inst/doc/wolves_ex.R

In MixSIAR: Bayesian Mixing Models in R

## ---- eval=FALSE--------------------------------------------------------------
#  library(MixSIAR)
#  mixsiar.dir <- find.package("MixSIAR")
#  paste0(mixsiar.dir,"/example_scripts")

## ---- eval=FALSE--------------------------------------------------------------
#  source(paste0(mixsiar.dir,"/example_scripts/mixsiar_script_wolves.R"))

## -----------------------------------------------------------------------------
library(MixSIAR)

## -----------------------------------------------------------------------------
# Replace the system.file call with the path to your file
mix.filename <- system.file("extdata", "wolves_consumer.csv", package = "MixSIAR")

# Load the mixture/consumer data
mix <- load_mix_data(filename=mix.filename, 
                     iso_names=c("d13C","d15N"), 
                     factors=c("Region","Pack"), 
                     fac_random=c(TRUE,TRUE), 
                     fac_nested=c(FALSE,TRUE), 
                     cont_effects=NULL)

## -----------------------------------------------------------------------------
# Replace the system.file call with the path to your file
source.filename <- system.file("extdata", "wolves_sources.csv", package = "MixSIAR")

# Load the source data
source <- load_source_data(filename=source.filename,
                           source_factors="Region", 
                           conc_dep=FALSE, 
                           data_type="means", 
                           mix)

## -----------------------------------------------------------------------------
# Replace the system.file call with the path to your file
discr.filename <- system.file("extdata", "wolves_discrimination.csv", package = "MixSIAR")

# Load the discrimination/TDF data
discr <- load_discr_data(filename=discr.filename, mix)

## ---- eval=FALSE--------------------------------------------------------------
#  # Make an isospace plot
#  plot_data(filename="isospace_plot", plot_save_pdf=TRUE, plot_save_png=FALSE, mix,source,discr)

## -----------------------------------------------------------------------------
# Calculate the convex hull area, standardized by source variance
calc_area(source=source,mix=mix,discr=discr)

## ---- eval=FALSE--------------------------------------------------------------
#  # default "UNINFORMATIVE" / GENERALIST prior (alpha = 1)
#  plot_prior(alpha.prior=1,source)

## ---- eval=FALSE--------------------------------------------------------------
#  # Write the JAGS model file
#  model_filename <- "MixSIAR_model.txt"   # Name of the JAGS model file
#  resid_err <- TRUE
#  process_err <- TRUE
#  write_JAGS_model(model_filename, resid_err, process_err, mix, source)

## ---- eval=FALSE--------------------------------------------------------------
#  run <- list(chainLength=200000, burn=150000, thin=50, chains=3, calcDIC=TRUE)

## ---- eval=FALSE--------------------------------------------------------------
#  jags.1 <- run_model(run="test", mix, source, discr, model_filename)

## ---- eval=FALSE--------------------------------------------------------------
#  jags.1 <- run_model(run="normal", mix, source, discr, model_filename)

## ---- eval=FALSE--------------------------------------------------------------
#  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 = FALSE)

## ---- eval=FALSE--------------------------------------------------------------
#  output_JAGS(jags.1, mix, source, output_options)