updts

.Rbuildignore

@@ -2,6 +2,7 @@
 ^\.Rproj\.user$
 vignette\surrosurv.Rnw
 vignette\surrosurv.bbl
+vignette\Sweave.sty
 vignette\surrosurv.log
 vignette\surrosurv.syntex.gz
 ^\.travis\.yml$

DESCRIPTION

@@ -2,8 +2,8 @@ Package: surrosurv
 Type: Package
 Title: Evaluation of Failure Time Surrogate Endpoints in Individual Patient Data
     Meta-Analyses
-Version: 1.1.23
-Date: 2017-08-16
+Version: 1.1.25
+Date: 2017-12-13
 Authors@R: c(
   person("Federico", "Rotolo", email="[email protected]", 
           role=c("aut", "cre")),

NAMESPACE

@@ -38,6 +38,8 @@ S3method(print, conv)
 S3method(loocv, data.frame)
 
 S3method(confint, surrosurv)
+S3method(convals, surrosurv)
+S3method(convergence, surrosurv)
 S3method(loocv, surrosurv)
 S3method(predict, surrosurv)
 S3method(print, surrosurv)

R/convergence.R

@@ -1,10 +1,9 @@
-#####################################################################################
-#####################################################################################
-#####################################################################################
-convals <- function(x) {
-  if (!'surrosurv' %in% class(x))
-    stop('x must be of class surrosurv')
-
+# ---------------------------------------------------------------------------- #
+convals <- function(x, ...) UseMethod('convals')
+# ---------------------------------------------------------------------------- #
+
+# ---------------------------------------------------------------------------- #
+convals.surrosurv <- function(x, ...) {
   models <- c('Clayton', 'Plackett', 'Hougaard', 'Poisson')
   models <-
     models[sapply(models, function(y)
@@ -82,27 +81,30 @@ convals <- function(x) {
   class(fitRES) <- 'conv'
   return(fitRES)
 }
+# ---------------------------------------------------------------------------- #
 
-#####################################################################################
-#####################################################################################
-#####################################################################################
-convergence <- function(x, kkttol = 1e-2, kkt2tol = 1e-8) {
-  if (!'surrosurv' %in% class(x))
-    stop('x must be of class surrosurv')
-
+
+# ---------------------------------------------------------------------------- #
+convergence <- function(x, kkttol = 1e-2, kkt2tol = 1e-8, ...)
+  UseMethod('convergence')
+# ---------------------------------------------------------------------------- #
+
+
+# ---------------------------------------------------------------------------- #
+convergence.surrosurv <- function(x, kkttol = 1e-2, kkt2tol = 1e-8, ...) {
   ConvRES <- convals(x)
   checkConvRES <- cbind(ConvRES[, 1, drop = FALSE] <= kkttol,
                         ConvRES[, 2:3] > kkt2tol)
 
   class(checkConvRES) <- 'conv'
   return(checkConvRES)
 }
+# ---------------------------------------------------------------------------- #
 
-#####################################################################################
-#####################################################################################
-#####################################################################################
 
+# ---------------------------------------------------------------------------- #
 print.conv <- function(x, na.print = '---', ...) {
   class(x) <- 'matrix'
   print(x, na.print = na.print, ...)
-}
+}
+# ---------------------------------------------------------------------------- #

man/convergence.Rd

@@ -1,6 +1,8 @@
 \name{convergence}
 \alias{convergence}
+\alias{convergence.surrosurv}
 \alias{convals}
+\alias{convals.surrosurv}
 \title{
   Assesses the convergence of fitted models for surrogacy evaluation
 }
@@ -13,8 +15,8 @@
     are positive definite.
 }
 \usage{
-  convals(x)
-  convergence(x, kkttol = 1e-2, kkt2tol = 1e-8)
+  \method{convals}{surrosurv}(x, ...)
+  \method{convergence}{surrosurv}(x, kkttol = 1e-2, kkt2tol = 1e-8, ...)
 }
 \arguments{
   \item{x}{
@@ -31,6 +33,9 @@
       are positive definite.
     The threshold is for the minimum of the eigenvalues.
   }
+  \item{...}{
+    Further parameters (not implemented)
+  }
 }
 
 \value{