findSwitches {dowser} | R Documentation |
findSwitches
Phylogenetic bootstrap function.
findSwitches(
clones,
permutations,
trait,
igphyml,
fixtrees = FALSE,
downsample = TRUE,
tip_switch = 20,
nproc = 1,
dir = NULL,
id = NULL,
modelfile = NULL,
build = "pratchet",
exec = NULL,
quiet = 0,
rm_temp = TRUE,
palette = NULL,
resolve = 2,
rep = NULL,
keeptrees = FALSE,
lfile = NULL,
seq = NULL,
boot_part = "locus",
force_resolve = FALSE,
...
)
clones |
tibble |
permutations |
number of bootstrap replicates to perform |
trait |
trait to use for parsimony models |
igphyml |
location of igphyml executible |
fixtrees |
keep tree topologies fixed? (bootstrapping will not be perfomed) |
downsample |
downsample clones to have a maximum specified tip/switch ratio? |
tip_switch |
maximum allowed tip/switch ratio if downsample=TRUE |
nproc |
number of cores to parallelize computations |
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 |
quiet |
amount of rubbish to print to console |
rm_temp |
remove temporary files (default=TRUE) |
palette |
a named vector specifying colors for each state |
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 |
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 |
Tree building details are the same as getTrees.
If keeptrees=TRUE
(default) the returned object will contain a list
named "trees" which contains a list of estimated tree objects for each
bootstrap replicate. The object is structured like:
trees[[<replicate>]][[<tree index>]]. If igphyml
is specified
(as well as trait
), the returned object
will contain a tibble
named "switches" containing switch count
information. This object can be passed to testSP and other functions
to perform parsimony based trait value tests.
A list of trees and/or switch counts for each bootstrap replicate.
Uses output from formatClones with similar arguments to getTrees. Output can be visualized with plotTrees, and tested with testPS, testSC, and testSP.
## Not run:
data(ExampleAirr)
ExampleAirr$sample_id <- sample(ExampleAirr$sample_id)
clones <- formatClones(ExampleAirr, trait="sample_id")
igphyml <- "~/apps/igphyml/src/igphyml"
btrees <- findSwitches(clones[1:2,], permutations=10, nproc=1,
igphyml=igphyml, trait="sample_id")
plotTrees(btrees$trees[[4]])[[1]]
testPS(btrees$switches)
## End(Not run)