removed calls from some objects

pkg/caret/R/avNNet.R

@@ -37,7 +37,6 @@ avNNet.formula <- function (formula, data, weights, ...,
                         ...)
   res$terms <- Terms
   res$coefnames <- colnames(x)
-  res$call <- match.call()
   res$na.action <- attr(m, "na.action")
   res$contrasts <- cons
   res$xlevels <- .getXlevels(Terms, m)

pkg/caret/R/bagFDA.R

@@ -7,7 +7,6 @@ function(x, y, weights = NULL, B = 50, keepX = TRUE, ...)
 {
   requireNamespaceQuietStop("mda")
   requireNamespaceQuietStop("earth")
-   funcCall <- match.call(expand.dots = TRUE)
    if(!is.matrix(x)) x <- as.matrix(x)
    if(!is.vector(y) & !is.factor(y)) y <- as.vector(y)   
    if(!is.vector(y) & !is.factor(y)) y <- factor(y[,1])
@@ -40,13 +39,12 @@ function(x, y, weights = NULL, B = 50, keepX = TRUE, ...)
    oob <- matrix(unlist(oobList), ncol = length(oobList[[1]]), byrow = TRUE)
    colnames(oob) <- names(oobList[[1]])
    if(keepX) x <- x else x <- NULL
-   structure(list(fit = btFits, B = B, oob = oob, call = funcCall, x = x, levels = levels(y), dots = list(...)), class = "bagFDA")
+   structure(list(fit = btFits, B = B, oob = oob, x = x, levels = levels(y), dots = list(...)), class = "bagFDA")
 }
 
 "bagFDA.formula" <-
 function (formula, data = NULL, B = 50, keepX = TRUE, ..., subset, weights, na.action = na.omit) 
 {
-   funcCall <- match.call(expand.dots = TRUE)
 
    if (!inherits(formula, "formula")) 
      stop("method is only for formula objects")
@@ -67,15 +65,13 @@ function (formula, data = NULL, B = 50, keepX = TRUE, ..., subset, weights, na.a
    if (xint > 0)  x <- x[, -xint, drop = FALSE]
 
    out <- bagFDA.default(x, y, w, B = B, keepX = keepX, ...)
-   out$call <- funcCall
    out
 }
 
 
 "print.bagFDA" <-
 function (x, ...) 
 {
-    cat("\nCall:\n", deparse(x$call), "\n\n", sep = "")
     if(!is.null(x$x))cat("Data:\n   # variables:\t", dim(x$x)[2], "\n   # samples:\t", dim(x$x)[1], "\n")
     cat(
       "\nModel:",
@@ -152,16 +148,14 @@ function(object, ...)
       }))
    modelInfo <- cbind(numTerms, numVar)
    colnames(modelInfo) <- c("Num Terms", "Num Variables")
-   out <- list(modelInfo = modelInfo, oobStat = oobStat, bagMARSCall = object$call)
+   out <- list(modelInfo = modelInfo, oobStat = oobStat)
    class(out) <- "summary.bagFDA"
    out
 }
 
 "print.summary.bagFDA" <-
 function(x, digits = max(3, getOption("digits") - 3), ...)
 {
-   cat("\nCall:\n", deparse(x$bagMARSCall), "\n\n", sep = "")
-
    oobStat <- apply(x$oob, 2, function(x) quantile(x, probs = c(0, 0.025, .25, .5, .75, .975, 1)))
    cat("Out of bag statistics:\n\n")
    print(x$oobStat, digits = digits)

pkg/caret/R/icr.R

@@ -24,7 +24,6 @@ icr.formula <- function (formula, data, weights, ...,
     res <- icr.default(x, y, weights = w, thresh = thresh, ...)
     res$terms <- Terms
     res$coefnames <- colnames(x)
-    res$call <- match.call()
     res$na.action <- attr(m, "na.action")
     res$contrasts <- cons
     res$xlevels <- .getXlevels(Terms, m)

pkg/caret/R/knn3.R

@@ -7,7 +7,7 @@ knn3.default <- function(x, ...)
 
