bootstrapTrees {dowser} | R Documentation |
Deprecated! Please use findSwitches instead.
Description
bootstrapTrees
Phylogenetic bootstrap function.
Usage
bootstrapTrees(
clones,
bootstraps,
nproc = 1,
trait = NULL,
dir = NULL,
id = NULL,
modelfile = NULL,
build = "pratchet",
exec = NULL,
igphyml = NULL,
fixtrees = FALSE,
quiet = 0,
rm_temp = TRUE,
palette = NULL,
resolve = 2,
rep = NULL,
keeptrees = TRUE,
lfile = NULL,
seq = NULL,
downsample = FALSE,
tip_switch = 20,
boot_part = "locus",
force_resolve = FALSE,
...
)
Arguments
clones |
tibble |
bootstraps |
number of bootstrap replicates to perform |
nproc |
number of cores to parallelize computations |
trait |
trait to use for parsimony models (required if
|
dir |
directory where temporary files will be placed (required
if |
id |
unique identifer for this analysis (required if
|
modelfile |
file specifying parsimony model to use |
build |
program to use for tree building (phangorn, dnapars) |
exec |
location of desired phylogenetic executable |
igphyml |
location of igphyml executible if trait models desired |
fixtrees |
keep tree topologies fixed? (bootstrapping will not be perfomed) |
quiet |
amount of rubbish to print to console |
rm_temp |
remove temporary files (default=TRUE) |
palette |
deprecated |
resolve |
how should polytomies be resolved? 0=none, 1=max parsminy, 2=max ambiguity + polytomy skipping, 3=max ambiguity |
rep |
current bootstrap replicate (experimental) |
keeptrees |
keep trees estimated from bootstrap replicates? (TRUE) |
lfile |
lineage file input to igphyml if desired (experimental) |
seq |
column name containing sequence information |
downsample |
downsample clones to have a maximum specified tip/switch ratio? |
tip_switch |
maximum allowed tip/switch ratio if downsample=TRUE |
boot_part |
is "locus" bootstrap columns for each locus separately |
force_resolve |
continue even if polytomy resolution fails? |
... |
additional arguments to be passed to tree building program |
Value
A list of trees and/or switch counts for each bootstrap replicate.