Fix for issue #44 warning when contrasts are not a list in bas.lm and…

… bas.glm

NEWS.md

@@ -1,10 +1,15 @@
 #  BAS 1.5.4
 
-# Features
+## Features
 
-Modified prior probabilities to adjust for the number of variables always included when 
+* Modified prior probabilities to adjust for the number of variables always included when 
 using include.always.  [Pull request #41](https://github.com/merliseclyde/BAS/pull/41) by Don van de Bergh.  [Issue #40](https://github.com/merliseclyde/BAS/issues/40)
 
+## Bug Fixes 
+
+* 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](https://github.com/merliseclyde/BAS/issues/44)
+
 ## Other 
 
 * Put ORCID in quotes in author list (per R-dev changes)

R/bas_glm.R

@@ -61,6 +61,7 @@ normalize.initprobs.glm <- function(initprobs, glm.obj) {
 #' @param weights optional vector of weights to be used in the fitting process.
 #' May be missing in which case weights are 1.
 #' @param subset subset of data used in fitting
+#' @param contrasts an optional list. See the contrasts.arg of `model.matrix.default()`.
 #' @param offset a priori known component to be included in the linear
 #' predictor; by default 0.
 #' @param na.action a function which indicates what should happen when the data
@@ -226,7 +227,7 @@ normalize.initprobs.glm <- function(initprobs, glm.obj) {
 #' @rdname bas.glm
 #' @export
 bas.glm <- function(formula, family = binomial(link = "logit"),
-                    data, weights, subset, offset, na.action = "na.omit",
+                    data, weights, subset, contrasts=NULL, offset, na.action = "na.omit",
                     n.models = NULL,
                     betaprior = CCH(alpha = .5, beta = as.numeric(nrow(data)), s = 0),
                     modelprior = beta.binomial(1, 1),

R/bas_lm.R

@@ -113,6 +113,7 @@ normalize.n.models <- function(n.models, p, initprobs, method, bigmem) {
 #' @param weights an optional vector of weights to be used in the fitting
 #' process. Should be NULL or a numeric vector. If non-NULL, Bayes estimates
 #' are obtained assuming that Y ~ N(Xb, sigma^2 diag(1/weights)).
+#' @param contrasts an optional list. See the contrasts.arg of `model.matrix.default()`.
 #' @param na.action a function which indicates what should happen when the data
 #' contain NAs. The default is "na.omit".
 #' @param n.models number of models to sample either without replacement
@@ -439,6 +440,7 @@ bas.lm <- function(formula,
                    data,
                    subset,
                    weights,
+                   contrasts=NULL,
                    na.action = "na.omit",
                    n.models = NULL,
                    prior = "ZS-null",