tumopp: Run tumopp

In heavywatal/rtumopp: R interface to tumopp, a tumor growth simulator in C++

Run tumopp

Description

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 = getOption("tumopp.cache", character(0))
)

## 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. ⁠~/.cache/tumopp⁠ for TRUE, tempdir() for any FALSE-like values.
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.

heavywatal/rtumopp documentation built on Aug. 27, 2024, 11:50 a.m.