From 4b09a70dd541187010ee3ffa4c7cfc00253908c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Facundo=20Mu=C3=B1oz?= <facundo.munoz@orleans.inra.fr>
Date: Fri, 13 Feb 2015 15:41:47 +0100
Subject: [PATCH] Removed duplicated methods not correctly merged from deev and
 master branches

---
 NAMESPACE                     |  1 -
 R/AllGeneric.R                |  2 --
 R/generics.R                  | 10 ----------
 R/metagene-class.R            |  1 +
 R/remlf90-class.R             | 30 ++++++++++--------------------
 man/Extract.metagene.Rd       |  4 ++--
 man/as.data.frame.metagene.Rd |  4 ++--
 man/as.data.frame.pedigree.Rd |  4 ++--
 man/get_ntraits.Rd            |  4 ++--
 man/get_pedigree.Rd           | 11 ++---------
 man/ngenerations.Rd           |  4 ++--
 man/nindividuals.Rd           |  4 ++--
 man/plot.metagene.Rd          |  4 ++--
 man/read.metagene.Rd          |  4 ++--
 14 files changed, 29 insertions(+), 58 deletions(-)
 delete mode 100644 R/generics.R

diff --git a/NAMESPACE b/NAMESPACE
index fc21f6b..6e52299 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,7 +10,6 @@ S3method(extractAIC,remlf90)
 S3method(fitted,remlf90)
 S3method(fixef,remlf90)
 S3method(get_ntraits,metagene)
-S3method(get_pedigree,breedR)
 S3method(get_pedigree,metagene)
 S3method(get_pedigree,remlf90)
 S3method(logLik,remlf90)
diff --git a/R/AllGeneric.R b/R/AllGeneric.R
index dd0e73e..4983e6b 100644
--- a/R/AllGeneric.R
+++ b/R/AllGeneric.R
@@ -5,11 +5,9 @@
 #' @param ... Arguments to be passed to methods.
 #' @references \code{\link[pedigreemm]{pedigree-class}} from package
 #'   \code{pedigreemm}
-#' @family metagene
 #' @export
 get_pedigree <- function(x, ...) UseMethod('get_pedigree')
 
-
 #' Extract the number of traits
 #' @param x a metagene object.
 #' @param ... Arguments to be passed to methods.
diff --git a/R/generics.R b/R/generics.R
deleted file mode 100644
index 1d1470a..0000000
--- a/R/generics.R
+++ /dev/null
@@ -1,10 +0,0 @@
-
-#' Get the Pedigree from an object
-#' 
-#' Returns an object from the formal class \code{pedigree}.
-#' @param x object to extract pedigree from
-#' @param ... Arguments to be passed to methods.
-#' @references \code{\link[pedigreemm]{pedigree-class}} from package
-#'   \code{pedigreemm}
-#' @export
-get_pedigree <- function(x, ...) UseMethod('get_pedigree')
diff --git a/R/metagene-class.R b/R/metagene-class.R
index 0759408..3200c23 100644
--- a/R/metagene-class.R
+++ b/R/metagene-class.R
@@ -231,6 +231,7 @@ nindividuals.metagene <- function(x, exclude.founders = FALSE, ...) {
 }
 
 #' @describeIn get_pedigree Get the pedigree from a \code{metagene} object
+#' @family metagene
 #' @export
 get_pedigree.metagene <- function(x, ...) {
   return(with(x$Data, pedigreemm::pedigree(sire=dad, dam=mum, label=self)))
diff --git a/R/remlf90-class.R b/R/remlf90-class.R
index e1ee3db..5bf8370 100644
--- a/R/remlf90-class.R
+++ b/R/remlf90-class.R
@@ -584,19 +584,6 @@ remlf90 <- function(fixed,
 #### Interface methods ####
 #%%%%%%%%%%%%%%%%%%%%%%%%%#
 
-#' @describeIn get_pedigree Get the pedigree from a remlf90 object
-#' @export
-get_pedigree.remlf90 <- function(x, ...) {
-  ped <- x$effects$genetic$ped
-  if( !is.null(ped) ) {
-    map <- attr(ped, 'map')
-    ped <- with(ped,
-                pedigreemm::pedigree(sire=sire, dam=dam, label=self))
-    attr(ped, 'map') <- map
-  }
-  return(ped)
-}
-
 #' @export
 coef.remlf90 <- function(object, ...) { 
   unlist(c(lapply(fixef(object),
@@ -665,14 +652,17 @@ fixef.remlf90 <- function (object, ...) {
 }
 
