buildBeast - Read in a directory from a BEAST run. Runs treeannotator and loganalyser.

Description¶

Read in a directory from a BEAST run. Runs treeannotator and loganalyser.

Usage¶

buildBeast(
data,
beast,
time,
template,
dir,
id,
mcmc_length = 1e+06,
resume_clones = NULL,
trait = NULL,
asr = FALSE,
posterior = c("none", "all", "parameters", "trees_with_traits", "trees"),
log_every = "auto",
include_germline = TRUE,
nproc = 1,
quiet = 0,
burnin = 10,
low_ram = TRUE,
germline_range = c(-10000, 10000),
java = TRUE,
seed = NULL,
log_target = 10000,
trees = NULL,
tree_states = FALSE,
start_edge_length = 100,
start_date = NULL,
max_start_date = NULL,
germline_trait_value = "?",
...
)

Arguments¶

data

a list of airrClone objects

beast

location of beast binary directory (beast/bin)

time

Name of sample time column

template

XML template

dir

directory where temporary files will be placed.

id

unique identifer for this analysis

mcmc_length

Number of MCMC steps

resume_clones

Clones to resume for mcmc_length more steps

trait

Trait column used

asr

Log ancestral sequences?

posterior

Read un full distribution of parameters and trees? Can be “none” to just have summary objects, “all” to have parameters, trees, and trees_with_traits, or a vector with the desired combination of “parameters”, “trees_with_traits”, and “trees”.

log_every

Frequency of states logged. auto will divide mcmc_length by log_target

include_germline

Include germline in analysis?

nproc

Number of cores for parallelization. Uses at most 1 core per tree.

quiet

Amount of rubbish to print to console

burnin

Burnin percent (default 10)

low_ram

run with less memory (slightly slower)

germline_range

Possible date range of germline tip

java

Use the -java flag for BEAST run

seed

Use specified seeed for the -seed option for BEAST

log_target

Target number of samples over mcmc_length

trees

optional list of starting trees, either phylo objects or newick strings

tree_states

Use states vector for starting tree

start_edge_length

edge length to use for all branches in starting tree

start_date

Starting date of time tree if desired

max_start_date

Maximum starting date of time tree if desired

germline_trait_value

trait value for germline, default ‘?’ for ambiguous

…

Additional arguments for XML writing functions

Value¶

The input clones tibble with an additional column for the bootstrap replicate trees.

See also¶

getTimeTrees