NEWS.md

BAS (development version)

BAS 1.7.5

Features

Version 1.7.5 of the BAS package adds an internal function to count the number of models that satisfy "hereditary" constraints. This is used in the force.heredity option in bas.lm to reduce the number of models considered in the sampling process and should reduce the memory requirements and speed up the sampling process. This currently works only for factors included in the model formula, but not with factors always included in the model orwith other hereditaty constraints such as with polynomials. (theforce.heredity option does work with these other constraints). This is a first step in reducing the number of models aallocated in the sampling process. Future updates will include other hereditary constraints.

• added hexagon sticker

• add copyright to source files to satisfy OpenSSF Best Practice

Bug Fixes

• fixed (issue #89) reported as Error on CRAN Check page for compiling BAS under R-devel with clang19. Removed legacy definitions of MACHEPS and MAXNUM from Cephes and replaced with DLB_EPSILON and DBL_MAX in R. Files in src/ mconf.h and const.c are no longer used and will be reomved from in the future.

• fixed (issue #87) prior inclusion probabilities using a Bernoulli prior other than 0.5 were incorrect if include.always was used to include some variables always.
  Added unit test in test-priorprobs.R

BAS 1.7.3

• reverted back to code using SETLENGTH (issue #82) to address stack imbalance issues seen in interactive checks and not flagged in R CMD check.

BAS 1.7.2

• added method="AMCMC" for bas.lm to use adaptive independent Metropolis Hastings for sampling models. With option importance.sampling = TRUE the adaptive independent proposal and be used for importance sampling with improved estimation of model probabilities and inclusion probabilities based on the Horivitz-Thompsom / Hajek estimator.

• added unit tests for link functions implemented in family.c

• fixed (issue #81) Removed legacy definitions of ‘PI’ and ‘Free’ and replaced with‘M_PI’ and ‘R_Free’ to comply with ‘STRICT_R_HEADERS’ prevent package removal on 9/23/2024

• fixed (issue #82) avoid SETLENGTH as non-API function when truncating vectors

BAS 1.7.1

Minor Improvements and Fixes

• Initialized vector se via memset and disp = 1.0 in fit_glm.c (issue #72)

• Initialized variables in hyp1f1.c from testthat (issue #75)

• Removed models that have zero prior probability in bas.lm and bas.glm (issue #74)

• Fixed error in bayesglm.fit to check arguments x or y for correct type before calling C and added unit test (issue #67)

BAS 1.6.6

New Features

• Added support for Gamma regression for bas.glm, with unit tests and example (Code contributed by @betsyberrson)

• added error if supplied initial model for the bas.lm sampling methods "MCMC" and "MCMC+BAS" had prior probability zero.

• fixed printing problems as identified via checks

• fixed indexing error for bas.lm and method = "MCMC+BAS" as bas.lm using method = "MCMC+BAS" crashed with a segmentation fault if bestmodel is not NULL or the null model. GitHub issue #69

• fixed error in predict.bas with se.fit=TRUE if there is only one predictor. GitHub issue #68 reported by @AleCarminati added unit test to test-predict.R

• Fixed error in coef for bas.glm objects when using a betaprior of class IC, including AIC and BIC Github issue #65

• Fixed error when using Jeffreys prior in bas.glm with the include.always option and added unit test in test-bas-glm.R.
  Github issue #61

• Fixed error for extracting coefficients from the median probability model when a formula is passed as an object rather than a literal, and added a unit test to test-coefficients.R Github issues #39 and #56

BAS 1.6.4

Changes

• skipped test on CRAN that fails to show a warning in the non full rank case when pivot=FALSE for bas.lm as default uses pivoting and documentation indicates that pivot=FALSE should only be used in the full rank case so that users should not encounter this issue in practice. Users will continue to see a warning of NA's are returned, but should be aware that not all platforms may produce a warning (such as M1mac). Github issue #62

BAS 1.6.3

Changes

• Added checks and unit-tests to see if modelprior is of class 'prior' resolving Github Issue #57

• Removed polevl.c, psi.c and gamma.c from Cephes as no longer used after switching to R's internal functions

BAS 1.6.2

• replaced deprecated DOUBLE_EPS with DBL_EPSILON for R 4.2.0 release (in two places) so restore on CRAN

BAS 1.6.1

Changes

• replaced deprecated DOUBLE_EPS with DBL_EPSILON for R 4.2.0 release

• fixed warnings from CRAN checks for under R devel (use of | and if with class)

• added a function trCCH that uses integration to compute the normalizing constant in the Truncated Compound Confluent Hypergeometric distribution that provides the correct normalizing constant for Gordy (1998) and is more stable for large values compared to the current phi1 function. This is now used in the TCCH prior for bas.glm.

