remove a function

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GFR
 Title: GFR (Genomic Functional Regression)
-Version: 0.9-15
+Version: 0.9-16
 Date: 2018-02-16
 Authors@R: c(person("Francisco Javier", "Luna-Vazquez", email = "frahik@gmail.com", role = c("aut", "cre")),
              person("Osval Antonio", "Montesinos-Lopez", email= "oamontes1@ucol.mx", role = "aut"),
@@ -34,7 +34,6 @@ Collate:
   Information.R
   Interface.R
   Maize_GFR.R
-  MTME.R
   Utils.R
   Wheat_GFR.R
   WheatI_GFR.R
@@ -49,7 +48,6 @@ Imports:
   truncnorm,
   tidyr,
   dplyr,
-  BMTME,
   IBCF.MTME,
   doParallel,
   foreach,

NAMESPACE

@@ -1,16 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(boxplot,BFRCV)
-S3method(boxplot,MTMECV)
 S3method(plot,BFR)
 S3method(plot,BFRCV)
-S3method(plot,MTMECV)
 S3method(predict,BFR)
 S3method(print,BFRCV)
 S3method(residuals,BFR)
 S3method(summary,BFR)
 S3method(summary,BFRCV)
-S3method(summary,MTMECV)
 export(BFR)
 export(Bspline.Basis)
 export(CV.KFold)
@@ -20,7 +17,6 @@ export(CV.StratifiedByFrac)
 export(ETAGenerate)
 export(FFR)
 export(Fourier.Basis)
-export(MTME)
 export(cholesky)
 export(cleanDat)
 export(detectCores)

R/CrossValidation.R

@@ -9,16 +9,6 @@
 NULL
 
 
-#' Cross-validation with K Folds
-#'
-#' @name CV.KFold
-#' @rdname CV.KFold
-#' @keywords internal
-#' @export
-#' @importFrom BMTME CV.KFold
-#' @usage CV.KFold(data, DataSetID = 'Line', K = 5, set_seed =  123)
-NULL
-
 #' Cross-validation with K Folds
 #'
 #' @name CV.KFold

R/Generic_Methods.R

@@ -66,49 +66,6 @@ summary.BFR <- function(object,...){
 }
 
 
-#' @title Summary.MTMECV
-#'
-#' @description Solo es una prueba
-#'
-#' @param object \code{MTMECV object} Objeto MTMECV, resultado de ejecutar MTME()
-#' @param ... Further arguments passed to or from other methods.
-#' @param information compact, extended, complete
-#'
-#' @importFrom stats cor
-#' @importFrom dplyr summarise group_by select '%>%' mutate_if funs
-#'
-#' @export
-summary.MTMECV <- function(object, information = 'compact', digits = 4, ...){
-  if (!inherits(object, "MTMECV")) Stop("This function only works for objects of class 'MTMECV'")
-
-  object$results %>%
-    group_by(Environment, Trait, Partition) %>%
-    summarise(Pearson = cor(Predicted, Observed, use = 'pairwise.complete.obs'),
-              MSEP = mean((Predicted - Observed)^2, na.rm = T)) %>%
-    select(Environment, Trait, Partition, Pearson, MSEP) %>%
-    mutate_if(is.numeric, funs(round(., digits))) %>%
-    as.data.frame() -> presum
-
-  presum %>%  group_by(Environment, Trait) %>%
-    summarise(SE_MSEP = sd(MSEP, na.rm = T)/sqrt(n()), MSEP = mean(MSEP, na.rm = T),
-              SE_Pearson = sd(Pearson, na.rm = T)/sqrt(n()), Pearson = mean(Pearson, na.rm = T))  %>%
-    select(Environment, Trait, Pearson, SE_Pearson, MSEP, SE_MSEP) %>%
-    mutate_if(is.numeric, funs(round(., digits))) %>%
-    as.data.frame() -> finalSum
-
-  out <- switch(information,
-                compact = finalSum,
-                complete = presum,
-                extended = {
-                  finalSum$Partition <- 'All'
-                  presum$Partition <- as.character(presum$Partition)
-                  presum$SE_Pearson <- NA
-                  presum$SE_MSEP <- NA
-                  rbind(presum, finalSum)
-                }
-  )
-  return(out)
-}
 
