run_modern: Run the modern (calibration) model

In ncahill89/BTF: Run the Bayesian Transfer Function

Run the modern (calibration) model

Description

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

test_modern_mod <- run_modern(
  modern_elevation = NJ_modern_elevation,
  modern_species = NJ_modern_species,
  n.iter = 10,
  n.burnin = 1,
  n.thin = 1
)

ncahill89/BTF documentation built on Oct. 4, 2022, 5:18 a.m.