Save and load a DenMark fit — denmark

cmdstanr keeps posterior draws in CSV files (by default in a temporary folder that disappears when R closes). denmark_save() reads everything into memory first, so the saved object can be reloaded and post-processed in a later session.

Usage

denmark_save(obj, file)

denmark_load(file)

Arguments

obj: A denmark object from DenMark().
file: Path of the .rds file.

Value

denmark_save() returns file invisibly; denmark_load() returns the denmark object.

Examples

toy <- denmark_toy_data()
tissue <- denmark_alpha_shape(toy$x, toy$y)
tumor <- subset(toy, celltype == "Tumor", select = -celltype)
fit <- DenMark(tumor, gene = "geneA", boundary = tissue,
               grid_size = 10, basis = 10,
               chains = 2, iter_warmup = 300, iter_sampling = 300,
               seed = 2024, quiet = TRUE)
f <- tempfile(fileext = ".rds")
denmark_save(fit, f)
fit2 <- denmark_load(f)
denmark_summary(fit2)
#>     variable         mean        sd       q2.5        q25        q50       q75
#> 1      beta0  5.601331528 0.3097492  4.9325404  5.4181133 5.61098860 5.8053836
#> 2      beta1 -0.006866258 0.5578875 -1.3494302 -0.3105288 0.07316074 0.3673002
#> 3     ell[1]  0.605010793 0.1502094  0.3779487  0.5024737 0.58196906 0.6884403
#> 4     ell[2]  0.771993891 0.2643356  0.4080575  0.5885706 0.72639588 0.8915657
#> 5 Astar[2,1]  0.633226952 0.1356900  0.3432107  0.5478936 0.65264227 0.7333021
#> 6   sigma[1]  0.996146048 0.2059037  0.6932623  0.8644840 0.95049295 1.0908011
#> 7   sigma[2]  1.334124248 0.3150556  0.8565963  1.1129229 1.28822175 1.5008512
#>       q97.5     rhat ess_bulk ess_tail                               label
#> 1 6.1774899 1.003058 582.9498 369.4042             intercept, cell density
#> 2 0.8390978 1.002995 507.7903 351.3187               intercept, expression
#> 3 0.9516199 1.010649 321.4436 419.2502         length-scale, density field
#> 4 1.4692636 1.005955 351.7718 339.1145      length-scale, expression field
#> 5 0.8651198 1.009571 291.8595 459.4095 rho: density-expression correlation
#> 6 1.5280511 1.001273 292.4361 359.8197                   SD, density field
#> 7 2.0902071 1.008189 241.4411 251.0961                SD, expression field