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Backward-compatible wrapper of the original DenMark interface

Source: R/fit.R
DenMarkmain.Rd

Keeps scripts written for the original interface running. L1 and L2 are no longer needed (they are computed from the data) and are only checked.

Usage

DenMarkmain(
  grid_size,
  dataset,
  basis,
  boundfactor,
  L1 = NULL,
  L2 = NULL,
  denmark_version = "M2",
  ...
)

Arguments

grid_size

Grid cells per axis, or c(nx, ny).

dataset

Data frame with columns x, y and one expression column.

basis

HSGP basis functions per axis, or c(m1, m2).

boundfactor

HSGP boundary factor (>= 1).

L1, L2

Optional half-ranges, only checked against the data.

denmark_version

"M2" (the default) fits the DenMark model; any other value is taken as the path to a Stan file (as in the earlier tutorial) and passed to DenMark() as stan_file.

...

Further arguments passed to DenMark().

Value

An object of class denmark, see DenMark().

Examples

toy <- denmark_toy_data()
tissue <- denmark_alpha_shape(toy$x, toy$y)
tumor <- toy[toy$celltype == "Tumor", c("x", "y", "geneA")]
fit <- DenMarkmain(grid_size = 10, dataset = tumor,
                   basis = 10, boundfactor = 1.5, boundary = tissue,
                   chains = 2, iter_warmup = 300, iter_sampling = 300,
                   seed = 2024, quiet = TRUE)
fit$rhat
#>      beta0      beta1     ell[1]     ell[2] Astar[2,1]   sigma[1]   sigma[2] 
#>   1.003058   1.002995   1.010649   1.005955   1.009571   1.001273   1.008189