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Making functional examples for the new cross behaviour
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@janaobsteter
janaobsteter committed Apr 7, 2023
1 parent 07fe8f4 commit 55b6b8c
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125 changes: 70 additions & 55 deletions R/Functions_L0_auxilary.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6329,32 +6329,31 @@ createRandomCrossPlan <- function(IDs, drones, nDrones) {
#' basePop <- createVirginQueens(founderGenomes)
#'
#' # Create three virgin MultiColony objects with locations
#' virginColonies1 <- createMultiColony(basePop[1:30],
#' location = Map(c, runif(100, 0, 2*pi), runif(100, 0, 2*pi)))
#' virginColonies2 <- createMultiColony(basePop[31:60],
#' location = Map(c, runif(100, 0, 2*pi), runif(100, 0, 2*pi)))
#' virginColonies3 <- createMultiColony(basePop[61:100],
#' location = Map(c, runif(100, 0, 2*pi), runif(100, 0, 2*pi)))
#'
#' virginColonies1 <- createMultiColony(basePop[1:30])
#' virginColonies1 <- setLocation(virginColonies1,
#' location = Map(c, runif(30, 0, 2*pi), runif(30, 0, 2*pi)))
#' virginColonies2 <- createMultiColony(basePop[31:60])
#' virginColonies2 <- setLocation(virginColonies2,
#' location = Map(c, runif(30, 0, 2*pi), runif(30, 0, 2*pi)))
#' virginColonies3 <- createMultiColony(basePop[61:90])
#' virginColonies3 <- setLocation(virginColonies3,
#' location = Map(c, runif(30, 0, 2*pi), runif(30, 0, 2*pi)))
#' virginColonies4 <- createMultiColony(basePop[91:120])
#' virginColonies4 <- setLocation(virginColonies4,
#' location = Map(c, runif(30, 0, 2*pi), runif(30, 0, 2*pi)))
#'
#' # Create drone colonies
#' droneColonies <- createMultiColony(basePop[101:200])
#' droneColonies1 <- createMultiColony(basePop[201:300], location = Map(c, runif(100, 0, 2*pi), runif(100, 0, 2*pi)))
#' droneColonies <- createMultiColony(basePop[121:200])
#' droneColonies <- setLocation(droneColonies, location = Map(c, runif(80, 0, 2*pi), runif(80, 0, 2*pi)))
#' # Create some drones to mate initial drone colonies with
#' droneGroups <- pullDroneGroupsFromDCA(createDrones(basePop[201:300], nInd = 20),
#' n = nColonies(droneColonies),
#' nDrones = nFathersPoisson)
#' droneColonies <- cross(droneColonies, drones = droneGroups)
#'
#'
#' # PROBLEM: If we don't allow for cross plan to include drone ID, how can we cross initial drone colonies via
#' mating plan (we can only create drones from MapPop queens or mated queens in a colony).
#'
#' # Create a random cross plan
#' crossPlan <- createCrossPlan(x = droneColonies,
#' droneColonies = droneColonies1,
#' spatial = FALSE,
#' nDPC = 10)
#' droneColonies <- cross(x = droneColonies,
#' droneColonies = droneColonies1,
#' crossPlan = crossPlan)
#' droneColonies <- buildUp(droneColonies, nWorkers = 1000, nDrones = 1000)
#' #mating plan (we can only create drones from MapPop queens or mated queens in a colony).
#'
#' #' # Plot the colonies in space
#' virginLocations <- as.data.frame(getLocation(c(virginColonies1, virginColonies2, virginColonies3), collapse = T))
Expand All @@ -6365,23 +6364,37 @@ createRandomCrossPlan <- function(IDs, drones, nDrones) {
#'
#' ggplot(data = locations, aes(x = V1, y = V2, colour = Type)) + geom_point()
#'
#' # Cross according to a cross plan with drone IDs
#' crossPlan1 <- createCrossPlan(x = virginColonies1,
#' droneColonies = droneColonies,
#' spatial = TRUE,
#' radius = 1.5)
#' colonies1 <- crossDroneID(virginColonies1,
#' drones = getDrones(droneColonies, collapse = TRUE),
#' crossPlan = crossPlan1)
#'
#' # Cross according to a cross plan with colony IDs and SAMPLE the existing drones from them
#' crossPlan2 <- createCrossPlan(x = virginColonies2,
#' droneColonies = droneColonies,
#' spatial = TRUE,
#' radius = 1.5,
#' createDrones = FALSE)
#'
#' # Plot the crossing for the first colony in the crossPlan2
#' # Cross according to a pre-existing spatial cross plan
#' # Cross plan can be created either manually or via the function createCrossPlan
#'
#' # Cross according to a random cross plan regardless of colonies locations
#' crossPlanRandom <- createCrossPlan(x = virginColonies1,
#' droneColonies = droneColonies,
#' spatial = FALSE)
#'
#' # Plot the crossing for the first colony in the crossPlan
#' virginLocations1 <- as.data.frame(getLocation(virginColonies1, collapse = T))
#' virginLocations1$Type <- "Virgin"
#' droneLocations <- as.data.frame(getLocation(droneColonies, collapse = T))
#' droneLocations$Type <- "Drone"
#' locations1 <- rbind(virginLocations1, droneLocations)
#'
#' # Blue marks the target virgin colony and blue marks the drone colonies in the chosen radius
#' ggplot(data = locations1, aes(x = V1, y = V2, shape = Type )) +
#' geom_point(colour = ifelse(rownames(locations1) %in% crossPlanRandom[[1]],
#' "red",
