Merge pull request PranaGeo#17 from yilmazbrs/dev

Pulling Dev from Baris

DESCRIPTION

@@ -36,7 +36,7 @@ Collate:
     SpcList-Class.R
     SpcList-Methods.R
     geoSpectral.R
-RoxygenNote: 6.0.1
+RoxygenNote: 5.0.1
 Suggests:
     testthat,
     xlsx

R/SpcList-Methods.R

@@ -38,7 +38,7 @@
 #'
 #' 
 #' @usage 
-#' spc.plot.grid(x,FUN, nnrow, nncol, mar=c(4,4.5,1,0.5),oma = c(0,0,0,0), lab_cex, ...)
+#' spc.plot.grid(x,FUN, nnrow, nncol, mar,oma, lab_cex, ...)
 #' @param x	 a \code{SpcList} data 
 #' @param FUN a character string giving the name of the ploting function to be used. 
 #' Can be either of "spc.plot"
@@ -55,7 +55,7 @@
 #' spc.plot.grid(BL,"spc.plot",3,2)
 #' 
 setGeneric (name= "spc.plot.grid",
-		def=function(x,FUN, nnrow, nncol,...){standardGeneric("spc.plot.grid")})
+		def=function(x,FUN, nnrow, nncol,mar, oma, lab_cex,...){standardGeneric("spc.plot.grid")})
 setMethod("spc.plot.grid", "SpcList", function (x,FUN, nnrow, nncol, mar=c(4,4.5,1,0.5), 
 				oma = c(0,0,0,0), lab_cex, ...){
 			nb_spc = length(which(sapply(x, inherits, "Spectra")))
@@ -105,7 +105,7 @@ setMethod("spc.plot.grid", "SpcList", function (x,FUN, nnrow, nncol, mar=c(4,4.5
 #' is plotted with spc.plot() while remaining elements are overlaid with spc.lines().
 #' 
 #' @usage 
-#' spc.plot.overlay(x,lab_cex=1,leg_idx=T, type="l", lty=1,lwd=1, col, ...)
+#' spc.plot.overlay(object,lab_cex,leg_idx, type, lty,lwd, col, ...)
 #' @param x	 a \code{SpcList} data 
 #' @param lab_cex vector of character expansion sizes, used cyclically
 #' @param type character string (length 1 vector) or vector of 1-character strings indicating the type of plot for each column of y, 
@@ -124,7 +124,7 @@ setMethod("spc.plot.grid", "SpcList", function (x,FUN, nnrow, nncol, mar=c(4,4.5
 #' spc.plot.overlay(BL, col=c("red","blue","green","yellow","cyan","black"))
 #' 
 setGeneric (name= "spc.plot.overlay",
-		def=function(object, ...){standardGeneric("spc.plot.overlay")})
+		def=function(object,lab_cex, leg_idx, type, lty, lwd, col, ...){standardGeneric("spc.plot.overlay")})
 setMethod("spc.plot.overlay", "SpcList", function (object, lab_cex=1,leg_idx=T, type="l", lty=1,lwd=1, col, ...){
 			if(missing(col))
 				col = 1:length(object)
@@ -207,7 +207,7 @@ setMethod("spc.plot.overlay", "SpcList", function (object, lab_cex=1,leg_idx=T,
 #' 
 #' 
 setGeneric (name= "spc.plot.depth.overlay",
-		def=function(object,X,...){standardGeneric("spc.plot.depth.overlay")})
+		def=function(object,X,lab_cex,...){standardGeneric("spc.plot.depth.overlay")})
 setMethod("spc.plot.depth.overlay", "SpcList", function (object, X, lab_cex, ...){
 			if(missing(lab_cex))
 				lab_cex = 1
@@ -244,8 +244,6 @@ setMethod("spc.plot.depth.overlay", "SpcList", function (object, X, lab_cex, ...
 #' Subsetting can be achieved using the implementation of the R function subset() for \code{Spectra} and SpcList classes
 #'It is possible to perform a row-wise selection
 #'
-#' @usage 
-#' subset(x,y,select,...)
 #' 
 #' 
 #' @param drop passed on to [ indexing operator. Default is FALSE 
@@ -507,8 +505,6 @@ setMethod("spc.getheader", signature = "list", def = function (object,name){
 #' @description
 #' Function sets or changes the value of a field in the header slot of \code{spclist} object
 #'
-#'@usage 
-#' spc.setheader(x,name,...)<-value
 #'
 #' @param value Object of class SpcList
 #' @param x A \code{SpcList} object 
@@ -544,8 +540,6 @@ setReplaceMethod(f="spc.setheader", signature="list",
 #' @description
 #'  Updates or changes the value of a field in the header slot of \code{spclist} object 
 #'
-#' @usage 
-#' spc.updateheader(object,name,...)<-value
 #' @param ... arguments to be passed to or from other methods 
 #' @param object A \code{Spectra} objec 
 #' @param name of the header field to be updated

