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MixSIAR 3.1.12.9000

MINOR IMPROVEMENTS

  • split output_JAGS function into several functions that can return objects for later manipulation #235

MixSIAR 3.1.12

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

MixSIAR 3.1.11

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

MixSIAR 3.1.10

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

MixSIAR 3.1.9

Nothing changed, just trying to get new Zenodo DOI (3.1.8 failed)

MixSIAR 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

MixSIAR 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

MixSIAR 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

MixSIAR 3.1.7 (2016-08-15)

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)

MixSIAR 3.1.6 (2016-06-24)

VERY MINOR IMPROVEMENTS

  • CRAN submission
  • added files for CRAN submission (cran-comments.md, NEWS.md)
  • fixed broken links found when checking for CRAN submission

MixSIAR 3.1.5 (2016-06-21)

VERY MINOR IMPROVEMENTS

  • Changed "Isotopes" to "Tracers" in GUI

MixSIAR 3.1.4 (2016-06-21)

BUG FIX

  • Fixed bug #72 by using utils::globalVariables(), created when making changes to pass R CMD check for CRAN submission

MixSIAR 3.1.3 (2016-06-01)

MINOR IMPROVEMENTS

  • Tests via testthat package (see "tests/testthat" folder)
  • Changes to pass R CMD check for submission to CRAN

MixSIAR 3.1.2 (2016-03-16)

MINOR IMPROVEMENTS

  • download latest release by default (instead of master)
  • updated citation info

MixSIAR 3.1.1 (2016-03-11)

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

MixSIAR 3.1.0 (2016-03-09)

NEW FEATURES

  • Converted to R package structure, so can now run MixSIAR with:

library(MixSIAR) mixsiar_gui()

MixSIAR 3.0.2 (2015-11-19)

BUG FIX

  • Problem loading mix/consumer data in the GUI version (#48)

MixSIAR 3.0.1 (2015-10-29)

BUG FIX

  • Fixed an error that applies with source data = means and the "Resid*Process" error structure (affects Wolves, Killer whale, and Isopod examples)

MixSIAR 3.0.0 (2015-10-29)

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