Merge pull request #581 from janaobsteter/devel

Merging the remaining changes to prepare the package for CRAN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SIMplyBee
 Type: Package
 Title: 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
   person("Jana", "Obšteter", email = "[email protected]",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1511-3916")),
@@ -26,9 +26,10 @@ 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
-Depends: R (>= 3.3.0), AlphaSimR (>= 1.3.2)
-RoxygenNote: 7.3.1
+Imports: methods, R6, stats, utils, extraDistr (>= 1.9.1), RANN, Rcpp (>= 0.12.7)
+Depends: R (>= 3.3.0), AlphaSimR (>= 1.5.3)
+LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
+RoxygenNote: 7.3.2
 Suggests: 
     rmarkdown,
     knitr,

NAMESPACE

@@ -204,6 +204,7 @@ export(swarmPUnif)
 exportClasses(Colony)
 exportClasses(MultiColony)
 import(AlphaSimR)
+import(Rcpp)
 importFrom(R6,R6Class)
 importFrom(extraDistr,rtpois)
 importFrom(methods,"slot<-")
@@ -217,8 +218,10 @@ importFrom(methods,setValidity)
 importFrom(methods,show)
 importFrom(methods,slot)
 importFrom(methods,validObject)
+importFrom(stats,na.omit)
 importFrom(stats,rbeta)
 importFrom(stats,rnorm)
 importFrom(stats,rpois)
 importFrom(stats,runif)
 importFrom(utils,packageVersion)
+useDynLib(SIMplyBee, .registration = TRUE)

NEWS.md

@@ -1,54 +1,68 @@
-# SIMplyBee version 0.4.0 #
+---
+editor_options: 
+  markdown: 
+    wrap: 72
+---
 
-* 2023-MM-DD TODO
+# SIMplyBee version 0.4.0
 
-## Major changes ##
+-   2024-08-23
 
-* createColony() and createMultiColony() do not have the location argument
-  anymore; use setLocation() instead; by default, location is now c(0, 0) PR#500
+## Major changes
 
-## New features ##
+-   createColony() and createMultiColony() do not have the location
+    argument anymore; use setLocation() instead; by default, location is
+    now c(0, 0) PR#500
 
-* In setLocation(MultiColony) we can set one location (numeric) or multiple
-  (list or data.frame) PR#500
-
-* getLocation(MultiColony) got the collapse argument
-  Commit#f4e629c3e8920948ad576eae3615a86b26300790
+## New features
 
-* We can now sample location of a swarm - see sampleLocation and radius
-  arugments in swarm() PR#500 PR#502
-
-* New function rcircle() to sample a random point within a circle with a given
-  radius PR#502
-
-* Removed the function createRandomCrossPlan() - that option is now included in the newly added createCrossPlan() fuction
+-   In setLocation(MultiColony) we can set one location (numeric) or
+    multiple (list or data.frame) PR#500
 
-* Added the funcionality for spatially-aware mating of honeybee colonies. The new funcionality is included in the createCrossPlan(), that allows to create the cross plan according to the colonies' locations, and in the cross() function, that crosses bees according to their location
-
+-   getLocation(MultiColony) got the collapse argument
+    Commit#f4e629c3e8920948ad576eae3615a86b26300790
 
-## Bug fixes ##
-* Bug fix - get*Haplo() functions were returning diploid drones when input was a Pop-class
+-   We can now sample location of a swarm - see sampleLocation and
+    radius arguments in swarm() PR#500 PR#502
 
+-   New function rcircle() to sample a random point within a circle with
+    a given radius PR#502
 
-*
+-   Removed the function createRandomCrossPlan() - that option is now
+    included in the newly added createCrossPlan() fuction
 
+-   Added the **functionality for spatially-aware mating** of honeybee
+    colonies. The new functionality is included in the
+    createCrossPlan(), that allows to create the cross plan according to
+    the colonies' locations, and in the cross() function, that crosses
+    bees according to their location. This did not break the old
+    functionality of the cross function.
+
+-  Unified setMisc and getMisc behaviour to comply with the new AlphaSimR behaviour
 
