Run the modern (calibration) model

Usage

run_modern(
  modern_elevation = NULL,
  modern_species = NULL,
  scale_x = FALSE,
  sigma_z_priors = NULL,
  dx = 0.1,
  ChainNums = seq(1, 3),
  n.iter = 40000,
  n.burnin = 10000,
  n.thin = 15,
  validation.run = FALSE,
  fold = 1
)

Arguments

modern_elevation: A dataframe of modern elevations
modern_species: A dataframe of modern counts (to be sorted with sort_modern)
scale_x: Set to TRUE to scale elevation data to have mean 0 and sd 1
sigma_z_priors: priors for foram variability (if available)
dx: The elevation interval for spacing the spline knots. Defaults to 0.2
ChainNums: The number of MCMC chains to run
n.iter: The number of iterations
n.burnin: The number of burnin samples
n.thin: The number of thinning
validation.run: Defaults to FALSE. Set to TRUE if running a validation
fold: Fold number for cross validation (CV)

Value

a list of objects including data, parameter values and scaling information

Examples

# \donttest{
test_modern_mod <- run_modern(
  modern_elevation = NJ_modern_elevation,
  modern_species = NJ_modern_species,
  n.iter = 10,
  n.burnin = 1,
  n.thin = 1
)
#> Start chain ID  1 
#> Compiling model graph
#>    Resolving undeclared variables
#>    Allocating nodes
#> Graph information:
#>    Observed stochastic nodes: 175
#>    Unobserved stochastic nodes: 3136
#>    Total graph size: 20460
#> 
#> Initializing model
#> 
#> Hooraah, Chain 1 has finished! 
#> Start chain ID  2 
#> Compiling model graph
#>    Resolving undeclared variables
#>    Allocating nodes
#> Graph information:
#>    Observed stochastic nodes: 175
#>    Unobserved stochastic nodes: 3136
#>    Total graph size: 20460
#> 
#> Initializing model
#> 
#> Hooraah, Chain 2 has finished! 
#> Start chain ID  3 
#> Compiling model graph
#>    Resolving undeclared variables
#>    Allocating nodes
#> Graph information:
#>    Observed stochastic nodes: 175
#>    Unobserved stochastic nodes: 3136
#>    Total graph size: 20460
#> 
#> Initializing model
#> 
#> Hooraah, Chain 3 has finished! 
#> Run complete! 
# }