finalize update for dropping always included variables issue #23

NEWS.md

@@ -4,7 +4,9 @@
 
 * Added option to force lower order terms to be included if higher order terms are present (hierarchical constraint).  Currently only supported with `method='MCMC'` and `method='BAS'` with `bas.lm` and `bas.glm`.  Updated Vignette to illustrate. [enhancement #19](https://github.com/merliseclyde/BAS/issues/19)
 
-* Added option `drop.always.included` to `image.bas` so that variables that are always included are not shown.  The intercept is no longer shown as well. [enhancement #23](https://github.com/merliseclyde/BAS/issues/23)
+* 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](https://github.com/merliseclyde/BAS/issues/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](https://github.com/merliseclyde/BAS/issues/23)
 
 ## Bugs
 

R/image.bas.R

@@ -25,9 +25,9 @@
 #' @param color The color scheme for image intensities. The value "rainbow"
 #' uses the rainbow palette. The value "blackandwhite" produces a black and
 #' white image (greyscale image)
-#' @param subset indices of variables to include in plot; (excludes the intercept)
+#' @param subset indices of variables to include/exclude in plot
 #' @param drop.always.included logical variable to drop variables that are
-#' always in the model.  TRUE by default.
+#' always forced into the model.  FALSE by default.
 #' @param offset numeric value to add to intensity
 #' @param digits number of digits in posterior probabilities to keep
 #' @param vlas las parameter for placing variable names; see par
@@ -49,14 +49,14 @@
 #' require(graphics)
 #' data("Hald")
 #' hald.ZSprior =  bas.lm(Y~ ., data=Hald,  prior="ZS-null")
-#' image(hald.ZSprior, subset=-1)
+#' image(hald.ZSprior, drop.always.included=TRUE) #drop the intercept
 #'
 #' @rdname image.bas
 #' @family bas methods
 #' @family bas plots
 #' @method image bas
 #' @export
-image.bas <- function (x, top.models=20, intensity=TRUE, prob=TRUE, log=TRUE, rotate=TRUE, color="rainbow", subset=NULL, drop.always.included = TRUE,
+image.bas <- function (x, top.models=20, intensity=TRUE, prob=TRUE, log=TRUE, rotate=TRUE, color="rainbow", subset=NULL, drop.always.included = FALSE,
                        offset=.75, digits=3, vlas=2,plas=0,rlas=0, ...)
 {
   postprob = x$postprobs
@@ -67,10 +67,14 @@ image.bas <- function (x, top.models=20, intensity=TRUE, prob=TRUE, log=TRUE, ro
   nvar <- ncol(which.mat)
 
 
-  if (is.null(subset)) subset=2:nvar
-  keep = x$include.always
-  subset = subset[!subset %in% keep]
-  if (length(subset) == 0) stop("no models in subset to show; modify subset or drop.always.included")
+  if (is.null(subset)) subset=1:nvar
+  if (drop.always.included) {
+    keep = x$include.always
+    if (is.null(keep)) keep = 1
+    subset = subset[!subset %in% keep]
+    if (length(subset) == 0) stop("no models in subset to show; modify subset or drop.always.included")
+  }
+
   which.mat =  which.mat[,subset, drop=FALSE]
   nvar = ncol(which.mat)
   namesx = x$namesx[subset]
@@ -84,8 +88,9 @@ image.bas <- function (x, top.models=20, intensity=TRUE, prob=TRUE, log=TRUE, ro
     # fix problem when scale has duplicate zeros
     zeros = which(scale == 0.0)
     nzeros = length(zeros)
+
     if (nzeros > 1) {
-      scale[zeros] = seq(scale[zeros[1]-1],0,length=nzeros)/1000
+      scale[zeros] = seq(scale[zeros[1]-1],0.0,length=nzeros)/1000
     }
   }
 

R/plot.bas.R

@@ -38,6 +38,10 @@
 #' plots; see also 'panel' above
 #' @param label.pos positioning of labels, for the left half and right half of
 #' the graph respectively, for plots 1-4
+#' @param subset indices of variables to include/exclude in plot of marginal posterior
+#' inclusion probabilities (NULL).
+#' @param drop.always.included logical variable to drop marginal posterior inclusiond probabilities
+#' for variables that are always forced into the model.  FALSE by default.
 #' @author Merlise Clyde, based on plot.lm by John Maindonald and Martin
 #' Maechler
 #' @seealso \code{\link{plot.coef.bas}} and \code{\link{image.bas}}.
@@ -65,7 +69,7 @@ plot.bas = function (x, which = c(1:4),
   id.n = 3,
   labels.id = NULL,
   cex.id = 0.75,  add.smooth = getOption("add.smooth"),
-  label.pos = c(4, 2))
+  label.pos = c(4, 2), subset=NULL, drop.always.included=FALSE)
 {
     if (!inherits(x, "bas"))
       stop("use only with \"bas\" objects")
@@ -168,10 +172,19 @@ plot.bas = function (x, which = c(1:4),
         text.id(dim[show.m], logmarg[show.m], show.m)
     }
     if (show[4]) {
-      probne0 = x$probne0
-      variables = 1:x$n.vars
+
+      if (is.null(subset)) subset=1:x$n.vars
+      if (drop.always.included) {
+        keep = x$include.always
+        if (is.null(keep)) keep = 1
+        subset = subset[!subset %in% keep]
+        if (length(subset) == 0) stop("no models in subset to show; modify subset or drop.always.included")
+      }
+      probne0 = x$probne0[subset]
+      nvars = length(subset)
+      variables = 1:nvars
       ylim <- c(0,1)
-      colors=rep(0, x$n.vars)
+      colors=rep(0, nvars)
       colors[probne0 > .5] = col.in
       colors[probne0 <= .5] = col.ex
 
@@ -182,7 +195,7 @@ plot.bas = function (x, which = c(1:4),
            ylim = ylim, ...)
       if (one.fig)
         title(sub = sub.caption, ...)
-      mtext(x$namesx, side=1, line=0.25, at=variables, las=2, cex=cex.lab, ...)
+      mtext(x$namesx[subset], side=1, line=0.25, at=variables, las=2, cex=cex.lab, ...)
       mtext(caption[4], 3, 0.25)
       #if (id.n > 0)
        # text.id(dim[show.m], logmarg[show.m], show.m)