Tom", "Carruthers", email = "tom@bluematterscience.com", role = "aut"),
   person("Adrian", "Hordyk", email = "adrian@bluematterscience.com", role = "aut"))
-Date: 2021-09-03
+Date: 2021-09-16
 Maintainer: Quang Huynh <quang@bluematterscience.com>
 Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 
   'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, 

NEWS.md

@@ -2,6 +2,11 @@ The latest release of the SAMtool package is available on [CRAN](https://CRAN.R-
 
 ## SAMtool 1.2.2
 - The `make_interim_MP` function is added to generate MPs that adjust the TAC between periodic assessments using the index.
+- An additional posfun to `SP` is added to avoid negative biomass situations.
+- Fix sampling of recruitment deviations for projections in `RCM` so that the mean is one in normal space. This error was apparent when autocorrelation was very large.
+- Assessment and RCModel objects now save the package version as attributes.
+- Shortcut function now reports year-specific reference points for the harvest control rule.
+- HCR returns TAC = NA when a control point or target point is negative.
 
 ## SAMtool 1.2.1
 - `HCR_segment` allows for creating control rules with any number of linear segments.

R/HCRs.R

@@ -132,7 +132,7 @@ HCR_segment <- function(Assessment, reps = 1, OCP_type = c("SSB_SSB0", "SSB_SSBM
         }
       }
 
-      if(exists("Fout", inherits = FALSE) && !is.na(F_out)) {
+      if(exists("Fout", inherits = FALSE) && !is.na(Fout)) {
         if(Fout > 0) {
           if(!exists("SE", inherits = FALSE) || !length(SE)) SE <- 0
           FM <- trlnorm(reps, Fout, SE/Fout)

R/z_MPs.R

@@ -1,10 +1,12 @@
 
 #' Make a custom management procedure (MP)
 #'
-#' Function operator that combines a function of class \code{Assess} and a function of
-#' class \code{HCR} to create a management procedure (MP) with constant TAC between assessments. 
-#' Use \link{make_interim_MP} to use an interim procedure to adjust the TAC between assessments using an index. The resulting function
-#' can then be tested in closed-loop simulation via \code{\link[MSEtool]{runMSE}}.
+#' Function operator that creates a management procedure (MP) by combining an assessment model (function of class \code{Assess}) with
+#' a harvest control rule (function of class \code{HCR}). The resulting function can then be tested in closed-loop simulation via 
+#' \code{\link[MSEtool]{runMSE}}. Use \code{make_MP} to specify constant TAC between assessments; the frequency of
+#' assessments is specified in \code{OM@@interval}. Use \code{make_interim_MP} to use an interim procedure to adjust the TAC between 
+#' assessments using an index (Huynh et al. 2020), with the frequency of assessments specified in argument \code{assessment_interval} when 
+#' making the MP; ensure that \code{OM@@interval <- 1}.
 #'
 #' @param .Assess Assessment model, a function of class \code{Assess}.
 #' @param .HCR Harvest control rule, a function of class \code{HCR}.