added hindcast cross validation (#149)

Bump version to 1.3.7

Added functionality for hindcast analysis

Co-authored-by: Alex Kokkalis <alko@aqua.dtu.dk>

make.description.R

@@ -3,7 +3,7 @@ date <- format(Sys.Date(), "%Y-%m-%d")
 cat('Package: spict
 Type: Package
 Title: Stochastic surplus Production model in Continuous-Time (SPiCT)
-Version: 1.3.6
+Version: 1.3.7
 Date:', date, '
 Authors@R: c(person(given="Martin Waever",
                     family="Pedersen",

spict/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: spict
 Type: Package
 Title: Stochastic surplus Production model in Continuous-Time (SPiCT)
-Version: 1.3.6
-Date: 2022-06-06 
+Version: 1.3.7
+Date: 2022-09-06 
 Authors@R: c(person(given="Martin Waever",
                     family="Pedersen",
                     email="wpsgodd@gmail.com",
@@ -40,4 +40,4 @@ Suggests:
 LazyData: true
 Encoding: UTF-8
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1

spict/NAMESPACE

@@ -10,6 +10,7 @@ export(annual)
 export(calc.bmsyk)
 export(calc.gamma)
 export(calc.influence)
+export(calc.mase)
 export(calc.om)
 export(calc.osa.resid)
 export(calc.tac)
@@ -31,6 +32,7 @@ export(get.par)
 export(get.spline)
 export(get.version)
 export(guess.m)
+export(hindcast)
 export(invlogit)
 export(invlogp1)
 export(likprof.spict)
@@ -63,6 +65,7 @@ export(plotspict.fb)
 export(plotspict.ffmsy)
 export(plotspict.growth)
 export(plotspict.hcr)
+export(plotspict.hindcast)
 export(plotspict.infl)
 export(plotspict.inflsum)
 export(plotspict.likprof)
@@ -100,5 +103,6 @@ export(write.aspic)
 exportClasses(spictcls)
 import(TMB)
 importFrom(ellipse,ellipse)
+importFrom(parallel,mclapply)
 importFrom(utils,packageDescription)
 useDynLib(spict)

spict/NEWS.md

@@ -1,7 +1,13 @@
-spict v1.3.7-pre (not released yet)
-============
+spict v1.3.7 (2021-08-12)
+
+New features
+
+* Added functionality for performing and plotting hindcast analysis 
+  introducing the functions `hindcast()` and `plotspict.hindcast`.
 
 Bug fixes:
+
+
 * fixed retro when last year's observations where missing
 
 spict v1.3.6 (2021-06-06)

spict/R/checkinp.R

@@ -1200,6 +1200,12 @@ check.inp <- function(inp, verbose = TRUE, mancheck = TRUE){
     ## Simulate using fitted object (env$last.par)?
     if(!"sim.fit" %in% names(inp)) inp$sim.fit <- TRUE
 
+    ##
+    if(!"iuse" %in% names(inp) || length(inp$iuse) != length(unlist(inp$obsI)))
+        inp$iuse <- rep(TRUE, length(unlist(inp$obsI)))
+
+
+
     # Reorder parameter list
     inp$parlist <- list(logm=inp$ini$logm,
                         mu=inp$ini$mu,