Usage
clumpp(sr, k, align.algorithm = "greedy", sim.stat = "g", greedy.option = "ran.order", repeats = 100, order.by.run = 0, label = NULL, delete.files = TRUE)
Arguments
sr
result from structure or folder name containing
STRUCTURE output files. k
choice of k in sr to combine.
align.algorithm
algorithm to be used for aligning the runs. Can be
"full.search", "greedy", or "large.k".
sim.stat
pairwise matrix similarity statistic to be used. Can be
"g" or "g.prime".
greedy.option
input order of runs to be tested. Required if
align.algorithm is "greedy" or "large.k". Valid choices are:
all |
| test all possible input orders of runs (note that this
option increases the run-time sub-stantially unless R is small). |
ran.order |
test a specified number of random input orders of
runs set by the repeats parameter. |
repeats
the number of input orders of runs to be tested. Only used if
align.algorithm is "greedy" or "large.k", and greedy.option
is "ran.order".
order.by.run
permute the clusters according to the cluster order of
a specific run. Set this parameter to a number from 1 to the number of
runs in sr.
label
label to use for input and output files.
delete.files
logical. Delete all files when CLUMPP is finished?