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)
set.seed(24601L)
result = tumopp::tumopp("-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 1.36 -1
## 2 0 0 0 2 1 1.36 2.04 -1
## 3 0 0 1 3 1 1.36 2.37 -1
## 4 0 0 0 4 2 2.04 2.69 -1
## 5 -1 1 0 5 2 2.04 3.07 -1
## 6 0 0 1 6 3 2.37 3.48 -1
## 7 1 0 2 7 3 2.37 3.15 -1
## 8 0 0 0 8 4 2.69 3.41 -1
## 9 0 -1 -1 9 4 2.69 3.52 -1
## 10 -1 1 0 10 5 3.07 4.43 -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 = tumopp::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::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