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_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)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.