 
-#' @describeIn get_pedigree Get the pedigree from a \code{breedR} object
+#' @describeIn get_pedigree Get the pedigree from a remlf90 object
 #' @export
-get_pedigree.breedR <- function(x, ...) {
-  if( !x$components$pedigree )
-    stop(paste('No genetic component in', substitute(x)))
-  
-  return(with(x$effects$genetic$ped,
-              pedigreemm::pedigree(sire=sire, dam=dam, label=self)))
+get_pedigree.remlf90 <- function(x, ...) {
+  ped <- x$effects$genetic$ped
+  if( !is.null(ped) ) {
+    map <- attr(ped, 'map')
+    ped <- with(ped,
+                pedigreemm::pedigree(sire=sire, dam=dam, label=self))
+    attr(ped, 'map') <- map
+  }
+  return(ped)
 }
 
 
diff --git a/man/Extract.metagene.Rd b/man/Extract.metagene.Rd
index b8050f0..852f9f7 100644
--- a/man/Extract.metagene.Rd
+++ b/man/Extract.metagene.Rd
@@ -35,8 +35,8 @@ Subset data
 Other metagene: \code{\link{as.data.frame.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{nindividuals}};
   \code{\link{plot.metagene}}; \code{\link{read.metagene}}
 }
diff --git a/man/as.data.frame.metagene.Rd b/man/as.data.frame.metagene.Rd
index b146e0a..77ccc34 100644
--- a/man/as.data.frame.metagene.Rd
+++ b/man/as.data.frame.metagene.Rd
@@ -30,8 +30,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{Extract.metagene}}, \code{\link{[.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{nindividuals}};
   \code{\link{plot.metagene}}; \code{\link{read.metagene}}
 }
diff --git a/man/as.data.frame.pedigree.Rd b/man/as.data.frame.pedigree.Rd
index 66930f3..c93f3ea 100644
--- a/man/as.data.frame.pedigree.Rd
+++ b/man/as.data.frame.pedigree.Rd
@@ -26,8 +26,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{Extract.metagene}}, \code{\link{[.metagene}};
   \code{\link{as.data.frame.metagene}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{nindividuals}};
   \code{\link{plot.metagene}}; \code{\link{read.metagene}}
 }
diff --git a/man/get_ntraits.Rd b/man/get_ntraits.Rd
index d0d1705..7a03fb9 100644
--- a/man/get_ntraits.Rd
+++ b/man/get_ntraits.Rd
@@ -21,8 +21,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{as.data.frame.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{nindividuals}};
   \code{\link{plot.metagene}}; \code{\link{read.metagene}}
 }
diff --git a/man/get_pedigree.Rd b/man/get_pedigree.Rd
index d01523c..c912531 100644
--- a/man/get_pedigree.Rd
+++ b/man/get_pedigree.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/AllGeneric.R, R/metagene-class.R, R/remlf90-class.R
 \name{get_pedigree}
 \alias{get_pedigree}
-\alias{get_pedigree.breedR}
 \alias{get_pedigree.metagene}
 \alias{get_pedigree.remlf90}
 \title{Get the Pedigree from an object}
@@ -11,7 +10,7 @@ get_pedigree(x, ...)
 
 \method{get_pedigree}{metagene}(x, ...)
 
-\method{get_pedigree}{breedR}(x, ...)
+\method{get_pedigree}{remlf90}(x, ...)
 }
 \arguments{
 \item{x}{object to extract pedigree from}
@@ -23,15 +22,9 @@ Returns an object from the formal class \code{pedigree}.
 }
 \section{Methods (by class)}{
 \itemize{
-<<<<<<< HEAD
-\item \code{metagene}: Get the pedigree from a metagene object
-
-\item \code{remlf90}: Get the pedigree from a remlf90 object
-=======
 \item \code{metagene}: Get the pedigree from a \code{metagene} object
 
-\item \code{breedR}: Get the pedigree from a \code{breedR} object
->>>>>>> dev
+\item \code{remlf90}: Get the pedigree from a remlf90 object
 }}
 \references{
 \code{\link[pedigreemm]{pedigree-class}} from package
diff --git a/man/ngenerations.Rd b/man/ngenerations.Rd
index dc105c3..c2b3906 100644
--- a/man/ngenerations.Rd
+++ b/man/ngenerations.Rd
@@ -21,8 +21,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{as.data.frame.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{nindividuals}}; \code{\link{plot.metagene}};
   \code{\link{read.metagene}}
 }
diff --git a/man/nindividuals.Rd b/man/nindividuals.Rd
index 8f031cc..4061c64 100644
--- a/man/nindividuals.Rd
+++ b/man/nindividuals.Rd
@@ -21,8 +21,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{as.data.frame.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{plot.metagene}};
   \code{\link{read.metagene}}
 }
diff --git a/man/plot.metagene.Rd b/man/plot.metagene.Rd
index 095c409..f4beb09 100644
--- a/man/plot.metagene.Rd
+++ b/man/plot.metagene.Rd
@@ -24,8 +24,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{as.data.frame.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{nindividuals}};
   \code{\link{read.metagene}}
 }
diff --git a/man/read.metagene.Rd b/man/read.metagene.Rd
index 01d5515..93bd67c 100644
--- a/man/read.metagene.Rd
+++ b/man/read.metagene.Rd
@@ -28,8 +28,8 @@ Other metagene: \code{\link{$.metagene}},
   \code{\link{as.data.frame.metagene}};
   \code{\link{as.data.frame.pedigree}};
   \code{\link{get_ntraits}}; \code{\link{get_pedigree}},
-  \code{\link{get_pedigree.breedR}},
-  \code{\link{get_pedigree.metagene}};
+  \code{\link{get_pedigree.metagene}},
+  \code{\link{get_pedigree.remlf90}};
   \code{\link{ngenerations}}; \code{\link{nindividuals}};
   \code{\link{plot.metagene}}
 }