Update NEWS to use markdown

2 files changed, 76 insertions, 152 deletions

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-
-Changes in version 1.5.2 (2021-06-18)
-
- * Remove View function due to problematic interactions with RStudio
-
- * Improvements to traceplot and densityplot
-
- * Make sure output is reproducible when parallel=FALSE
-
- * Minor bugfixes
-
-Changes in version 1.5.1 (2019-07-30)
-
- * Fix issue when chains adapted for different numbers of iterations
-
- * Fix crash when DIC was requested but JAGS couldn't calculate it
-
- * Stop auto-converting 1 row/1 col matrices into vectors
-
- * Improve pp.check plotting function
-
- * Add some warnings about functions and arguments that will be deprecated soon
-
-Changes in version 1.5.0 (2018-09-09)
-
- * Fix issues with NAs in parameters.
-
- * Fix missing arguments in autojags().
-
- * Handle errors in output processing so that samples are not lost completely.
-
- * Make sure a specified random seed is used for initial value functions.
-
- * Fix error where summary stats were printed in the wrong order for some parameters.
-
- * Don't collapse 1 row/1col matrices into vectors automatically.
-
-Changes in version 1.4.9 (2017-12-08)
-
- * Fix bug with DIC output introduced in 1.4.7.
-
-Changes in version 1.4.8 (2017-11-17)
-
- * Minor changes to prep for CRAN submission.
-
-Changes in version 1.4.7 (2017-08-17)
-
- * Fix more issues with random seeds and problems with DIC.
-
-Changes in version 1.4.6 (2017-05-26)
-
- * Fix issue with setting seed affecting other random number generation.
-
-Changes in version 1.4.5 (2017-02-08)
-
- * Allow turning deviance/DIC monitoring on/off when updating an existing model. Overhaul handling of adaptation; default to running a sequence of adapt() calls until JAGS reports adapation is adequate. Suggest minimum of 1000 adaptation iterations otherwise in man pages. Change output of summary function. Add ability to control factories.
-
-Changes in version 1.4.4 (2018-11-10)
-
- * Change default approach to generating random seeds. Add S3 method for View() and convert traceplot() to an S3 method from S4.
-
-Changes in version 1.4.3 (2016-09-15)
-
- * Fix to allow running in parallel when dependencies are in non-standard libraries. Fix bug when updating jagsbasic class.
-
-Changes in version 1.4.2 (2016-02-21)
-
- * Changes to NAMESPACE to get clean build check on R-devel.
-
-Changes in version 1.4.1 (2016-02-20)
-
- * Add ability to specify number of CPU cores to use when running in parallel.
-
-Changes in version 1.4.0 (2016-02-10)
-
- * Fix a problem where saving output for a single scalar parameter broke output processing.
-
-Changes in version 1.3.9 (2016-01-21)
-
- * Fix a problem where nonscalar estimated parameters with missing (i.e., non-estimated) values broke the display of summary stats.
-
-Changes in version 1.3.8 (2015-07-13)
-
- * Explicitly import functions from default packages to meet new standards for building with R-devel. Change minimum required version of rjags to 3-13.
-
-Changes in version 1.3.7 (2015-06-11)
-
- * Add verbose argument to functions to allow suppression of all text output in the console as the function runs.
-
-Changes in version 1.3.6 (2015-05-06)
-
- * Change method for closing connection to clusters when running in parallel to avoid closing unrelated connections. Adjust output for jags.basic.
-
-Changes in version 1.3.5 (2015-03-26)
-
- * Fix problem with max.iter argument in autojags(). Clarify documentation and output for autojags().
-
-Changes in version 1.3.4 (2015-03-21)
-
- * Add option save.all.iter in autojags() function to combine MCMC samples from all iterative updates into final posterior.
-
-Changes in version 1.3.3 (2015-02-24)
-
- * Fix issue with calculating stats that sometimes occurred with a constant posterior distribution.
-
-Changes in version 1.3.2 (2015-01-29)
-
- * Fix error where autojags did not handle NA rhat values properly. Added more helpful warning when at least one rhat value = NA.
-
-Changes in version 1.3.1 (2015-01-15)
-
- * Minor wording changes.
-
-Changes in version 1.3 (2014-12-01)
-
- * Add warning and fix issue with traceplot when number of saved iterations after thinning was rounded up by JAGS (because it wasn't an integer). Several small fixes to clean up code and get R CMD check to run cleanly.
-
-Changes in version 1.2 (2014-11-19)
-
- * Add some failsafes/warnings.
-
-Changes in version 1.1 (2014-07-28)
-
- * Clean up / modularize code. Add an auto-updating function autojags(). Several small bugfixes.
