summary_stat: Summary statistics from posterior of MixSIAR model

In brianstock/MixSIAR: Bayesian Mixing Models in R

Description

summary_stat prints and saves summary statistics

Usage

summary_stat(
  combined,
  toprint = "all",
  groupby = "factor",
  meanSD = TRUE,
  quantiles = c(0.025, 0.25, 0.5, 0.75, 0.975),
  savetxt = TRUE,
  filename = "summary_statistics"
)

Arguments

combined	list, output from combine_sources function
toprint	vector, which parameters to print? Options are: "p" to print stats for proportions only (all factors), "global" to only print overall proportions, "fac1" to only print factor 1 proportions, "fac2" to print factor 2 proportions. Set = "epsilon" to print multiplicative error term only. Default = "all", prints stats for all model parameters.
groupby	character, group stats by "factor" or "source"? I.e. in wolves example, group proportions by Region 1, Region 2, Region 3 (groupby="factor") vs. Deer, Marine Mammals, Salmon (groupby="source"). Currently only "factor" is implemented.
meanSD	TRUE/FALSE, print mean and SD for the parameters?
quantiles	vector, which quantiles to print. Default = c(0.025, 0.25, 0.5, 0.75, 0.975).
savetxt	TRUE/FALSE, save results as .txt file (in working directory)?
filename	character, file name to save results as (.txt will be appended automatically)

See Also

combine_sources and plot_intervals

Examples

## Not run: 
# first run mantis shrimp example
# combine 6 sources into 2 groups of interest (hard-shelled vs. soft-bodied)
#   'hard' = 'clam' + 'crab' + 'snail'           # group 1 = hard-shelled prey
#   'soft' = 'alphworm' + 'brittlestar' + 'fish' # group 2 = soft-bodied prey
combined <- combine_sources(jags.1, mix, source, alpha.prior=alpha, 
                groups=list(hard=c("clam","crab","snail"), soft=c("alphworm","brittlestar","fish")))

summary_stat(combined)
summary_stat(combined, savetxt=FALSE)
summary_stat(combined, meanSD=FALSE)
summary_stat(combined, quantiles=c(.05,.5,.95))
summary_stat(combined, toprint="fac1")
summary_stat(combined, toprint="p")
summary_stat(combined, toprint="global")

## End(Not run)

brianstock/MixSIAR documentation built on Oct. 23, 2020, 4:48 a.m.