 knn3.formula <- function (formula, data, subset, na.action, k = 5, ...) 
 {
-    cl <- match.call()
+
     if (missing(formula) ||
         (length(formula) != 3) ||
         (length(attr(terms(formula[-2], data = data), "term.labels")) < 1) ||
@@ -36,7 +36,6 @@ knn3.formula <- function (formula, data, subset, na.action, k = 5, ...)
     RET <- list(learn = list(y = y, X = x))
     RET$k <- k
     RET$terms <- Terms
-    RET$call <- match.call(expand.dots = TRUE)
     RET$contrasts <- attr(x, "contrasts")
     RET$xlevels <- xlev
     RET$theDots <- list(...)
@@ -51,8 +50,6 @@ knn3.data.frame <- function(x, y, k = 5, ...)
 {
   x <- as.matrix(x)
   out <- knn3(x, y = y, k = k, ...)
-  call <- match.call(expand.dots = TRUE)
-  out$call <- call
   out
 }
 
@@ -63,7 +60,6 @@ knn3.matrix <- function(x, y, k = 5, ...)
     RET <- list(learn = list(y = y, X = x))
     RET$k <- k
     RET$terms <- NULL
-    RET$call <- match.call(expand.dots = TRUE)
     RET$contrasts <- NULL
     RET$xlevels <- NULL
     RET$theDots <- list(...)    
@@ -74,7 +70,6 @@ knn3.matrix <- function(x, y, k = 5, ...)
 print.knn3 <- function (x, ...) 
 {
    cat(x$k, "-nearest neighbor classification model\n", sep = "")
-   printCall(x$call)
    cat("Training set class distribution:\n")
    print(table(x$learn$y))
 

pkg/caret/R/knnreg.R

@@ -7,7 +7,6 @@ knnreg.default <- function(x, ...)
 
 knnreg.formula <- function (formula, data, subset, na.action, k = 5, ...) 
 {
-  cl <- match.call()
   if (missing(formula) ||
       (length(formula) != 3) ||
       (length(attr(terms(formula[-2],  data = data), "term.labels")) < 1) ||
@@ -36,7 +35,6 @@ knnreg.formula <- function (formula, data, subset, na.action, k = 5, ...)
   RET <- list(learn = list(y = y, X = x))
   RET$k <- k
   RET$terms <- Terms
-  RET$call <- match.call(expand.dots = TRUE)
   RET$contrasts <- attr(x, "contrasts")
   RET$xlevels <- xlev
   RET$theDots <- list(...)
@@ -54,7 +52,6 @@ knnreg.matrix <- function(x, y, k = 5, ...)
   RET <- list(learn = list(y = y, X = x))
   RET$k <- k
   RET$terms <- NULL
-  RET$call <- match.call(expand.dots = TRUE)
   RET$contrasts <- NULL
   RET$theDots <- list(...)    
   class(RET) <- "knnreg"
@@ -69,7 +66,6 @@ knnreg.data.frame <- function(x, y, k = 5, ...)
   RET <- list(learn = list(y = y, X = x))
   RET$k <- k
   RET$terms <- NULL
-  RET$call <- match.call(expand.dots = TRUE)
   RET$contrasts <- NULL
   RET$theDots <- list(...)    
   class(RET) <- "knnreg"
@@ -79,7 +75,6 @@ knnreg.data.frame <- function(x, y, k = 5, ...)
 print.knnreg <- function (x, ...) 
 {
   cat(x$k, "-nearest neighbor regression model\n", sep = "")
-  printCall(x$call)
   invisible(x)
 }
 

pkg/caret/R/pcaNNet.R

@@ -32,7 +32,6 @@ pcaNNet.formula <- function (formula, data, weights, ...,
     res <- pcaNNet.default(x, y, weights = w, thresh = thresh, ...)
     res$terms <- Terms
     res$coefnames <- colnames(x)
-    res$call <- match.call()
     res$na.action <- attr(m, "na.action")
     res$contrasts <- cons
     res$xlevels <- .getXlevels(Terms, m)

pkg/caret/R/plsda.R

@@ -173,6 +173,5 @@ print.plsda <- function (x, ...) {
   switch(x$probMethod,
          softmax = cat("\nThe softmax function was used to compute class probabilities.\n"),
          Bayes = cat("\nBayes rule was used to compute class probabilities.\n"))
-  printCall(x$call)
   invisible(x)
 }

pkg/caret/inst/NEWS.Rd

@@ -13,6 +13,7 @@
 		\item A new argument to \code{lift} called \code{cuts} was added to allow more control over what thresholds are used to calculat the curve.
 		\item The \code{cuts} argument of \code{calibration} now accepts a vector of cut points.
 		\item Jason Schadewald noticed and fixed a bug in the man page for \code{dummyVars}
+		\item Call objects were remoed from the following models: \code{avNNet}, \code{bagFDA}, \code{icr}, \code{knn3}, \code{knnreg}, \code{pcaNNet}, and \code{plsda}.
 	}
 }