-# SIMplyBee version 0.3.0 #
+-  Added new C++ function isHeterozygous() to speed up the SIMplyBee function isCsdHeterozygous()
 
-* 2022-12-05 First public/CRAN version of the package
+## Bug fixes
 
-## Major changes ##
+-   Bug fix - get\*Haplo() functions were returning diploid drones when
+    input was a Pop-class
 
-* ~2 years of work went into this first public version!
+-   
 
-## New features ##
+# SIMplyBee version 0.3.0
 
-* Many;) See the vignettes and help pages.
+-   2022-12-05 First public/CRAN version of the package
 
-## Bug fixes ##
+## Major changes
 
-* Many bugs and issues squashed - see https://github.com/HighlanderLab/SIMplyBee/issues.
-  Please contribute to the development of this package.
+-   \~2 years of work went into this first public version!
 
+## New features
 
+-   Many;) See the vignettes and help pages.
 
+## Bug fixes
+
+-   Many bugs and issues squashed - see
+    <https://github.com/HighlanderLab/SIMplyBee/issues>. Please
+    contribute to the development of this package.

R/Class-Colony.R

@@ -16,27 +16,27 @@ setClassUnion("integerOrNumericOrLogicalOrCharacter", c("integer", "numeric", "l
 #'
 #' @slot id integer, unique ID of the colony
 #' @slot location numeric, location of the colony (x, y)
-#' @slot queen \code{\link{Pop-class}}, the queen of the colony (we use
+#' @slot queen \code{\link[AlphaSimR]{Pop-class}}, the queen of the colony (we use
 #'   its misc slot for queen's age and drones (fathers) she mated with)
-#' @slot virginQueens \code{\link{Pop-class}}, virgin queens of the
+#' @slot virginQueens \code{\link[AlphaSimR]{Pop-class}}, virgin queens of the
 #'   colony
-#' @slot drones \code{\link{Pop-class}}, drones of the colony
-#' @slot workers \code{\link{Pop-class}}, workers of the colony
+#' @slot drones \code{\link[AlphaSimR]{Pop-class}}, drones of the colony
+#' @slot workers \code{\link[AlphaSimR]{Pop-class}}, workers of the colony
 #' @slot split logical, has colony split
 #' @slot swarm logical, has colony swarmed
 #' @slot supersedure logical, has colony superseded
 #' @slot collapse logical, has colony collapsed
 #' @slot production logical, is colony productive
 #' @slot misc list, available for storing extra information about the colony
 #'
-#' @param object \code{\link{Colony-class}}
-#' @param x \code{\link{Colony-class}}
-#' @param ... \code{NULL}, \code{\link{Colony-class}}, or
-#'   \code{\link{MultiColony-class}}
+#' @param object \code{\link[SIMplyBee]{Colony-class}}
+#' @param x \code{\link[SIMplyBee]{Colony-class}}
+#' @param ... \code{NULL}, \code{\link[SIMplyBee]{Colony-class}}, or
+#'   \code{\link[SIMplyBee]{MultiColony-class}}
 #'
-#' @seealso \code{\link{createColony}}
+#' @seealso \code{\link[SIMplyBee]{createColony}}
 #'
-#' @return \code{\link{Colony-class}} or \code{\link{MultiColony-class}}
+#' @return \code{\link[SIMplyBee]{Colony-class}} or \code{\link[SIMplyBee]{MultiColony-class}}
 #'
 #' @examples
 #' founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 100)
@@ -157,8 +157,8 @@ setMethod(
 #' @rdname combineNULLAndPop
 #' @title Combine a NULL and AlphaSimR population
 #'
-#' @param x NULL or \code{\link{Pop-class}}
-#' @param ... list of NULL or \code{\link{Pop-class}} objects
+#' @param x NULL or \code{\link[AlphaSimR]{Pop-class}}
+#' @param ... list of NULL or \code{\link[AlphaSimR]{Pop-class}} objects
 #'
 #' @description This combine \code{c()} method is a hack to combine NULL and an
 #'   AlphaSimR population object \code{c(NULL, pop)} (\code{c(pop, NULL)} works

