getTimeTrees - Estimate time trees by running BEAST on each clone
Applies XML template to each clone
Description¶
getTimeTrees Tree building function.
Usage¶
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 = "?",
...
)
Arguments¶
- clones
- a tibble of
airrCloneobjects, the output of formatClones - template
- XML template
- beast
- location of beast binary directory (beast/bin)
- dir
- directory where temporary files will be placed.
- id
- unique identifer for this analysis
- time
- Name of sample time column
- mcmc_length
- Number of MCMC steps
- log_every
- Frequency of states logged. “auto” will divide mcmc_length by log_target
- burnin
- Burnin percent (default 10)
- trait
- Trait column to be used
- resume_clones
- Clones to resume for
mcmc_lengthmore steps - nproc
- Number of cores for parallelization. At most 1 core/tree can be used.
- quiet
- amount of rubbish to print to console
- rm_temp
- remove temporary files (default=TRUE)
- include_germline
- Include germline sequence in analysis?
- seq
- Sequence column in data
- 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 from MCMC chain
- tree_states
- Use
statesvector for starting tree - trees
- optional list of starting trees, either phylo objects or newick strings
- germline_trait_value
- trait value for germline, default ‘?’ for ambiguous
- …
- Additional arguments passed to tree building programs
Value¶
A tibble with a column of phylo objects and parameters column
Details¶
For examples and vignettes, see https://dowser.readthedocs.io