finished wolves and geese vignettes

brianstock · Mar 11, 2016 · e1911f3 · e1911f3
1 parent fab6561
commit e1911f3
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Showing 7 changed files with 143 additions and 507 deletions.
diff --git a/inst/doc/geese_ex.R b/inst/doc/geese_ex.R
@@ -4,39 +4,36 @@ mixsiar.dir <- find.package("MixSIAR")
 paste0(mixsiar.dir,"/example_scripts")
 
 ## ---- eval=FALSE---------------------------------------------------------
-#  source(paste0(mixsiar.dir,"/example_scripts/mixsiar_script_wolves.R"))
+#  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", "wolves_consumer.csv", package = "MixSIAR")
+mix.filename <- system.file("extdata", "geese_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)
+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", "wolves_sources.csv", package = "MixSIAR")
+source.filename <- system.file("extdata", "geese_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)
+						   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", "wolves_discrimination.csv", package = "MixSIAR")
+discr.filename <- system.file("extdata", "geese_discrimination.csv", package = "MixSIAR")
 
-# Load the discrimination/TDF data
 discr <- load_discr_data(filename=discr.filename, mix)
 
 ## ---- eval=FALSE---------------------------------------------------------
@@ -53,43 +50,18 @@ calc_area(source=source,mix=mix,discr=discr)
 
 ## ---- eval=FALSE---------------------------------------------------------
 #  # Write the JAGS model file
-#  model_filename <- "MixSIAR_model.txt"   # Name of the JAGS model file
+#  model_filename <- "MixSIAR_model.txt"
 #  resid_err <- TRUE
-#  process_err <- TRUE
+#  process_err <- FALSE
 #  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,
 #                      alpha.prior = 1, resid_err, process_err)
 
 ## ---- eval=FALSE---------------------------------------------------------
-#  jags.1 <- run_model(run="normal", mix, source, discr, model_filename,
-#                      # alpha.prior = 1, resid_err, process_err)
-
-## ---- 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)
+#  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)