-
-Changes in version 1.00 (2014-05-21)
-
- * Update to new package name ('jagsUI'). Implement update function. Bugfixes. Final release prior to CRAN upload.
-
-Changes in version 0.01-7 (2014-05-12)
-
- * Fix setting the random seed so it actually works. Allow running MCMC chains in parallel. Various bugfixes.
-
-Changes in version 0.01-6 (2014-05-09)
-
- * Overhaul calculation of statistics to speed things up. Minor bugfixes.
-
-Changes in version 0.01-5 (2014-05-06)
-
- * Bugfixes. Changed primary function name to 'jags' from 'simplejags' for simplicity. Also edited several other function names. Added a summary table to the output object.
-
-Changes in version 0.01-4 (2014-05-01)
-
- * Improve processing of input data to avoid some common errors. Changed traceplots() function to traceplot() to be more consistent with similar packages. Added ability to calculate DIC and pD for JAGS models. Cleaned up the print method.
-
-Changes in version 0.01-3 (2014-04-17)
-
- * Simplify output object so that indexed parameters are contained in their own array rather than many separate list objects. Adjust other functions to match this change. Clean up the printed text / progress bars in R console.
-
-Changes in version 0.01-2 (2014-04-08)
-
- * Fix problem where some components of output object were vectors instead of lists (and change print function accordingly). Add option for simplejags() to save input data and initial values in model output object for future use (store.data).
diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 0000000..3f936d0
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,76 @@
+# jagsUI 1.6.0
+
+ * Extensive refactoring of internal code
+ * Don't drop output dimensions when only one parameter saved
+ * Summary method now returns the summary matrix
+ * Add tests
+ * Add vignette
+
+# jagsUI 1.5.2
+
+ * Remove View function due to problematic interactions with RStudio
+ * Improvements to traceplot and densityplot
+ * Make sure output is reproducible when parallel=FALSE
+ * Minor bugfixes
+
+# jagsUI 1.5.1
+
+ * Fix issue when chains adapted for different numbers of iterations
+ * Fix crash when DIC was requested but JAGS couldn't calculate it
+ * Stop auto-converting 1 row/1 col matrices into vectors
+ * Improve pp.check plotting function
+ * Add some warnings about functions and arguments that will be deprecated soon
+
+# jagsUI 1.5.0
+
+ * Fix issues with NAs in parameters.
+ * Fix missing arguments in autojags().
+ * Handle errors in output processing so that samples are not lost completely.
+ * Make sure a specified random seed is used for initial value functions.
+ * Fix error where summary stats were printed in the wrong order for some parameters.
+ * Don't collapse 1 row/1col matrices into vectors automatically.
+
+# jagsUI 1.4.9
+
+ * Fix bug with DIC output introduced in 1.4.7.
+
+# jagsUI 1.4.8
+
+ * Minor changes to prep for CRAN submission.
+ * Fix more issues with random seeds and problems with DIC.
+ * Fix issue with setting seed affecting other random number generation.
+ * Allow turning deviance/DIC monitoring on/off when updating an existing model.
+ * Overhaul handling of adaptation; default to running a sequence of adapt() calls until JAGS reports adapation is adequate. Suggest minimum of 1000 adaptation iterations otherwise in man pages. 
+ * Change output of summary function. Add ability to control factories.
+
+# jagsUI 1.4.4
+
+ * Change default approach to generating random seeds. 
+ * Add S3 method for View() 
+ * Convert traceplot() to an S3 method from S4.
+ * Fix to allow running in parallel when dependencies are in non-standard libraries. 
+ * Fix bug when updating jagsbasic class.
+
+# jagsUI 1.4.2
+
+ * Changes to NAMESPACE to get clean build check on R-devel.
+ * Add ability to specify number of CPU cores to use when running in parallel.
+ * Fix a problem where saving output for a single scalar parameter broke output processing.
+ * Fix a problem where nonscalar estimated parameters with missing (i.e., non-estimated) values broke the display of summary stats.
+ * Explicitly import functions from default packages to meet new standards for building with R-devel. 
+ * Change minimum required version of rjags to 3-13.
+
+# jagsUI 1.3.7
+
+ * Add verbose argument to functions to allow suppression of all text output in the console as the function runs.
+ * Change method for closing connection to clusters when running in parallel to avoid closing unrelated connections.
+ * Adjust output for jags.basic.
+ * Fix problem with max.iter argument in autojags(). Clarify documentation and output for autojags().
+ * Add option save.all.iter in autojags() function to combine MCMC samples from all iterative updates into final posterior.
+ * Fix issue with calculating stats that sometimes occurred with a constant posterior distribution.
+ * Fix error where autojags did not handle NA rhat values properly.
+ * Added more helpful warning when at least one rhat value = NA.
+
+# jagsUI 1.3.1
+
+ * Initial CRAN upload.