• Rewrote phi1 function to use direct numerical integration (phi1_int) when Wald statistic is large so that marginal likelihoods are not NA as suggested by Daniel Heeman and Alexander Ly (see below). This should improve stability of estimates of Bayes Factors and model probabilities from bas.glm that used the HyperTwo function, including coefficient priors for hyper.g.n(), robust(), and intrinsic(). Added additional unit tests.

• Added thin as an option for bas.glm

• added unit tests and examples to show the connections between the special functions trCCH, phi1, 1F1 and 2F1

Bug Fixes

• added internal function for phi1_int when the original HyperTwo function returns NA Issue #55 See more details above.

• corrected the shrinkage estimate under the CCH prior that did not include terms involving the beta function.

BAS 1.6.0

Changes

• update FORTRAN code to be compliant with USE_FC_LEN_T for character strings

Bug Fixes

• fixed warning in src code for log_laplace_F21 which had an uninitialized variable leading to NaN being returned from R function hypergeometric2F1

BAS 1.5.5

Changes

• Fixed WARNING under fedora-clang-devel. Added climate.dat file to package for building vignette so that package does not violate CRAN's policy for accessing internet resources and is more permanent if file location/url changes locally.

• Fixed testthat errors under Solaris. Default settings for force.heredity is set back to FALSE in bas.lm and bas.glm so that methods work on all platforms. For Solaris, users who wish to impose the force.heredity constraint may use the post-processing function.

BAS 1.5.4

Features

• Modified prior probabilities to adjust for the number of variables always included when using include.always. Pull request #41 by Don van de Bergh. Issue #40

Bug Fixes

• Fixed valgrind error in src/ZS_approx_null_np.c for invalid write noted in CRAN checks

• fixed function declaration type-mismatch and argument errors identified by LTO noted in CRAN checks

• Added contrast=NULL argument to bas.lm and bas.glm so that non-NULL contrasts do not trigger warning in model.matrix as of R 3.6.0. Bug #44

• Added check for sample size equal to zero due to subsetting or missing data Bug #37

Other

• Put ORCID in quotes in author list (per R-dev changes)

BAS 1.5.3

Bug Fixes

Fixed errors identified on cran checks https://cran.r-project.org/web/checks/check_results_BAS.html

• initialize R2_m = 0.0 in lm_mcmcbas.c (lead to NA's with clang on debian and fedora )

• switch to default of pivot = TRUE in bas.lm, adding tol as an argument to control tolerance in cholregpovot for improved stability across platforms with singular or nearly singular designs.

• valgrind messages: Conditional jump or move depends on uninitialized value(s). Initialize vectors allocated via R_alloc in lm_deterministic.c and glm_deterministic.c.

BAS 1.5.2

Features

• Included an option pivot=TRUE in bas.lm to fit the models using a pivoted Cholesky decomposition to allow models that are rank-deficient. Enhancement #24 and Bug #21. Currently coefficients that are not-estimable are set to zero so that predict and other methods will work as before. The vector rank is added to the output (see documentation for bas.lm) and the degrees of freedom methods that assume a uniform prior for obtaining estimates (AIC and BIC) are adjusted to use rank rather than size.

• Added option force.heredity=TRUEto force lower order terms to be included if higher order terms are present (hierarchical constraint) for method='MCMC' and method='BAS' with bas.lm and bas.glm. Updated Vignette to illustrate. enhancement #19. Checks to see if parents are included using include.always pass issue #26.

• Added option drop.always.included to image.bas so that variables that are always included may be excluded from the image. By default all are shown enhancement #23

• Added option drop.always.included and subset to plot.bas so that variables that are always included may be excluded from the plot showing the marginal posterior inclusion probabilities (which=4). By default all are shown enhancement #23

• update fitted.bas to use predict so that code covers both GLM and LM cases with type='link' or type='response'

• Updates to package for CII Best Practices Badge certification

• Added Code Coverage support and more extensive tests using test_that.

