template to each clonegetTimeTrees Tree building function.
getTimeTrees(
clones,
template,
beast,
dir,
id,
time,
mcmc_length = 3e+07,
log_every = "auto",
burnin = 10,
trait = NULL,
resume_clones = NULL,
nproc = 1,
quiet = 0,
rm_temp = FALSE,
include_germline = TRUE,
seq = "sequence",
germline_range = c(-10000, 10000),
java = TRUE,
seed = NULL,
log_target = 10000,
tree_states = FALSE,
trees = NULL,
germline_trait_value = "?",
...
)A tibble with a column of phylo objects and parameters column
a tibble of airrClone objects, the output of
formatClones
XML template
location of beast binary directory (beast/bin)
directory where temporary files will be placed.
unique identifer for this analysis
Name of sample time column
Number of MCMC steps
Frequency of states logged. "auto" will divide mcmc_length by log_target
Burnin percent (default 10)
Trait column to be used
Clones to resume for mcmc_length more steps
Number of cores for parallelization. At most 1 core/tree can be used.
amount of rubbish to print to console
remove temporary files (default=TRUE)
Include germline sequence in analysis?
Sequence column in data
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 from MCMC chain
Use states vector for starting tree
optional list of starting trees, either phylo objects or newick strings
trait value for germline, default '?' for ambiguous
Additional arguments passed to tree building programs
For examples and vignettes, see https://dowser.readthedocs.io
getTrees, readBEAST