Description Usage Arguments Value
output_JAGS
processes the mixing model output, prints and saves (in the
working directory):
diagnostics
summary statistics
posterior density plots
pairs plot
trace/XY plots
1 2 3 4 5 6 7 8 9 10 11 12 | output_JAGS(
jags.1,
mix,
source,
output_options = list(summary_save = TRUE, summary_name = "summary_statistics",
sup_post = FALSE, plot_post_save_pdf = TRUE, plot_post_name = "posterior_density",
sup_pairs = FALSE, plot_pairs_save_pdf = TRUE, plot_pairs_name = "pairs_plot", sup_xy
= TRUE, plot_xy_save_pdf = FALSE, plot_xy_name = "xy_plot", gelman = TRUE, heidel =
FALSE, geweke = TRUE, diag_save = TRUE, diag_name = "diagnostics", indiv_effect =
FALSE, plot_post_save_png = FALSE, plot_pairs_save_png = FALSE, plot_xy_save_png =
FALSE, diag_save_ggmcmc = TRUE)
)
|
jags.1 |
rjags model object, output from |
mix |
output from |
source |
output from |
output_options |
list containing options for plots and saving:
|
p.both
– only if 2 fixed effects OR 1 fixed + 1 random, otherwise NULL
).
p.both
holds the MCMC chains for the estimated proportions at the different factor levels. Dimensions = [n.draws, f1.levels, f2.levels, n.sources].
Calculated by combining the ilr offsets from global intercept: ilr.both[,f1,f2,src] = ilr.global[,src] + ilr.fac1[,f1,src] + ilr.fac2[,f2,src] And then transforming from ilr- to proportion-space.
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