Bugs

• fixed issue #36 Errors in prior = "ZS-null" when R2 is not finite or out of range due to model being not full rank. Change in gexpectations function in file bayesreg.c

• fixed issue #35 for method="MCMC+BAS" in bas.glm in glm_mcmcbas.c when no values are provided for MCMC.iterations or n.models and defaults are used. Added unit test in test-bas-glm.R

• fixed issue #34 for bas.glm where variables in include.always had marginal inclusion probabilities that were incorrect. Added unit test in test-bas-glm.R

• fixed issue #33 for Jeffreys prior where marginal inclusion probabilities were not renormalized after dropping intercept model

• fixed issue #32 to allow vectorization for phi1 function in R/cch.R and added unit test to "tests/testthat/test-special-functions.R"

• fixed issue #31 to coerce g to be a REAL for g.prior prior and IC.prior in bas.glm; added unit-test "tests/testthat/test-bas-glm.R"

• fixed issue #30 added n as hyper-parameter if NULL and coerced to be a REAL for intrinsic prior in bas.glm; added unit-test

• fixed issue #29 added n as hyper-parameter if NULL and coerced to be a REAL for beta.prime prior in bas.glm; added unit-test

• fixed issue #28 fixed length of MCMC estimates of marginal inclusion probabilities; added unit-test

• fixed issue #27 where expected shrinkage with the JZS prior was greater than 1. Added unit test.

• fixed output include.always to include the intercept issue #26 always so that drop.always.included = TRUE drops the intercept and any other variables that are forced in. include.always and force.heredity=TRUE can now be used together with method="BAS".

• added warning if marginal likelihoods/posterior probabilities are NA with default model fitting method with suggestion that models be rerun with pivot = TRUE. This uses a modified Cholesky decomposition with pivoting so that if the model is rank deficient or nearly singular the dimensionality is reduced. Bug #21.

• corrected count for first model with method='MCMC' which lead to potential model with 0 probability and errors in image.

• coerced predicted values to be a vector under BMA (was a matrix)

• fixed size with using method=deterministic in bas.glm (was not updated)

• fixed problem in confint with horizontal=TRUE when intervals are point mass at zero.

Other

• suppress warning when sampling probabilities are 1 or 0 and the number of models is decremented
  Issue #25

• changed force.heredity.bas to re-normalize the prior probabilities rather than to use a new prior probability based on heredity constraints. For future, add new priors for models based on heredity. See comment on issue #26.

• Changed License to GPL 3.0

BAS 1.5.1 June 6, 2018

Features

• added S3 method variable.names to extract variable names in the highest probability model, median probability model, and best probability model for objects created by predict.

Bugs

• Fixed incorrect documentation in predict.basglm which had that type = "link" was the default for prediction issue #18

BAS 1.5.0 May 2, 2018

Features

• add na.action for handling NA's for predict methods issue #10

• added include.always as new argument to bas.lm. This allows a formula to specify which terms should always be included in all models. By default the intercept is always included.

• added a section to the vignette to illustrate weighted regression and the force.heredity.bas function to group levels of a factor so that they enter or leave the model together.

Bugs

• fixed problem if there is only one model for image function;
  github issue #11

• fixed error in bas.lm with non-equal weights where R2 was incorrect. issue #17

Deprecated

• deprecate the predict argument in predict.bas, predict.basglm and internal functions as it is not utilized

BAS 1.4.9 March 24, 2018

Bugs

• fixed bug in confint.coef.bas when parm is a character string
• added parentheses in betafamily.c line 382 as indicated in CRAN check for R devel

Features

• added option to determine k for Bayes.outlier if prior probability of no outliers is provided

BAS 1.4.8 March 10, 2018

Bugs

• fixed issue with scoping in eval of data in predict.bas if dataname is defined in local env.

• fixed issue 10 in github (predict for estimator='BPM' failed if there were NA's in the X data. Delete NA's before finding the closest model.

• fixed bug in 'JZS' prior - merged pull request #12 from vandenman/master

• fixed bug in bas.glm when default betaprior (CCH) is used and inputs were INTEGER instead of REAL

• removed warning with use of 'ZS-null' for backwards compatibility

Features added

• updated print.bas to reflect changes in print.lm

• Added Bayes.outlier function to calculate posterior probabilities of outliers using the method from Chaloner & Brant for linear models.

BAS 1.4.7 October 22, 2017

Updates

• Added new method for bas.lm to obtain marginal likelihoods with the Zellner-Siow Priors for "prior= 'JZS' using QUADPATH routines for numerical integration. The optional hyper parameter alpha may now be used to adjust the scaling of the ZS prior where g ~ G(1/2, alpha*n/2) as in the BayesFactor package of Morey, with a default of alpha=1 corresponding to the ZS prior used in Liang et al (2008). This also uses more stable evaluations of log(1 + x) to prevent underflow/overflow.

• Priors ZS-full for bas.lm is planned to be deprecated.