 
 #' @title Summary.BFRCV
@@ -335,84 +292,3 @@ boxplot.BFRCV <- function(x, select = 'Pearson', ordered = TRUE, ...){
     boxplot(plot.y, col = "grey", ylab = ylab, ...)
   }
 }
-
-#' @title boxplot.MTMECV
-#'
-#' @description Solo es una prueba
-#'
-#' @param x \code{MTMECV object} Objeto MTMECV, resultado de ejecutar MTME()
-#' @param select \code{string} Pearson or MSEP
-#' @param ordered \code{logic} TRUE or FALSE
-#' @param ... Further arguments passed to or from other methods.
-#'
-#' @importFrom graphics boxplot
-#' @export
-boxplot.MTMECV <- function(x, select = 'Pearson', ordered = TRUE, ...){
-  ### Check that object is compatible
-  if (!inherits(x, "MTMECV")) Error("This function only works for objects of class 'MTMECV'")
-
-  results <- summary(x, 'complete')
-
-  switch (select,
-          Pearson = {
-            plot.y <- results$Pearson
-            ylab <- "Pearson's Correlation"
-          }, MSEP = {
-            plot.y <- results$MSEP
-            ylab <- "MSEP Average"
-          }, CC = {
-            plot.y <- results$CC
-            ylab <- "Classification correct average"
-          },
-          Error('Error in select parameter.')
-  )
-
-  if (length(unique(results$Env)) > 1) {
-    results$TxE <- paste0(results$Trait, '_', results$Env)
-
-    if (ordered && select != 'MSEP') {
-      results$TxE  <- with(results, reorder(TxE , Pearson, median, na.rm = T))
-    } else if (ordered && select == 'MSEP') {
-      results$TxE  <- with(results, reorder(TxE , MSEP, median, na.rm = T))
-    }
-
-    boxplot(plot.y ~ results$TxE, col = "grey", ylab = ylab, ...)
-  }else{
-    boxplot(plot.y, col = "grey", ylab = ylab, ...)
-  }
-}
-
-
-#' @title Plot MTMECV graph
-#'
-#' @description Plot from MTMECV object
-#'
-#' @param x \code{MTMECV object} MTMECV object, result of use the MTME() function
-#' @param select \code{character} By default ('Pearson'), plot the Pearson Correlations of the MTME Object, else ('MSEP'), plot the MSEP of the MTMECV Object.
-#' @param ... Further arguments passed to or from other methods.
-#'
-#' @importFrom graphics arrows axis plot
-#' @export
-plot.MTMECV <- function(x, select = 'Pearson', ...){
-  ### Check that object is compatible
-  if (!inherits(x, "MTMECV")) Error("This function only works for objects of class 'MTMECV'")
-
-  results <- summary(x)
-  results <- results[order(results[, select]),]
-
-  if (select == "Pearson") {
-    results$SE <- 1.96 * results$SE_Pearson
-    ylab <- "Pearson's Correlation"
-  } else if (select == "MSEP") {
-
-    results$SE <- 1.96 * results$SE_MSEP[which(results$Fold == 'Average_all')]
-    ylab <- select
-  }
-  x.labels <- paste0(results$Trait, '_', results$Env)
-  plot.x <- 1:length(x.labels)
-  plot(plot.x, results[, select], ylim = range(c(results[, select] - results$SE, results[, select] + results$SE)),
-       type = 'p', ylab = ylab, xlab = '', xaxt = "n", ...)
-  axis(1, at = plot.x, labels = x.labels, las = 2)
-  arrows(plot.x, results[, select] - results$SE, plot.x, results[, select] + results$SE, code = 3, length = 0.02, angle = 90)
-}
-