STb_summary() — STb_summary • STbayes

Create a useful summary table for STbayes fit. Contains estimates on log and linear scale for lambda_0 (intrinsic rate) and s' (social transmission rate). Includes estimated s (relative strength of social transmission).

Usage

STb_summary(
  fit,
  depth = 1,
  prob = 0.95,
  ignore_params = c("lp__", "idx", "log_lik", "log_lik_matrix", "count_ST", "psocn_sum",
    "acquisition_time", "z_ID", "Rho_ID", "v_ID", ".chain", ".iteration", ".draw",
    "s_prime"),
  digits = 3,
  CI_method = c("HPDI", "PI")
)

Arguments

fit: CmdStanMCMC model fit
depth: integer depth of multidimensional parameters to extract
prob: double limits for HPD of estimates (default = 0.95)
ignore_params: character vector of parameters to ignore
digits: integer of digits to round to
CI_method: "HPDI" for highest density interval or "PI" for quantiles (equal tails). Defaults to HPDI.

Value

Summary table

Examples

data_list <- import_user_STb(STbayes::event_data, STbayes::edge_list)
model_obj <- generate_STb_model(data_list)
fit <- fit_STb(data_list,
    model_obj,
    parallel_chains = 4,
    chains = 4,
    cores = 4,
    iter = 4000,
    refresh = 2000
)
STb_summary(fit, prob = 0.95, digits = 3, CI_method = "HPDI")