• replaced math functions to use portable C code from Rmath and consolidated header files

BAS 1.4.6 May 24, 2017

Updates

• Added force.heredity.interaction function to allow higher order interactions to be included only if their "parents" or lower order interactions or main effects were included. Currently tested with two way interactions. This is implemented post-sampling; future updates will add this at the sampling stage which will reduce memory usage and sampling times by reducing the number of models under consideration.

Bugs

• Fixed unprotected ANS in C code in glm_sampleworep.c and sampleworep.c after call to PutRNGstate and possible stack imbalance in glm_mcmc.

• Fixed problem with predict for estimator=BPM when newdata was one row

BAS 1.4.5 March 28, 2017

Bugs

• Fixed non-conformable error with predict when new data was from a dataframe with one row.

• Fixed problem with missing weights for prediction using the median probability model with no new data.

BAS 1.4.4 March 14, 2017

Updates

• Extract coefficient summaries, credible intervals and plots for the HPM and MPM in addition to the default BMA by adding a new estimator argument to the coef function. The new n.models argument to coef provides summaries based on the top n.models highest probability models to reduce computation time. 'n.models = 1' is equivalent to the highest probability model.

• use of newdata that is a vector is now deprecated for predict.bas; newdata must be a dataframe or missing, in which case fitted values based on the dataframe used in fitting is used

• factor levels are handled as in lm or glm for prediction when there may be only level of a factor in the newdata

Bugs

• fixed issue for prediction when newdata has just one row

• fixed missing id in plot.bas for which=3

BAS 1.4.3 February 18, 2017

Updates

• Register symbols for foreign function calls
• bin2int is now deprecated
• fixed default MCMC.iteration in bas.lm to agree with documentation
• updated vignette to include more examples, outlier detection, and finding the best predictive probability model
• set a flag for MCMC sampling renormalize that selects whether the Monte Carlo frequencies are used to estimate posterior model and marginal inclusion probabilities (default renormalize = FALSE) or that marginal likelihoods time prior probabilities that are renormalized to sum to 1 are used. (the latter is the only option for the other methods); new slots for probne0.MCMC, probne0.RN, postprobs.RN and postprobs.MCMC.

Bug fixes

• fixed problem with prior.bic, robust, and hyper.g.n where default had missing n that was not set in hyperparameters
• fixed error in predict and plot for GLMs when family is provided as a function

BAS 1.4.2 October 12, 2016

Updates

• added df to the object returned by bas.glm to simplify coefficients function.

Bug Fixes

• corrected expected value of shrinkage for intrinsic, hyper-g/n and TCCH priors for glms

BAS 1.4.1 September 17, 2016

Bug Fixes

• the modification in 1.4.0 to automatically handle NA's led to errors if the response was transformed as part of the formula; this is fixed

Features

• added subset argument to bas.lm and bas.glm

BAS 1.4.0 August 25, 2016

New features

• added na.action for bas.lm and bas.glm to omit missing data.
• new function to plot credible intervals created by confint.pred.bas or confint.coef.bas. See the help files for an example or the vignette.
• added se.fit option in predict.basglm.
• Added testBF as a betaprior option for bas.glm to implement Bayes Factors based on the likelihood ratio statistic's distribution for GLMs.
• DOI for this version is http://dx.doi.org/10.5281/zenodo.60948

BAS 1.3.0 July 15, 2016

New Features

A vignette has been added at long last! This illustrates several of the new features in BAS such as

• new functions for computing credible intervals for fitted and predicted values confint.pred.bas()
• new function for adding credible intervals for coefficients confint.coef.bas()
• added posterior standard deviations for fitted values and predicted values in predict.bas()

Deprecation

• deprecated use of type to specify estimator in fitted.bas and replaced with estimator so that predict() and fitted() are compatible with other S3 methods.
• updated functions to be of class bas to avoid NAMESPACE conflicts with other libraries

BAS 1.2.2 June 29, 2016

New Features

• added option to find "Best Predictive Model" or "BPM" for fitted.bas or predict.bas
• added local Empirical Bayes prior and fixed g-prior for bas.glm
• added diagnostic() function for checking convergence of bas objects created with method = "MCMC""
• added truncated power prior as in Yang, Wainwright & Jordan (2016)

Minor Changes

• bug fix in plot.bas that appears with Sweave
• bug fix in coef.bma when there is just one predictor

