[Mboost-commits] r788 - in pkg/mboostDevel: R man

[noreply at r-forge.r-project.org]

Author: hofner
Date: 2014-07-28 18:26:00 +0200 (Mon, 28 Jul 2014)
New Revision: 788

Modified:
   pkg/mboostDevel/R/confint.R
   pkg/mboostDevel/man/confint.Rd
Log:
improved interface of confint.mboost


Modified: pkg/mboostDevel/R/confint.R
===================================================================
--- pkg/mboostDevel/R/confint.R	2014-07-28 10:02:59 UTC (rev 787)
+++ pkg/mboostDevel/R/confint.R	2014-07-28 16:26:00 UTC (rev 788)
@@ -3,13 +3,21 @@
                            B = 1000, B.mstop = 25, newdata = NULL,
                            which = parm,
                            papply = ifelse(B.mstop == 0, mclapply, lapply),
-                           papply.mstop = mclapply,
-                           ...) {
+                           cvrisk_options = list(), ...) {
 
     which <- object$which(which, usedonly = FALSE)
     if (!all(which %in% object$which(NULL, usedonly = FALSE)))
         stop(sQuote("which"), " is wrongly specified")
 
+    if (!is.list(cvrisk_options))
+        stop(sQuote("cvrisk_options"), " must be a named list")
+    if (length(cvrisk_options) > 0 && is.null(names(cvrisk_options)))
+        stop(sQuote("cvrisk_options"), " must be a named list")
+    if ("folds" %in% names(cvrisk_options))
+        stop("One cannot modify the folds of the inner bootstrap")
+    if ("object" %in% names(cvrisk_options))
+        stop("One cannot specify the model (object) of the inner bootstrap")
+
     ## create new data and/or restructure data
     newdata <- .create_newdata(object, newdata, which)
 
@@ -25,13 +33,15 @@
                       risk = "inbag", trace = FALSE)
         if (B.mstop > 0) {
             ## <FIXME> are the weights handled correctly?
-            cvr <- cvrisk(mod, folds = cv(model.weights(mod), B = B.mstop),
-                          papply = papply.mstop, ...)
+            cvr <- do.call("cvrisk",
+                           args = c(list(object = mod,
+                                       folds = cv(model.weights(mod), B = B.mstop)),
+                                       cvrisk_options))
             mod[mstop(cvr)]
         }
         .predict_confint(mod, newdata = newdata, which = which)
     }
-    predictions <- papply(1:B, do_update)
+    predictions <- papply(1:B, do_update, ...)
     cat("\n")
 
     ## prepare returned object

Modified: pkg/mboostDevel/man/confint.Rd
===================================================================
--- pkg/mboostDevel/man/confint.Rd	2014-07-28 10:02:59 UTC (rev 787)
+++ pkg/mboostDevel/man/confint.Rd	2014-07-28 16:26:00 UTC (rev 788)
@@ -17,7 +17,7 @@
 \method{confint}{mboost}(object, parm = NULL, level = 0.95, B = 1000,
         B.mstop = 25, newdata = NULL, which = parm,
         papply = ifelse(B.mstop == 0, mclapply, lapply),
-        papply.mstop = mclapply, ...)
+        cvrisk_options = list(), ...)
 \method{plot}{mboost.ci}(x, which, level = x$level, ylim = NULL, type = "l", col = "black",
      ci.col = rgb(170, 170, 170, alpha = 85, maxColorValue = 255),
      raw = FALSE, print_levelplot = TRUE,...)
@@ -65,13 +65,12 @@
     computing resources if you use parallel computing for both, the
     inner and the outer bootstrap.
   }
-  \item{papply.mstop}{
-    (parallel) apply function for the inner bootstrap, defaults to
-    \code{\link[parallel]{mclapply}} if we use an inner bootstrap is to
-    determine the optimal stopping iteration. For details see
-    argument \code{papply} in \code{\link{cvrisk}}. Be careful with your
-    computing resources if you use parallel computing for both, the
-    inner and the outer bootstrap.
+  \item{cvrisk_options}{
+    (optionally) specify a named list with arguments to the inner
+    bootstrap. For example use \code{cvrisk_options = list(mc.cores =
+      2)} to specify that the \code{\link{mclapply}} function within
+    \code{\link{cvrisk}} uses 2 cores to compute the optimal
+    \code{mstop}.
   }
   \item{x}{
     a confidence interval object.
@@ -105,7 +104,7 @@
     logical, should the point estimtate (PE) be also returned?
   }
   \item{\dots}{
-    additional arguments
+    additional arguments to the outer bootstrap such as \code{mc.cores}.
   }
 }
 \details{