tumopp: Run tumopp

In heavywatal/tumorr: 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 = TRUE, cache = FALSE)

## 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	use cache if TRUE.
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/tumorr documentation built on April 2, 2024, 7:24 p.m.