BAS 1.2.1 April 16, 2016

• bug fix for method="MCMC" with truncated prior distributions where MH ratio was incorrect allowing models with 0 probability to be sampled.
• fixed error in Zellner-Siow prior (ZS-null) when n=p+1 or saturated model where log marginal likelihood should be 0

BAS 1.2.0 April 11, 2016

• removed unsafe code where Rbestmarg (input) was being overwritten in .Call which would end up in corruption of the constant pool of the byte-code (Thanks to Tomas Kalibera for catching this!)
• fixed issue with dimensions for use with Simple Linear Regression

BAS 1.1.0 March 31, 2016

New Features

• added truncated Beta-Binomial prior and truncated Poisson (works only with MCMC currently)
• improved code for finding fitted values under the Median
• deprecated method = "AMCMC" and issue warning message

Minor Changes

• Changed S3 method for plot and image to use class bas rather than bma to avoid name conflicts with other packages

BAS 1.09

- added weights for linear models
- switched LINPACK calls in bayesreg to LAPACK finally should be
faster
- fixed bug in intercept calculation for glms
- fixed inclusion probabilities to be a vector in the global EB
methods for linear models

BAS 1.08

- added intrinsic prior for GLMs
- fixed problems for linear models for p > n and R2 not correct

BAS 1.07

- added phi1 function from Gordy (1998)  confluent hypergeometric
function of two variables  also known as one of the Horn
hypergeometric functions or Humbert's phi1
- added Jeffrey's prior on g
- added the general tCCH prior and special cases of the hyper-g/n.
- TODO check shrinkage functions for all	

BAS 1.06

- new improved Laplace approximation for hypergeometric1F1
- added class basglm for predict
- predict function now handles glm output
- added dataframe option for newdata in predict.bas and predict.basglm
- renamed coefficients in output to be 'mle' in bas.lm to be consistent across
lm and glm versions so that predict methods can handle both
cases.  (This may lead to errors in other external code that
expects object$ols or object$coefficients)
- fixed bug with initprobs that did not include an intercept for bas.lm

BAS 1.05

- added thinning option for MCMC method for bas.lm
- returned posterior expected shrinkage for bas.glm
- added option for initprobs = "marg-eplogp" for using marginal
SLR models to create starting probabilities or order variables
especially for p > n case
- added standalone function for hypergeometric1F1 using Cephes
library and a Laplace approximation
-Added class "BAS" so that predict and fitted functions (S3
methods) are not masked by functions in the BVS package: to do
modify the rest of the S3 methods.

BAS 1.04

- added bas.glm for model averaging/section using mixture of g-priors for
GLMs.  Currently limited to Logistic Regression
- added Poisson family for glm.fit

BAS 1.0

- cleaned up  MCMC method code

BAS 0.93

- removed internal print statements in bayesglm.c
- Bug fixes in AMCMC algorithm

BAS 0.92

- fixed glm-fit.R  so that hyper parameter for BIC is numeric

BAS 0.91

- added new AMCMC algorithm

BAS 0.91

- bug fix in bayes.glm

BAS 0.90

- added C routines for fitting glms

BAS 0.85

- fixed problem with duplicate models if n.models was > 2^(p-1) by

restricting n.models

- save original X as part of object so that fitted.bma gives the

correct fitted values (broken in version 0.80)

BAS 0.80

- Added `hypergeometric2F1` function that is callable by R
- centered X's in bas.lm so that the intercept has the correct

shrinkage - changed predict.bma to center newdata using the mean(X) - Added new Adaptive MCMC option (method = "AMCMC") (this is not stable at this point)

BAS 0.7

-Allowed pruning of model tree to eliminate rejected models

BAS 0.6

- Added MCMC option to create starting values for BAS (`method = "MCMC+BAS"`)

BAS 0.5

-Cleaned up all .Call routines so that all objects are duplicated or

allocated within code

BAS 0.45

- fixed ch2inv that prevented building on Windows in bayes glm_fit

BAS 0.4

- fixed FORTRAN calls to use F77_NAME macro 
- changed  allocation of objects for .Call to prevent some objects from being overwritten.  

BAS 0.3

- fixed EB.global function to include prior probabilities on models
- fixed update function 

BAS 0.2

- fixed predict.bma to allow newdata to be a matrix or vector with the

column of ones for the intercept optionally included. - fixed help file for predict - added modelprior argument to bas.lm so that users may now use the beta-binomial prior distribution on model size in addition to the default uniform distribution - added functions uniform(), beta-binomial() and Bernoulli() to create model prior objects - added a vector of user specified initial probabilities as an option for argument initprobs in bas.lm and removed the separate argument user.prob