Read in a directory from a BEAST run. Runs treeannotator and loganalyser.
buildBeast(
data,
beast,
time,
template,
dir,
id,
mcmc_length = 1e+06,
resume_clones = NULL,
trait = NULL,
asr = FALSE,
full_posterior = FALSE,
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,
...
)The input clones tibble with an additional column for the bootstrap replicate trees.
a list of airrClone objects
location of beast binary directory (beast/bin)
Name of sample time column
XML template
directory where temporary files will be placed.
unique identifer for this analysis
Number of MCMC steps
Clones to resume for mcmc_length more steps
Trait column used
Log ancestral sequences?
Read un full distribution of parameters and trees?
Frequency of states logged. auto will divide mcmc_length by log_target
Include germline in analysis?
Number of cores for parallelization. Uses at most 1 core per tree.
Amount of rubbish to print to console
Burnin percent (default 10)
run with less memory (slightly slower)
Possible date range of germline tip
Use the -java flag for BEAST run
Use specified seeed for the -seed option for BEAST
Target number of samples over mcmc_length
optional list of starting trees, either phylo objects or newick strings
Use states vector for starting tree
edge length to use for all branches in starting tree
Starting date of time tree if desired
Maximum starting date of time tree if desired
Additional arguments for XML writing functions
getTimeTrees