This file lists notable changes to Tetrad IV since version 4.3.6.

4.3.6

* Rendered Bayes updater interface less clunky. Fixed the problem of category
buttons not shading correctly in Java 1.5 and Macs. Added a notification to let
the user know when they're trying to update a Bayes IM that's not completely
specified.

* Repaired the help button for searches so that it actually opens up the help
file for those searches. Corrected help files for most searches.

* Lined up columnar output in regression editor for platforms in which it was
not lined up.

* Specified null hypotheses for SEM chi square tests where used in the
interface (SEM estimator, parameters tab of pattern searches).

* Removed some items from the interface that weren't working correctly: Logistic
regression, Structural EM, CEFS. (These will be re-added when the underlying
issues are fixed.)

4.3.6-1

* Added this change log to the downloads page.

* Improved the discretizer some. If no variables are selected, all variables are
discretized. The displayed number of categories is now synced with the number
of bins displayed for discretizing continuous data.

* Changed "unfaithful" to "ambiguous" for CPC, to reflect the fact that for
finite sample sizes it's detecting (and underlining) examples of near-unfaithfulness,
not necessarily unfaithfulness per se. (Made similar change to CFCI.)

* Fixed knowledge in FCI so that if X<-oY and Forbidden(X-->Y), the edge will
be oriented as X<->Y.

* Modified the case expander so that it can expand cases for mixed data set.

* Reorganized the tools menu of the Data Editor a bit and added a gadget to
split datasets by cases.

4.3.6-2

* Put the BPC algorithm back from last August to fix a subtle bug in recent
versions.

* Modified reading for discrete data so that categories for defined variables
are treated as fixed. For example, if a variable X is defined to have categories
"true" and "false," and in the data column for X the string "red" appears, this
string is treated as a missing value for the column rather as an additional
category for the column. Also, in variable definitions, the syntax for a
definition of categories is changed from X:0=off,1=on to X:off,on.

* Any session node that in the editor interface edits parameter values has been
tagged as un uncancellable operation for now so that parameter values can be
passed to the simulation algorithm. Hopefully a better way of doing this will
be conceived of eventually.

4.3.6-6

* Modified simulation study behavior so that it logs while traversing the
execution tree. This involved adding logging behavior to relevant modules,
including updating.

* Fixed knowledge bug in PC. Now knowledge is invoked to determine whether a
set S of variables consists entirely of potential parents of X or potential
parents of Y, before using that set as a conditioning set to remove the edge
from X to Y. Previously, it was insisted that S consist of potential parents
of both X and Y.

4.3.6-7

* Fixed a bug in use of knowledge in PC. Used to be that for removing A---B,
it was insisted that variables in the conditioning set be potential parents
of both A and B. Now it is insisted that they all be potential parents of A or
of B.

* Added a gadget to interpolate means of columns for missing values in the
data editor.

* Added support in SEM IM to automatically enter and calculate variable
intercepts for acyclic models. The underlying model is still parameterized
using variable means, so the intercepts are calculated.

* Added GUI support for viewing either means or intercepts in the SEM IM Editor
for acyclic SEMs. Fixed some old labeling problems for popup mean editors.

* A bug in the construction of SEM PM's was fixed. When a graph was provided
for constructing a SEM PM that contained edges not directed or bidirected,
these edges were stripped from the graph. Now an exception is thrown.

4.3.6-8

* Add new data loading interface to support mixed tabular data loading, and
faster loading of large discrete data sets, among other things.

* Fixed bug in classifier, in which the target of classification was required
to be in the test set for Bayesian classification.

4.3.6-9

* Added knowledge sensitivity to MBFS.

* Added stats tabs for discrete pattern-based searches.

* Added tool to pattern-producing search editors to let the user automatically
add orientations implied by local orientation changes.

* Added an experimental score-based reorientation procedure.

* Added checks for tabular data checks and covariance matrices so that if
these are manually edited, downstream models (like searches) are invalidated.

* Added a rudimentary graph history mechanism to the pattern searches.

* Fixed bug where when classifier editor was closed and reopened, recent
classifications were no longer displayed.

* Added "graph properties" menu item to pattern searches.

* Modified the layered drawing layout so that it lays out all connected
components and does some heuristic edge uncrossing for successive tiers.

4.3.7-0

Stable version--no changes.

4.3.7-1

* Added checks for missing values for continuous independence tests.

* Fixed bug in data editor in which empty data tabs were sometimes inserted
into the list.

* Added tool to do a global score-based reorientation for pattern-producing
searches.

* Moved the "close tab" feature in data editor to a right click on the tab to
be closed.

* Modified the missing data injector so that it works with mixed data sets.

* Clarified use of missing data in data editor and algorithms by writing a help
page and adding missing value checks to algorithms that don't explicitly
handle missing data.

* Fixed the parameter editor preventing EM Bayes Estimator from working in the
interface.

* Added a show/hide error term feature to the SEM IM editor.

* Added a regression missing data imputer to the data editor.

* In the SEM estimator, prefaced the gradient ascent optimizer by the
regression optimizer to give it a better starting point for cyclic models.

* Modified regression interpolator algorithm.

4.3.7-2

* Modified data loading algorithms so that initial spaces in lines are ignored.

* Changed name of Meek orient menu item back to Meek orient.

* Adjusted "whitespace" delimiter to include all whitespace characters. Adjusted
other delimiters to not automatically strip leading and trailing whitespace.

4.3.7-3

* Fixed DAGs in Pattern tool so that it works for GES.

* Fixed intermittent bug in SEM graph where exogenous nodes were sometimes
being returned as null.

* Added a copy graph gadget to the DAGs in Pattern.

* Added bidirected and undirected edge highligher tools to graph editors and
PC/GES search editors.

* Changed instruction for Bootstrap Sample to read, "with replacement."

4.3.7-4

* Added histograms for the data editor.

4.3.7-5

* Improved the interface for Multiple Linear Regression and Logistic Regression
with drag-and-drop variable selectors.

4.3.7-6

* Added menu item in PC/GES search editor to choose an arbitrary DAG in
a pattern.

* Moved items from Data-->Tools menu to a new Data Manipulation box,
including bootstrap sampler, discretizer, and several others. Changed some
editors to accomodate.

* Buttons re-added to regression editors to move variables.

* Added a tree view model selector for nodes with many models (e.g. data manip,
search).

* Switched the internal configuration to an XML file.

* Added menu item to save out histogram image.

* Fixed show/hide error terms problem in SEM PM.

* Fixed bug where variance parameters and values were not being shown in the
SEM PM and IM editors.

* Added Other Groups feature to knowledge editor.

* Revised the discretizer editor.

* Revised the regression editor to allow both drag-and-drop and button-press
variable moves.

4.3.7-7

* Fixed a bug preventing Bayes updater from working.

* Added MMHC (with GES in place of HC) to Tetrad; commented out of interface
for now.

4.3.8-0

4.3.8-1

* Problems of binding correct parameters to correct editors in SEM PM and SEM IM
fixed.

* New logging facility added that lets user log specific events.

4.3.8-4

* Rewrite tabular regression model and added covariance regression model.

* Fixed problem of not being able to run Purify, BPC, and Mimbuild from
covariance matrices.

4.3.8-6

--Uh, forgot to add several things. Will try to go back and add them.

* Changed data saver so that it can save out mixed data.

### INTERIM VERSION; MORE CHANGES WILL BE POSTED AS THEY ARE MADE ###