# dsem 2.0.1

* Fix an "out-of-bounds read" error identified by SAN
* Change NA to -1 for RAM passed as DATA_IMATRIX, because NA or NA_integer_ triggered a clang-ASAN
  WARNING "/TMB/include/convert.hpp:139:23: runtime error: nan is outside the range of representable values of type 'int'"
* Added a GitHub Action ./github/workflows/sanitizers-novignettes-auto.yaml that uses `error_on = "warning"` to 
  detect either "out-of-bounds" or "nan is outside the range" issues
* Remove `as_sem(.)` because `sem::sem(.)` appears to cause a UBSAN warning, and removing `sem` from IMPORTS

# dsem 2.0.0

* Changing `gmrf_parameterization = "gmrf_project"`, given V = t(G)*G,
  to invert Vinv = invertSparseMatrix(V) where Vinv is then dense and then 
  casting Vinv2 = asSparseMatrix( Vinv ),
  rather than a sparseLDLT for solve( V, I-P ), because the latter seems numerically
  unstable when P has a high condition number (e.g., the moose-wolf vignette in tinyVAST)
* Add option to specify a path based fixed at another variable
* Renamed `gmrf_parameterization = "conditional_krig"` as 
  `gmrf_parameterization = "mvn_project"` and confirmed it in simple case
* Renamed `gmrf_parameterization = "separable"` as `full` and `projection`
  as `project`
* Fixed bug where `predict` for `type="link"` was pulling `x_tj` rather than `z_tj`
  and therefore was missing the initial conditions, mean value, and only worked
  for `gmrf_parameterization = "separable"`
* Add `stabilize_Q` option to `dsem_control`, adding a diagonal component to 
  t(Gamma)*Gamma to ensure it's PD
* Added `gmrf_parameterization = "gmrf_project"` (which maintains sparsity
  while allowing latent variables with zero exogenous variance, or manifest
  variables with measurement error and zero exogenous variance), and which automatically
  switches to `separable` if no variables have zero variance
* Added an integrated test confirming that `gmrf_project`, `mvn_project` and `separable`
  (with a small extra non-zero variance inflation) are all identical in a logistic
  regression that involves loops (i.e., zero-variance for intermediate latent variable)
* Switching `dsem_control` to use `gmrf_parameterization = "gmrf_project"` 
  as default
* Turned off integrated-tests for `dsemRTMB` (which threw an error with updates
  to RTMB, and is not being used anyway)

# dsem 1.7.0

* Add option to turn off useless `NA/NaN function evaluation` function evaluations
  from `nlminb` (enabled by default, but overriden in `dsem_control`)
* Use `Matrix::bandSparse` to simplify logic in `make_matrices`
* Add experimental function `partition_variance`
* Extend `total_effect` to compute result for either pulse or press experiment
* Adding exploratory option `gmrf_parameterization = "conditional_krig"` that 
  excludes `family = "fixed"` variables from the GMRF density calculation 
  while still conditioning upon their value(s)

# dsem 1.6.0

* Export and document `make_matrices`
* Remove `ggm` from Imports (because it Imports `graph` which is not on CRAN)
  and instead define a locally copy of relevant functions.  Also adding Giovanni M.
  Marchetti (the maintainer of `ggm` as contributor in DESCRIPTION)
* Update `test_dsep(.)` to allow options for imputing missing data prior to test,
  and using default `impute_data = "by_test"` based on explorations to date
* Add example for `total_effect`
* Adding "model structura" vignette and re-organizing pkgdown page

# dsem 1.5.0

* Add option to simulate data with or without missingness pattern of original data
* Change `test_dsep(.)` to have option to impute missing data, and changing that
  to be the default behavior

# dsem 1.5.0

* Fix bug when adding missing variances (PR 36)
* Fix bug in detecting high ratio of variances (issue 35)
* Added `test_dsep(.)` to calculate a p-value for the probability that a
  a data set arose from the specified model (highly experimental)
* Added `total_effect(.)` to calculate total effects
* Fixed bug where dsem crashed when `quiet = FALSE` and running without data
  e.g., as qualitative network model
* Added vignette showing how to approximate diffusive movement using DSEM with
  paths among adjacent strata

# dsem 1.4.1

* Edits to allow DSEM to run when all path coefficients are fixed 
  (contributed by Maurice Goodman)

# dsem 1.4.0

* Adding option for lower and upper bounds
* Adding `stepwise_selection` for automated stepwise model selection
* Adding `plot` option to use `ggraph` as alternative to previous `igraph`
  option
* Adding `convert_equations` to extend `sem::specifyEquations` and simplify
  specification for large models
* Adding argument `prior_negloglike` as interface to specify Bayesian priors
  and/or likelihood penalties in `dsem`
* Adding `dsemRTMB` using RTMB as interchangeable alternative to `dsem` using
  TMB

# dsem 1.3.0

* Adding option to specify constant marginal variance, as alternative to existing
  calculation which results in a constant conditional variance but a changing marginal 
  variance along the causal graph

# dsem 1.2.1

* removing `checkDepPackageVersion(dep_pkg="Matrix", this_pkg="TMB")` from `.onLoad()`
  as requested by K. Kristensen

# dsem 1.2.0

* Adding option to specify covariance via argument `covs`
* Adding options to specify gmrf_parameterization="projection"
* Adding vigette outlining how to fit dynamic factor analysis
* Fix bug arising when `tsdata` had two or more columns sharing a single variable name
* Adding `make_dfa` helper function
* Updating bering_sea dataset to include extra year of cold-pool, and changing vignette
  to match the published specification and results
* Updating the lag indexing for the Klein-I model in the vignette to use positive values
  for lags, and updating saved MCMC results to match that corrected specification

# dsem 1.1.0

* Adding option to specify covariance in Gamma

# dsem 1.0.2

* Eliminate `eval` usage
* Add codecov Action and badge
* Change default behavior so that all variables in `tsdata` have a standard
  deviation by default

# dsem 1.0.1

* Fix bug in `simulate.dsem` to keep up with changing interface in `dsem`
* Update CITATION to indicate accepted paper
* Remove fit_tmb to eliminate cryptic warning messages and simplify code

# dsem 1.0.0

* Initial public release