R/Class-MultiColony.R

@@ -10,22 +10,22 @@ setClassUnion("integerOrNumericOrLogicalOrCharacter", c("integer", "numeric", "l
 #' @description An object holding a collection of honeybee colonies. It behaves
 #'   like a list.
 #'
-#' @slot colonies list, a collection of \code{\link{Colony-class}} objects
+#' @slot colonies list, a collection of \code{\link[SIMplyBee]{Colony-class}} objects
 #'
-#' @param object \code{\link{MultiColony-class}}
-#' @param x \code{\link{MultiColony-class}}
+#' @param object \code{\link[SIMplyBee]{MultiColony-class}}
+#' @param x \code{\link[SIMplyBee]{MultiColony-class}}
 #' @param i integer, numeric, logical, or character, index or ID to select
 #'   a colony (see examples)
 #' @param j not used
 #' @param drop not used
-#' @param value \code{\link{Colony-class}} or \code{\link{MultiColony-class}} to
+#' @param value \code{\link[SIMplyBee]{Colony-class}} or \code{\link[SIMplyBee]{MultiColony-class}} to
 #'   assign into \code{x} based on colony index or name \code{i}
-#' @param ... \code{NULL}, \code{\link{Colony-class}}, or
-#'   \code{\link{MultiColony-class}}
+#' @param ... \code{NULL}, \code{\link[SIMplyBee]{Colony-class}}, or
+#'   \code{\link[SIMplyBee]{MultiColony-class}}
 #'
-#' @seealso \code{\link{createMultiColony}}
+#' @seealso \code{\link[SIMplyBee]{createMultiColony}}
 #'
-#' @return \code{\link{MultiColony-class}} or \code{\link{Colony-class}}
+#' @return \code{\link[SIMplyBee]{MultiColony-class}} or \code{\link[SIMplyBee]{Colony-class}}
 #'
 #' @examples
 #' founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
@@ -206,7 +206,7 @@ setMethod(
 )
 
 # [ ----
-#' @describeIn MultiColony-class Extract a colony (one or more!) with an integer/numeric/logical index (position) (return \code{\link{MultiColony-class}})
+#' @describeIn MultiColony-class Extract a colony (one or more!) with an integer/numeric/logical index (position) (return \code{\link[SIMplyBee]{MultiColony-class}})
 setMethod(
   f = "[",
   signature(x = "MultiColony", i = "integerOrNumericOrLogical", j = "ANY", drop = "ANY"),
@@ -217,7 +217,7 @@ setMethod(
   }
 )
 
-#' @describeIn MultiColony-class Extract a colony (one or more!) with a character ID (name) (return \code{\link{MultiColony-class}})
+#' @describeIn MultiColony-class Extract a colony (one or more!) with a character ID (name) (return \code{\link[SIMplyBee]{MultiColony-class}})
 setMethod(
   f = "[",
   signature(x = "MultiColony", i = "character", j = "ANY", drop = "ANY"),
@@ -230,7 +230,7 @@ setMethod(
 )
 
 # [[ ----
-#' @describeIn MultiColony-class Extract a colony (just one!) with an integer/numeric/logical index (position) (return \code{\link{Colony-class}})
+#' @describeIn MultiColony-class Extract a colony (just one!) with an integer/numeric/logical index (position) (return \code{\link[SIMplyBee]{Colony-class}})
 setMethod(
   f = "[[",
   signature(x = "MultiColony", i = "integerOrNumericOrLogical"),
@@ -246,7 +246,7 @@ setMethod(
   }
 )
 
-#' @describeIn MultiColony-class Extract a colony (just one!) with a character ID (name) (return \code{\link{Colony-class}})
+#' @describeIn MultiColony-class Extract a colony (just one!) with a character ID (name) (return \code{\link[SIMplyBee]{Colony-class}})
 setMethod(
   f = "[[",
   signature(x = "MultiColony", i = "character"),