Level 0 function that returns alleles from the csd locus. See
SimParamBee
for more information about the csd locus.
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
)
Pop-class
, Colony-class
, or
MultiColony-class
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"
numeric, for how many individuals; if NULL
all individuals
are taken; this can be useful as a test of sampling individuals
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
logical, return haploid result for drones?
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.
logical, return only the unique set of csd alleles. This argument
interacts with collapse
. Default is FALSE
. See examples about
this behaviour.
SimParamBee
, global simulation parameters
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
If both collapse and unique are TRUE
, the function returns a
unique set of csd alleles in the entire population, colony, or multicolony
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
founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes, nCsdAlleles = 5)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
drones <- createDrones(x = basePop[1], nInd = 1000)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- cross(colony, drones = droneGroups[[1]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- buildUp(x = colony, nWorkers = 6, nDrones = 3)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- createMultiColony(basePop[3:4], n = 2)
#> Error in createMultiColony(basePop[3:4], n = 2): object 'basePop' not found
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- buildUp(x = apiary, nWorkers = 6, nDrones = 3)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Use getCsdAlleles on a Population
getCsdAlleles(getQueen(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(getWorkers(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Use getCsdAlleles on a Colony
getCsdAlleles(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, caste = "queen")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQueenCsdAlleles(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, caste = "workers")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getWorkersCsdAlleles(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Same aliases exist for all the castes!
getCsdAlleles(colony, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, collapse = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, collapse = TRUE, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Use getCsdAlleles on a MultiColony
getCsdAlleles(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(apiary, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(apiary, collapse = TRUE, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(apiary, nInd = 2)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found