# Get csd alleles Level 0 function that returns alleles from the csd locus. See `SimParamBee` for more information about the csd locus. ```r getCsdAlleles( x, caste = NULL, nInd = NULL, allele = "all", dronesHaploid = TRUE, collapse = FALSE, unique = FALSE, simParamBee = NULL ) getQueenCsdAlleles( x, allele = "all", unique = FALSE, collapse = FALSE, simParamBee = NULL ) getFathersCsdAlleles( x, nInd = NULL, allele = "all", dronesHaploid = TRUE, unique = FALSE, collapse = FALSE, simParamBee = NULL ) getVirginQueensCsdAlleles( x, nInd = NULL, allele = "all", unique = FALSE, collapse = FALSE, simParamBee = NULL ) getWorkersCsdAlleles( x, nInd = NULL, allele = "all", unique = FALSE, collapse = FALSE, simParamBee = NULL ) getDronesCsdAlleles( x, nInd = NULL, allele = "all", dronesHaploid = TRUE, unique = FALSE, collapse = FALSE, simParamBee = NULL ) ``` ## Arguments - `x`: `Pop-class`, `Colony-class`, or `MultiColony-class` - `caste`: NULL or character, NULL when `x` is a `Pop-class`, and character when `x` is a `Colony-class` or `MultiColony-class` with the possible values of "queen", "fathers", "workers", "drones", "virginQueens", or "all" - `nInd`: numeric, for how many individuals; if `NULL` all individuals are taken; this can be useful as a test of sampling individuals - `allele`: character, either "all" for both alleles or an integer for a single allele, use a value of 1 for female allele and a value of 2 for male allele - `dronesHaploid`: logical, return haploid result for drones? - `collapse`: logical, if `TRUE`, the function will return a set of csd alleles across the entire population, colony, or multicolony (not separately for each caste when `x` is a colony or each caste of each colony when `x` is a multicolony. This is a way to get one single object as an output across castes or colonies. Note this has nothing to do with the colony collapse. It's like `paste(..., collapse = TRUE)`. Default is `FALSE`. See examples about this behaviour. - `unique`: logical, return only the unique set of csd alleles. This argument interacts with `collapse`. Default is `FALSE`. See examples about this behaviour. - `simParamBee`: `SimParamBee`, global simulation parameters ## Returns matrix with haplotypes when `x` is `Pop-class`, list of matrices with haplotypes when `x` is `Colony-class` (list nodes named by caste) and list of a list of matrices with haplotypes when `x` is `MultiColony-class`, outer list is named by colony id when `x` is `MultiColony-class`; `NULL` when `x` is `NULL` ## Details If both collapse and unique are `TRUE`, the function returns a unique set of csd alleles in the entire population, colony, or multicolony ## Functions * `getQueenCsdAlleles()`: Access csd alleles of the queen * `getFathersCsdAlleles()`: Access csd alleles of the fathers * `getVirginQueensCsdAlleles()`: Access csd alleles of the virgin queens * `getWorkersCsdAlleles()`: Access csd alleles of the workers * `getDronesCsdAlleles()`: Access csd alleles of the drones ## Examples ```r founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100) SP <- SimParamBee$new(founderGenomes, nCsdAlleles = 5) basePop <- createVirginQueens(founderGenomes) drones <- createDrones(x = basePop[1], nInd = 1000) droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson) # Create a Colony and a MultiColony class colony <- createColony(x = basePop[2]) colony <- cross(colony, drones = droneGroups[[1]]) colony <- buildUp(x = colony, nWorkers = 6, nDrones = 3) apiary <- createMultiColony(basePop[3:4], n = 2) apiary <- cross(apiary, drones = droneGroups[c(2, 3)]) apiary <- buildUp(x = apiary, nWorkers = 6, nDrones = 3) # Use getCsdAlleles on a Population getCsdAlleles(getQueen(colony)) getCsdAlleles(getWorkers(colony)) # Use getCsdAlleles on a Colony getCsdAlleles(colony) getCsdAlleles(colony, caste = "queen") getQueenCsdAlleles(colony) getCsdAlleles(colony, caste = "workers") getWorkersCsdAlleles(colony) # Same aliases exist for all the castes! getCsdAlleles(colony, unique = TRUE) getCsdAlleles(colony, collapse = TRUE) getCsdAlleles(colony, collapse = TRUE, unique = TRUE) # Use getCsdAlleles on a MultiColony getCsdAlleles(apiary) getCsdAlleles(apiary, unique = TRUE) getCsdAlleles(apiary, collapse = TRUE, unique = TRUE) getCsdAlleles(apiary, nInd = 2) ```

getCsdAlleles function