One psock

.gitignore

@@ -13,6 +13,8 @@
 
 # Output files from R CMD build
 /*.tar.gz
+src/*.o
+src/*.so
 
 # Output files from R CMD check
 /*.Rcheck/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SIMplyBee
 Type: Package
 Title: 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes
-Version: 0.4.1
+Version: 0.5.0
 Authors@R: c(
   person("Jana", "Obšteter", email = "obsteter.jana@gmail.com",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1511-3916")),
@@ -26,8 +26,8 @@ URL: https://github.com/HighlanderLab/SIMplyBee
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Imports: methods, R6, stats, utils, extraDistr (>= 1.9.1), RANN, Rcpp (>= 0.12.7)
-Depends: R (>= 3.3.0), AlphaSimR (>= 1.5.3)
+Imports: methods, R6, stats, utils, extraDistr (>= 1.9.1), RANN, Rcpp (>= 0.12.7), foreach
+Depends: R (>= 3.3.0), AlphaSimR (>= 2.0.0)
 LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
 RoxygenNote: 7.3.2
 Suggests: 

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(SimParamBee)
 export(addCastePop)
+export(addCastePop_internal)
 export(addDrones)
 export(addVirginQueens)
 export(addWorkers)
@@ -69,13 +70,11 @@ export(getGv)
 export(getIbdHaplo)
 export(getId)
 export(getLocation)
-export(getMisc)
 export(getPheno)
 export(getPooledGeno)
 export(getQtlGeno)
 export(getQtlHaplo)
 export(getQueen)
-export(getQueenAge)
 export(getQueenCsdAlleles)
 export(getQueenCsdGeno)
 export(getQueenGv)
@@ -87,7 +86,6 @@ export(getQueenSegSiteGeno)
 export(getQueenSegSiteHaplo)
 export(getQueenSnpGeno)
 export(getQueenSnpHaplo)
-export(getQueenYearOfBirth)
 export(getSegSiteGeno)
 export(getSegSiteHaplo)
 export(getSnpGeno)
@@ -192,8 +190,6 @@ export(replaceWorkers)
 export(resetEvents)
 export(selectColonies)
 export(setLocation)
-export(setMisc)
-export(setQueensYearOfBirth)
 export(simulateHoneyBeeGenomes)
 export(split)
 export(splitPColonyStrength)
@@ -207,6 +203,9 @@ import(AlphaSimR)
 import(Rcpp)
 importFrom(R6,R6Class)
 importFrom(extraDistr,rtpois)
+importFrom(foreach,"%do%")
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)
 importFrom(methods,"slot<-")
 importFrom(methods,classLabel)
 importFrom(methods,is)

NEWS.md

@@ -4,6 +4,33 @@ editor_options:
     wrap: 72
 ---
 
+# SIMplyBee version 0.5.0
+
+-   2025-11-27
+
+## Major changes
+
+-   swarm/split/supersede do no longer store the year of the queen
+
+-   colonies with high inbreeding that do not produce a viable virgin
+    queens in max(10, SP\$nVirginQueens) attempts are removed in
+    swarm/supersede
+
+-   split no longer creates virgin queens in the split colonies but
+    returns colonies with workers and meta data, but no virgin queens
+
+-   createMultiColony() no longer creates an empty apiary, but it adds
+    empty colonies with IDs
+
+## New features
+
+-   parallelised all the major functions (so they run on
+    simParamBee\$nThreads cores) with PSOCK system. Since the parallelisation setup within functions
+    takes additional time, we recommend using a single threads for a small number of colonies
+
+## Bug fixes
+
+
 # SIMplyBee version 0.4.1
 
 -   2024-09-19
@@ -57,8 +84,6 @@ which caused an error. We now read in the locations from a csv file.
 -   Bug fix - get\*Haplo() functions were returning diploid drones when
     input was a Pop-class
 
--   
-
 # SIMplyBee version 0.3.0
 
 -   2022-12-05 First public/CRAN version of the package

R/Class-Colony.R

@@ -94,7 +94,8 @@ setClassUnion("ColonyOrNULL", c("Colony", "NULL"))
 
 setValidity(Class = "Colony", method = function(object) {
   errors <- character()
-  if ((ifelse(test = !is.null(slot(object, name = "queen")), yes = nInd(slot(object, name = "queen")), no = 0)) > 1) { #Don't use nQueen because of the SP problem
+  test <- !is.null(slot(object, name = "queen"))
+  if ((ifelse(test, yes = nInd(slot(object, name = "queen")), no = 0)) > 1) { #Don't use nQueen because of the SP problem
     errors <- c(errors, "There can be only one queen per colony!")
   }
   if (length(errors) == 0) {