NEWS.md

piecewiseSEM Change Log

2016-12-06 Version 1.2.1

• Bug fix: use of standardize = "scale" in sem.coefs with cbind in glmer
• Warning: use of poly polynomials in model formula
• Feature addition: support for models of class rq
• Bug fix: error in scaling of transformed variables in get.scaled.data
• Bug fix: sem.basis.set failed to remove variables regressed against their interaction
• Bug fix: multiple levels of grouping.vars in sem.fit

2016-10-11 Version 1.2.0

• Feature addition: new function acyclic to test for acyclic DAGs
• Feature addition: new function rsquared for easier calling of sem.model.fits
• Bug fix: order of adjacency matrix in get.sort.dag
• Feature addition: model class glmmTMB
• Bug fix: inclusion of transformed variables as additional boxes in sem.plot
• Bug fix: specification of invalid models in endogenous.reverse
• Feature addition: implemented two-column binding as response in GLM(M)s
• Bug fix: memory allocation error in sem.model.fits
• Bug fix: inclusion of entries in the basis set without corresponding models in the model list in endogenous.reverse
• Bug fix: crossed random effects in get.random.formula not returning correct random slopes
• Bug fix: gls models in sem.missing.paths could not update basis model

2016-07-05 Version 1.1.3

• Feature addition: report of intercepts in sem.coefs
• Bug fix: warning with random slopes not present as fixed effects in sem.model.fits
• Feature addition: new function endogenous.reverse to assist with independence claims among intermediate endogenous variables not fit to a normal distribution
• Bug fix: negative binomial models fail to return R2s in sem.model.fits
• Bug fix: Failed to index correct P-value in sem.missing.paths when categorical variables are present
• Bug fix: intermediate endogenous variables not properly removed from the basis set in sem.missing.paths

2016-06-06 Version 1.1.2

• Feature addition: significance indicators for P-value outputs
• Bug fix: remove random effects from get.scaled.data
• Feature addition: Use KRmodcomp from pbkrtest instead of get_LB_dff to calculate P-values for lmer models
• Bug fix: transformations for scaled coefficients no longer fails in sem.coefs
• Bug fix: all interactions now show up in sem.coefs when scaled
• Bug fix: random slopes as fixed effects not registering properly in sem.model.fits
• Bug fix: added \dontrun{} to all help files

2016-05-18 Version 1.1.1

• Reduced time it takes examples to run
• Stop: if duplicate responses are detected in the model list
• Temporary bug fix: returns lowest P-value for when d-sep tests include non-linear intermediate endogenous variables, only if family is not Gaussian
• Bug fix: reversed order of conditioning variables so they come first
• Bug fix: removed entries from the basis set that attempt to predict an interaction that does not appear in the model list

2016-03-10 Version 1.1.0

• Feature addition: rudimentary plotting using sem.plot
• Feature addition: support for glmmadmb models
• Feature addition: pbkrtest to reliably extract p-values from lme4 models
• Major Bug Fix: incorrect basis set specified by ggm::topSort; introduced sort.dag function, removed dependency on ggm
• Major Bug Fix: sem.basis.set now treats transformed variables as untransformed, resolving duplicate vars in the basis set
• Bug fix: resolved switched interactions (e.g., x1:x2 vs x2:x1) leading to duplicate vars in the basis set using get.dag
• Bug fix: fixed long standing bug with lmer models not returning p-values

2016-02-09 Version 1.0.4

• Bug fix: correlated errors among exogenous variables in sem.coefs
• Bug fix: correctly scale data from pgls models using get.scaled.data
• Bug fix: corrected basis set for models created with gls
• Feature addition: helper function get.scaled.model to get model from scaled coefficients
• Feature addition: (partial) correlations in sem.coefs
• Bug fix: passing of correlated errors to lavaan
• Bug fix: standardized coefficients for variables transformed in model formula

2016-01-20 Version 1.0.3

• Bug fix: get.model.control updated for latest versions of lme4 and nlme
• Bug fix: hand compute interactions in sem.lavaan using argument compute.int = TRUE
• Feature addition: function get.scaled.data to handle transformed variables in sem.coefs when standardize = "scale"

2016-01-15 Version 1.0.2

• Feature addition: added additional plotting arguments for partial.residuals
• Feature addition: AICc and delta AIC to sem.model.fits
• Bug fix: Offsets in model formula treated as predictors in d-sep tests

2015-12-13 Version 1.0.1

• Feature addition: AICc and delta AIC to sem.model.fits
• Bug fix: issue with interactions in basis set and d-sep tests in sem.missing.paths
• Bug fix: issue with fixed intercept models and calculating the basis set
• Bug fix: issue with offset() variables in sem.missing.paths
• Bug fix: transformed responses for partial residuals
• Bug fix: duplicated values in basis set (function DAG in ggm package)

2015-10-26 Version 1.0.0

• First release to CRAN

2015-10-23 Version 0.9.9

• Added vignette
• Fixed issue with design matrix including omitted observations and dropped levels in sem.model.fits
• Incorporated interactions into partial.resid
• Fixed bug with lme residuals in partial.resid and predict.sem
• Modified sem.coefs to return NA for standardized interactions

