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
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)
)
rjags model object, output from run_model
function
output from load_mix_data
output from load_source_data
list containing options for plots and saving:
summary_save
: Save the summary statistics as a txt file? Default = TRUE
summary_name
: Summary statistics file name (.txt will be appended). Default = "summary_statistics"
sup_post
: Suppress posterior density plot output in R? Default = FALSE
plot_post_save_pdf
: Save posterior density plots as pdfs? Default = TRUE
plot_post_name
: Posterior plot file name(s) (.pdf/.png will be appended) Default = "posterior_density"
sup_pairs
: Suppress pairs plot output in R? Default = FALSE
plot_pairs_save_pdf
: Save pairs plot as pdf? Default = TRUE
plot_pairs_name
: Pairs plot file name (.pdf/.png will be appended) Default = "pairs_plot"
sup_xy
: Suppress xy/trace plot output in R? Default = TRUE
plot_xy_save_pdf
: Save xy/trace plot as pdf? Default = FALSE
plot_xy_name
: XY/trace plot file name (.pdf/.png will be appended) Default = "xy_plot"
gelman
: Calculate Gelman-Rubin diagnostic test? Default = TRUE
heidel
: Calculate Heidelberg-Welch diagnostic test? Default = FALSE
geweke
: Calculate Geweke diagnostic test? Default = TRUE
diag_save
: Save the diagnostics as a .txt file? Default = TRUE
diag_name
: Diagnostics file name (.txt will be appended) Default = "diagnostics"
indiv_effect
: artifact, set to FALSE
plot_post_save_png
: Save posterior density plots as pngs? Default = FALSE
plot_pairs_save_png
: Save pairs plot as png? Default = FALSE
plot_xy_save_png
: Save xy/trace plot as png? Default = FALSE
diag_save_ggmcmc
: Save ggmcmc diagnostics as pdf? Default = TRUE
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.