Changes in version 3.1.12.9000 MINOR IMPROVEMENTS - split output_JAGS function into several functions that can return objects for later manipulation #235 Changes in version 3.1.12 (2020-10-20) MINOR IMPROVEMENTS - plot_continuous_var() has new arguments alphaCI (sets credible interval width) and exclude_sources_below, which allows you to remove sources from the plot whose median proportion is below a specified level for all values of the continuous variable (i.e. only plot sources with median contributions above 5%). BUG FIX - Fixed two bugs in plot_continuous_var() #198 and #212 Changes in version 3.1.11 (2020-05-13) MAJOR CHANGE For MixSIAR to remain on CRAN, had to remove the mixsiar_gui() function. mixsiar_gui() is now found in the new GitHub-only package MixSIARgui. devtools::install_github("brianstock/MixSIARgui", dependencies=T) # installs MixSIAR as dependency library(MixSIARgui) # also loads MixSIAR mixsiar_gui() MINOR IMPROVEMENTS - Allow output_JAGS() to suppress diagnostic pdf plots with output_options$diag_save_ggmcmc = FALSE - Allow plot_data() to return the ggplot object so that it can be modified by the user - 2 tweaks to make it clearer which sources receive which weights when using an informative prior - source names appear in plots from plot_prior() function - warning message that asks users to confirm the informative prior matches their alpha vector - Update/fix alligator ex - moved calc_eps() - add code to plot cont effect + random effects of individuals (mixsiar_script_alligator_length_ind.R) BUG FIX - Fix error when combining sources with > 9 sources Changes in version 3.1.10 (2018-04-13) MINOR IMPROVEMENTS - fixed minor mistakes in manual (new example datasets table) - scale mix and source tracer data (so can always use same priors regardless of scale of data) - update compare_models to work with loo 2.0.0 Changes in version 3.1.9 (2018-03-30) Nothing changed, just trying to get new Zenodo DOI (3.1.8 failed) Changes in version 3.1.8 MINOR IMPROVEMENTS - updated manual - new example: alligator diet, model comparison table with LOO/WAIC weights - new example: mantis shrimp diet, informative priors + combining sources - new function 'compare_models' to perform model selection based on LOO/WAIC weights, via 'loo' package - new function 'combine_sources' to aggregate sources a posteriori - new function 'summary_stat' to print summary of posterior after combining sources - new function 'plot_intervals' to plot CI of posterior after combining sources Changes in version 3.1.7.9001 MINOR IMPROVEMENTS - Removed attach.jags call (now directly use jags.1$BUGSoutput$sims.list) - Added epsilon (multiplicative error term) estimates to output (summary stats, posterior plots) BUG FIX - Fixed bug #129 by using MCMCpack::rdirichlet instead of compositions::rDirichlet.rcomp - Small changes to pass R CMD check Changes in version 3.1.7.9000 MINOR IMPROVEMENTS - Improved continuous effect output plots: 1) added 95% CI shading, 2) plot each level of fixed effect - Fixed bug with 1FE + 1RE: empty levels Heidelberger diagnostic (#100) - Fixed bug with 1FE + 1RE: posterior density plots saved over themselves - Added return value for output_JAGS function: now returns p.both if 1FE + 1RE VERY MINOR IMPROVEMENTS - Added check/error message: if sources by factor, sources must match for all factor levels - Updated CITATION and manual Changes in version 3.1.7 (2016-08-23) MINOR IMPROVEMENTS - Changed resid.prop prior from dchisqr(3) to dunif(0,20) VERY MINOR IMPROVEMENTS - Updated install instructions in README (install.packages) - Fixed error in Cladocera vignette (process vs. resid error) - Fixed link to manual to CRAN page (DESCRIPTION file) Changes in version 3.1.6 (2016-06-25) VERY MINOR IMPROVEMENTS - CRAN submission - added files for CRAN submission (cran-comments.md, NEWS.md) - fixed broken links found when checking for CRAN submission Changes in version 3.1.5 VERY MINOR IMPROVEMENTS - Changed "Isotopes" to "Tracers" in GUI Changes in version 3.1.4 BUG FIX - Fixed bug #72 by using utils::globalVariables(), created when making changes to pass R CMD check for CRAN submission Changes in version 3.1.3 MINOR IMPROVEMENTS - Tests via testthat package (see "tests/testthat" folder) - Changes to pass R CMD check for submission to CRAN Changes in version 3.1.2 MINOR IMPROVEMENTS - download latest release by default (instead of master) - updated citation info Changes in version 3.1.1 NEW FEATURES - Added vignettes for script examples, see browseVignettes("MixSIAR") MINOR IMPROVEMENTS - Tested package install on Windows, Mac, Linux - Revised install instructions - Couple minor bug fixes - Revised manual Changes in version 3.1.0 NEW FEATURES - Converted to R package structure, so can now run MixSIAR with: library(MixSIAR) mixsiar_gui() Changes in version 3.0.2 BUG FIX - Problem loading mix/consumer data in the GUI version (#48) Changes in version 3.0.1 BUG FIX - Fixed an error that applies with source data = means and the "Resid*Process" error structure (affects Wolves, Killer whale, and Isopod examples) Changes in version 3.0.0 NEW FEATURES - error structures now multivariate, with 3 options: "Residual only", "Residual * Process", "Process only (N=1)" - fixed coding of fixed effects (cases with 2FE, 1FE + 1RE) - new function plot_prior to plot uninformative vs. informative priors (included in GUI) - new function calc_area to calculate Brett (2014) normalized surface area - normalized continuous covariate - MCMC chains given different initial values (#35) - added new examples with fatty acids - new manual