posterior_summary: Summarize posterior samples

In StrattonCh/msocc: Package for Fitting and Analyzing Computationally Efficient Multi-scale Occupancy Models

Description

This function allows for easy summaries of the posterior samples drawn by msocc_mod.

Usage

posterior_summary(
  msocc_mod,
  burnin = 0,
  print = F,
  level = "overall",
  quantiles = c(0.025, 0.975),
  unique = T
)

Arguments

msocc_mod	output from msocc_mod (object of class msocc)
burnin	number of samples to discard as burnin when summarizing the posterior
print	should summaries be printed in the console?
level	one of c('overall', 'site', 'sample', 'rep'); which level of the design should be summarized?
quantiles	vector of quantiles for credibility intervals
unique	should only unique rows be printed?
n	number of rows to print in the console for the posterior summary

Value

object of class data.frame providing summaries of the posterior organized by site, sample, and replicate.

Examples

data(fung)

# prep data
fung.detect <- fung %>%
  dplyr::select(1:4)

site.df <- fung %>%
  dplyr::select(-sample, -pcr1, -pcr2) %>%
  dplyr::distinct(site, .keep_all = TRUE) %>%
  dplyr::arrange(site)

sample.df <- fung %>%
  dplyr::select(-pcr1, -pcr2) %>%
  dplyr::arrange(site, sample)

# model sample level occurence by frog density
fung_mod2 <- msocc_mod(wide_data = fung.detect, progress = T,
                       site = list(model = ~ 1, cov_tbl = site.df),
                       sample = list(model = ~ frogs, cov_tbl = sample.df),
                       rep = list(model = ~ 1, cov_tbl = sample.df),
                       num.mcmc = 1000, beta_bin = T)

# overall summary
posterior_summary(fung_mod2)

# site level
posterior_summary(fung_mod2, level = 'site')

# sample level
posterior_summary(fung_mod2, level = 'sample')

# rep level
posterior_summary(fung_mod2, level = 'rep')

StrattonCh/msocc documentation built on Dec. 22, 2020, 2:51 a.m.