Run tumopp — tumopp • tumopp

tumopp() returns full results with config columns in a data.frame. See tumopp("-h") or https://heavywatal.github.io/tumopp/group__params.html for the list of command options.

Usage

tumopp(args, ...)

# Default S3 method
tumopp(
  args = character(0L),
  ...,
  graph = getOption("tumopp.graph", TRUE),
  cache = NULL
)

# S3 method for class 'list'
tumopp(args, ..., graph = TRUE, mc.cores = getOption("mc.cores", 1L))

# S3 method for class 'data.frame'
tumopp(args, ..., graph = TRUE, mc.cores = getOption("mc.cores", 1L))

make_args(alt, const = NULL, times = 1L, each = 1L)

Arguments

args: command line arguments as a string vector or list of strings.
...: not used.
graph: add graph column if TRUE
cache: A parent directory to cache results. TRUE is equivalent to getOption("tumopp.cache", "~/.cache/tumopp"). tempdir() is used in other cases including the default (NULL), which is discarded at the end of an R session. Set FALSE to force tumopp to run and overwrite previous results if any.
mc.cores: The number of cores to use for concurrent execution.
alt: named list of altered arguments.
const: named list of constant arguments.
times, each: passed to rep()

Details

A population data.frame includes ancestral cells. Extant cells can be extracted by filtering with death == 0 or filter_extant() function. The sampling time, i.e., the end of a simulation, is typically the maximum value of birth time.

The default unit of time (birth and death columns) is the average cell cycle of newborn cells (given the parameter -b/--beta0 is set to 1). For example, step-wise tumor growth and integer values in the birth column will be observed if -k/--shape parameter is set to a very large value like 10**6. If you are considering some cell line whose average cell cycle is 4 days for example, then the unit of those columns can be interpreted as 4 days, or you can set --beta0=0.25 to change the unit to a day.

The omega column denotes the number of cell divisions allowed for each cell. Negative values denote unlimited proliferation potential.

make_args() returns argument combinations in a tibble.