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, ...)
# S3 method for default
tumopp(args = character(0L), ..., graph = TRUE, cache = FALSE)
# S3 method for list
tumopp(args, ..., graph = TRUE, mc.cores = getOption("mc.cores", 1L))
# S3 method for 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.