getTimeTreesIterate - Iteratively resume getTimeTrees until convergence, as defined by
all parameters (except those in ignore vector) having ESS
greater than or equal to the specified ess_cutoff
Description¶
getTimeTreesIterate Iteratively resume getTimeTrees til convergence.
Usage¶
getTimeTreesIterate(
clones,
template,
beast,
dir,
id,
time,
iterations = 10,
ess_cutoff = 200,
burnin = 10,
ignore = c("traitfrequencies"),
continue = FALSE,
posterior = c("none", "all", "parameters", "trees_with_traits", "trees"),
trait = NULL,
nproc = 1,
quiet = 0,
asr = FALSE,
low_ram = TRUE,
trim_ids = FALSE,
...
)
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
- iterations
- Maximum number of times to resume MCMC chain
- ess_cutoff
- Minimum number of ESS for all parameters
- burnin
- Burnin percent (default 10)
- ignore
- Vector of parameters to ignore for ESS calculation
- continue
- If TRUE, will check for iteration folder and resume from last iteration if found (default FALSE)
- 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”.
- trait
- Trait column to be used
- nproc
- Number of cores for parallelization. At most 1 core/tree can be used.
- quiet
- quiet notifications if > 0
- asr
- Log ancestral sequences?
- low_ram
- run with less memory (slightly slower)
- trim_ids
- remove last _ group from tips?
- …
- Additional arguments for getTimeTrees
Value¶
A tibble of tidytree and airrClone objects.
Details¶
For a full list of options (of which there are many more), see getTimeTrees
For examples and vignettes, see https://dowser.readthedocs.io