#' ifelse(rownames(locations1) == names(crossPlanRandom)[[1]], "blue", "black")),
#' size = 3) +
#' xlab("x") + ylab("y")
#'
#'
#' # Cross according to a spatial cross plan according to the colonies' locations
#' crossPlanSpatial <- createCrossPlan(x = virginColonies2,
#' droneColonies = droneColonies,
#' spatial = TRUE,
#' radius = 1.5)
#'
#' # Plot the crossing for the first colony in the crossPlan
#' virginLocations2 <- as.data.frame(getLocation(virginColonies2, collapse = T))
#' virginLocations2$Type <- "Virgin"
#' droneLocations <- as.data.frame(getLocation(droneColonies, collapse = T))
Expand All @@ -6390,28 +6403,30 @@ createRandomCrossPlan <- function(IDs, drones, nDrones) {
#'
#' # Blue marks the target virgin colony and blue marks the drone colonies in the chosen radius
#' ggplot(data = locations2, aes(x = V1, y = V2, shape = Type )) +
#' geom_point(colour = ifelse(rownames(locations2) %in% crossPlan2[[1]],
#' geom_point(colour = ifelse(rownames(locations2) %in% crossPlanSpatial[[1]],
#' "red",
#' ifelse(rownames(locations2) == names(crossPlan2)[[1]], "blue", "black")),
#' ifelse(rownames(locations2) == names(crossPlanSpatial)[[1]], "blue", "black")),
#' size = 3) +
#' xlab("x") + ylab("y")
#'
#' colonies2 <- crossColonyID(x = virginColonies2,
#' droneColonies = droneColonies,
#' createDrones = FALSE,
#' nFathers = 15,
#' crossPlan = crossPlan2)
#'
#' # Cross according to a cross plan with colony IDs and CREATE drones from them
#' crossPlan3 <- createCrossPlan(virginColonies = virginColonies3,
#' droneColonies = droneColonies,
#' spatial = TRUE,
#' radius = 1.5)
#' colonies3 <- crossColonyID(x = virginColonies3,
#' droneColonies = droneColonies,
#' createDrones = TRUE,
#' nFathers = 15,
#' crossPlan = crossPlan3)
#' colonies2 <- cross(x = virginColonies2,
#' droneColonies = droneColonies,
#' crossPlan = crossPlanSpatial)
#'
#'
#' # Cross according to a cross plan that is created internally within the cross function
#' # The cross plan is created at random, regardless the location of the colonies
#' colonies3 <- cross(x = virginColonies3,
#' droneColonies = droneColonies,
#' nDPC = 5)
#'
#' # Mate spatially with cross plan created internally by the cross function
#' colonies4 <- cross(x = virginColonies4,
#' droneColonies = droneColonies,
#' spatial = TRUE,
#' radius = 1,
#' nDPC = 5)
#'
#'
#' @export
createCrossPlan <- function(x,
Expand Down
16 changes: 8 additions & 8 deletions R/Functions_L1_Pop.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1207,7 +1207,8 @@ pullVirginQueens <- function(x, nInd = NULL, use = "rand", collapse = FALSE) {
#' queens. You can use \code{checkMating} to alert you about this situation.
#'
#' @seealso \code{\link{Colony-class}} on how we store the fathers along the
#' queen.
#' queen. For more examples for mating with either externally or internally created cross plan,
#' please see \code{\link{\createCrossPlan}}
#'
#' @return \code{\link{Pop-class}} with mated queen(s). The misc slot of the
#' queens contains additional information about the number of workers, drones,
Expand Down Expand Up @@ -1283,7 +1284,7 @@ pullVirginQueens <- function(x, nInd = NULL, use = "rand", collapse = FALSE) {
#' droneProducingColonies <- cross(droneProducingColonies, drones = droneGroups[10:15])
#' apiary2 <- createMultiColony(basePop[16:20])
#' # Create a random cross plan
#' randomCrossPlan <- createCrossPlan(virgin = apiary2,
#' randomCrossPlan <- createCrossPlan(x = apiary2,
#' droneColonies = droneProducingColonies,
#' spatial = FALSE, nDPC = 5)
#' apiary2 <- cross(x = apiary2,
Expand All @@ -1292,8 +1293,9 @@ pullVirginQueens <- function(x, nInd = NULL, use = "rand", collapse = FALSE) {
#' nFathers = 15)
#' nFathers(apiary2)
#'
#'
#' @seealso For crossing virgin queens according to a cross plan, see
#' \code{\link{createRandomCrossPlan}}.
#' \code{\link{createCrossPlan}}.
#' For crossing virgin queens on a mating stations, see
#' \code{\link{createMatingStationDCA}}
#'
Expand Down Expand Up @@ -1365,7 +1367,7 @@ cross <- function(x,
crossPlan_create <- is.null(drones) && (!is.null(droneColonies) && is.null(crossPlan))

if (crossPlan_create) {
crossPlan <- createCrossPlan(virgin = x,
crossPlan <- createCrossPlan(x = x,
droneColonies = droneColonies,
spatial = spatial,
radius = radius,
Expand Down Expand Up @@ -1506,15 +1508,13 @@ crossDroneID <- function(x,
#' @export
crossColonyID <- function(x,
droneColonies = NULL,
createDrones = FALSE,
nFathers = 15,
crossPlan = NULL,
checkMating = "error",
simParamBee = NULL) {
ret <- cross(x,
droneID = FALSE, drones = NULL,
colonyID = TRUE, droneColonies = droneColonies,
createDrones = createDrones,
drones = NULL,
droneColonies = droneColonies,
nFathers = nFathers,
crossPlan = crossPlan,
checkMating = checkMating,
Expand Down

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