2015-09-08 Version 0.9.8

• Added functions get.dag and get.basis.set
• Fixed issue with interactions in sem.missing.paths
• Fixed issue in sem.missing.paths where only 1 missing path returned NA instead of p-value
• Removed argument filter.exog = TRUE
• Fixed error for add.vars in get.dag
• Fixed issue with transformed variables and sem.coefs
• Fixed issue with lme4 models and sem.model.fits
• Fixed issue with incorrect independence claims in get.basis.set
• Fixed (nlme) merging error in partial.resid
• Fixed issue with glmmPQL and get.random.structure
• Added new citation (arXiv)

2015-07-31 Version 0.9.1

• Implemented workaround in sem.basis.set where output changed based on order of variables in formula with interactions
• Saturated models now return AIC (and AICc) values (with warning)
• Added standard errors on predictions for mixed models in predict.sem()
• Fixed typo in output for sem.fisher.c with incorrect df
• Fixed error with lme4 and gls models in partial.resid()
• Fixed error with lmerTest returning "merMod" objects
• New function predict.sem returns model predictions
• Fixed "unsupported model class" error for merModTest

2015-06-15 Version 0.9

• Major revisions and annotations to all functions to improve transparency and efficiency
• Included new helper functions get.random.formula() and get.model.control()
• Now reports df for all model types except glmer
• Included support for "gls" and phylogenetically independent contrast ("pgls") models
• Fixed deparse error in get.random.struture()
• Improved handling of gls() models

2015-04-27 Version 0.4.4

• Fixed issue with transformed corr.errors in get.basis.set
• get.sem.coefs now does range standardization
• get.sem.coefs now returns single table with significance values
• Improved handling of uneven observations in get.partial.resid
• get.partial.resid now accepts a single model in addition to a list of models
• get.lavaan.sem now supports additional arguments from lavaan

2015-01-26 Version 0.4.3

• Added new function to return R^2 and AIC values for component models in SEM
• get.partial.resid now returns residuals plot with fitted line

2015-01-03 Version 0.4.2

• get.missing.paths now returns more information for d-sep tests
• get.basis.set drops independence claims in the basis set where interactions predict their corresponding main effects
• get.fisher.c now reports k df and get.aic now reports K and n df
• Fixed rounding error that misreported Fisher's C
• Allow user-specified rounding using sig= argument in get.sem.fit, get.fisher.c, and get.aic

2014-12-19 Version 0.4.1

• Fixed minor bug in get.partial.resid where random effects threw an error for lme models
• Fixed interaction bug in filter.exogenous which was returning incompatible models from the basis set
• Fixed bug in get.sem.coefs where missing values returned NA for corr.errors
• Fixed issue with transformed/untransformed variables predicting one another in the basis set
• Fixed interaction bug in get.missing.paths, filter.exogenous, get.partial.resiod
• Now can supply single model control or list

2014-11-12 Version 0.4.0

• Fixed bug for transformed variables in get.partial.resid
• Can now specify an equation as input into get.partial.resid
• Fixed bug for transformed interaction terms in structured equations for get.basis.set
• Fixed bug for transformed variables when also specifying raw variables in corr.error
• Added model control arguments to get.sem.fit and get.partial.resid

2014-09-22 Version 0.3.2

• Added optional switch to display conditional variables in get.missing.paths
• Removed logLik df from get.aic output

2014-09-19 Version 0.3.1

• Incorporated multilevel data into get.sem.fit
• Fixed error when length(basis.set) = 1 and .progressBar = T
• Expanded interaction term in get.basis.set to include 20 letters instead of 10, and run them backwards
• Renamed variable names in filter.exogenous to better reflect what they are

2014-09-12 Version 0.2.6

• Incorporated transformed variables and multiple interactions into get.sem.coefs
• Fixed but with add.vars; many functions now require the user to supply a data.frame

2014-09-10 Version 0.2.5

• Standardized argument order across functions
• Improved handling of correlated errors in get.sem.coefs
• Incorporated correlated errors into get.sem.lavaan

2014-09-05 Version 0.2.3

• Fixed return of standardized coefficients in get.sem.coefs

2014-08-25 Version 0.2.2

• Added argument to define and quantify correlated errors
• Added new function get.partial.resid

2014-08-18 Version 0.1.5

• Added new function get.basis.set (replaced dag.updated)
• Improved handling of interactions in the basis set
• Improved handling of p-value rownames in get.missing.paths
• get.aic now returns df

2014-08-04 Version 0.1.4

• Added new functions get.aic, get.fisher.c, get.sem.coefs, get.lavaan.sem
• Added README.md
• Completed all existing .Rd files
• Updated .progressBar as to not conflict with existing function progressBar
• Altered handling of model formulae to collapse to a single character string

2014-08-03 Version 0.1.0

• Initial build of package
• Added CHANGELOG