added inst/doc to GitHub so can link vignettes

.gitignore

@@ -1,4 +1,3 @@
 .Rproj.user
 .Rhistory
 .RData
-inst/doc

R/load_mix_data.R

@@ -5,8 +5,12 @@
 #'
 #' @param filename csv file with the mixture/consumer data
 #' @param iso_names vector of isotope column headings in 'filename'
-#' @param random_effects vector of random effect column headings in 'filename'
-#' @param fixed_effects vector of fixed effect column headings in 'filename',
+#' @param factors vector of random/fixed effect column headings in 'filename'.
+#'          NULL if no factors.
+#' @param fac_random vector of TRUE/FALSE, TRUE if factor is random effect, FALSE
+#'          if fixed effect. NULL if no factors.
+#' @param fac_nested vector of TRUE/FALSE, TRUE if factor is nested within the
+#'          other. Only applies if 2 factors. NULL otherwise.
 #' @param cont_effects vector of continuous effect column headings in 'filename'
 #'
 #' @return \code{mix}, a list including:

inst/doc/geese_ex.R

@@ -0,0 +1,96 @@
+## ------------------------------------------------------------------------
+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,
+#                      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)
+
+## ---- eval=FALSE---------------------------------------------------------
+#  output_JAGS(jags.1, mix, source, output_options)
+