Basic usage
This is an R interface of tumopp, a tumor growth
simulator in C++. The parameter values and resulting populations are
returned in a nested tibble.
See ?tumopp for details.
library(tumopp)
result = tumopp("--seed=24601 -D3 -Cmoore -k10 -N1000")
colnames(result)
#> [1] "alpha0" "benchmark" "beta0" "coord" "delta0"
#> [6] "dimensions" "extinction" "interval" "local" "ma"
#> [11] "max" "max_time" "mb" "md" "mm"
#> [16] "mutate" "origin" "outdir" "path" "plateau"
#> [21] "prolif" "record" "resistant" "rho0" "sa"
#> [26] "sb" "sd" "seed" "shape" "sm"
#> [31] "symmetric" "treatment" "ua" "ub" "ud"
#> [36] "um" "verbose" "population" "graph"
result$population[[1L]] |> dplyr::arrange(id)
#> # A tibble: 1,999 × 8
#> x y z id ancestor birth death omega
#> <int> <int> <int> <int> <int> <dbl> <dbl> <int>
#> 1 0 0 0 1 0 0 1.28 -1
#> 2 0 0 0 2 1 1.28 2.18 -1
#> 3 1 1 0 3 1 1.28 1.89 -1
#> 4 1 1 0 4 3 1.89 3.14 -1
#> 5 1 2 1 5 3 1.89 2.80 -1
#> 6 1 0 1 6 2 2.18 3.20 -1
#> 7 -1 0 -1 7 2 2.18 3.13 -1
#> 8 1 2 1 8 5 2.80 3.80 -1
#> 9 2 3 2 9 5 2.80 3.92 -1
#> 10 -1 0 -1 10 7 3.13 4.82 -1
#> # ℹ 1,989 more rowsExplore parameter space
A parameter grid can be generated with make_args(). See
tumopp("--help") or C++
library documentation generated by doxygen for available
parameters.
.const = list(D = 3L, C = "hex", N = 1000L)
.alt = list(
k = c("1", "1e6"),
L = c("const", "linear", "step"),
P = c("random", "mindrag")
)
# Generate combinations of arguments
args_table = make_args(alt = .alt, const = .const, each = 1L) |> print()
#> # A tibble: 12 × 6
#> k L P D C N
#> <chr> <chr> <chr> <int> <chr> <int>
#> 1 1 const mindrag 3 hex 1000
#> 2 1 const random 3 hex 1000
#> 3 1 linear mindrag 3 hex 1000
#> 4 1 linear random 3 hex 1000
#> 5 1 step mindrag 3 hex 1000
#> 6 1 step random 3 hex 1000
#> 7 1e6 const mindrag 3 hex 1000
#> 8 1e6 const random 3 hex 1000
#> 9 1e6 linear mindrag 3 hex 1000
#> 10 1e6 linear random 3 hex 1000
#> 11 1e6 step mindrag 3 hex 1000
#> 12 1e6 step random 3 hex 1000
# Concurrent execution
results = tumopp(args_table)
results |>
dplyr::select(!c(outdir, seed, where(is.list))) |>
dplyr::select(where(\(x) dplyr::n_distinct(x) > 1L))
#> # A tibble: 12 × 4
#> args local path shape
#> <chr> <chr> <chr> <dbl>
#> 1 1 const mindrag 1
#> 2 2 const random 1
#> 3 3 linear mindrag 1
#> 4 4 linear random 1
#> 5 5 step mindrag 1
#> 6 6 step random 1
#> 7 7 const mindrag 1000000
#> 8 8 const random 1000000
#> 9 9 linear mindrag 1000000
#> 10 10 linear random 1000000
#> 11 11 step mindrag 1000000
#> 12 12 step random 1000000