Nothing
## ---- eval=FALSE--------------------------------------------------------------
# library(MixSIAR)
# mixsiar.dir <- find.package("MixSIAR")
# paste0(mixsiar.dir,"/example_scripts")
## ---- eval=FALSE--------------------------------------------------------------
# source(paste0(mixsiar.dir,"/example_scripts/mixsiar_script_geese.R"))
## -----------------------------------------------------------------------------
library(MixSIAR)
## -----------------------------------------------------------------------------
# Replace the system.file call with the path to your file
mix.filename <- system.file("extdata", "geese_consumer.csv", package = "MixSIAR")
mix <- load_mix_data(filename=mix.filename,
iso_names=c("d13C","d15N"),
factors="Group",
fac_random=FALSE,
fac_nested=FALSE,
cont_effects=NULL)
## -----------------------------------------------------------------------------
# Replace the system.file call with the path to your file
source.filename <- system.file("extdata", "geese_sources.csv", package = "MixSIAR")
source <- load_source_data(filename=source.filename,
source_factors=NULL,
conc_dep=TRUE,
data_type="means",
mix)
## -----------------------------------------------------------------------------
# Replace the system.file call with the path to your file
discr.filename <- system.file("extdata", "geese_discrimination.csv", package = "MixSIAR")
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"
# resid_err <- TRUE
# process_err <- FALSE
# write_JAGS_model(model_filename, resid_err, process_err, mix, source)
## ---- eval=FALSE--------------------------------------------------------------
# jags.1 <- run_model(run="test", mix, source, discr, model_filename,
# alpha.prior = 1, resid_err, process_err)
## ---- eval=FALSE--------------------------------------------------------------
# jags.1 <- run_model(run="short", mix, source, discr, model_filename,
# alpha.prior = 1, resid_err, process_err)
## ---- eval=FALSE--------------------------------------------------------------
# output_JAGS(jags.1, mix, source, output_options)
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