R/Spectra-Methods.R

@@ -555,8 +555,8 @@ setReplaceMethod("spc.colnames", signature = "Spectra", def = function (x,value)
 #' spc.plot(x)
 #' 
 #' 
-setGeneric("spc.plot",function(x,Y,...){standardGeneric("spc.plot")})
-setMethod("spc.plot", "Spectra", function (x, Y, maxSp, lab_cex,type="l",pch=19,lwd=2,cex=0.3,...){						
+setGeneric("spc.plot",function(x,Y,maxSp,lab_cex,xlab,ylab,type,pch,lwd,cex,...){standardGeneric("spc.plot")})
+setMethod("spc.plot", "Spectra", function (x, Y, maxSp, lab_cex,xlab,ylab,type="l",pch=19,lwd=2,cex=0.3,...){						
   if (length(x@InvalidIdx)==0)
     x@InvalidIdx = rep(FALSE,nrow(x@Spectra))
 
@@ -685,7 +685,7 @@ setMethod("spc.lines",signature = "Spectra",definition = function(x,...){
 #' 
 #compressHeader=T Compress the header (make multiple all-equal header elements as ONE	
 setGeneric (name= "spc.rbind",def=function(...){standardGeneric("spc.rbind")})
-setMethod("spc.rbind", signature = "Spectra", def = function (...,compressHeader=T){
+setMethod("spc.rbind", signature = "Spectra", def = function (...,compressHeader=TRUE){
   #Check that column names match
   DFL=sapply(list(...),function(x) names(x@data),simplify=F)
   if(!all(sapply(1:length(DFL),function(x) all(DFL[[x]]==DFL[[1]]))))
@@ -1234,7 +1234,6 @@ setMethod("spc.getheader", signature = "Spectra",
 #'
 #'@usage 
 #' spc.setheader(x,name,...)<-value
-#'
 #' @seealso \code{\link{spc.getheader}}
 #' @param value Object of class SpcHeader
 #' @param x A \code{Spectra} object 
@@ -1251,7 +1250,7 @@ setGeneric (name="spc.setheader<-",
 setReplaceMethod(f="spc.setheader", signature="Spectra",
                  definition=function(object,value){
                    stopifnot(class(value)=="SpcHeader")
-                   object@header<-value
+                   object@header<-value 
                    validObject(object)
                    return(object)
                  })
@@ -1276,7 +1275,7 @@ setReplaceMethod(f="spc.setheader", signature="Spectra",
 setGeneric (name="spc.updateheader<-",
             def=function(object,Name,value,...){standardGeneric("spc.updateheader<-")})
 setReplaceMethod(f="spc.updateheader", signature="Spectra",
-                 definition=function(object,Name,value){
+                 definition=function(object,Name,value,...){
                    hdr=spc.getheader(object)
                    hdr[[Name]]=value
                    spc.setheader(object)<-hdr
@@ -1462,8 +1461,6 @@ setMethod("spc.data2header", signature = "Spectra",
 #' @description
 #' Get  the header for data of each element  with a column
 #'
-#' @usage 
-#' spc.header2data(object,headerfield,dataname,...)
 #'
 #' 
 #' @param dataname list \code{Spectra} object
@@ -1488,7 +1485,7 @@ setMethod("spc.data2header", signature = "Spectra",
 #its elements will be pasted using paste(...,collapse="|"). If it is another 
 #type, only the first element will be taken.  
 setGeneric(name= "spc.header2data",
-           def=function(object,headerfield,dataname,...){standardGeneric("spc.header2data")})
+           def=function(object,headerfield,dataname,compress,...){standardGeneric("spc.header2data")})
 setMethod("spc.header2data", signature = "Spectra", 
           def=function(object,headerfield,dataname,compress=TRUE,...){
             if(missing(dataname))
@@ -1716,7 +1713,7 @@ setMethod("rep", signature(x = "Spectra"),
 #' spc.interp.spectral(sp[,lbd],c(430,450,500),show.plot=TRUE)
 #' 
 setGeneric (name= "spc.interp.spectral",
-            def=function(source1,target_lbd,...){standardGeneric("spc.interp.spectral")})
+            def=function(source1,target_lbd,show.plot,...){standardGeneric("spc.interp.spectral")})
 setMethod("spc.interp.spectral", signature = "Spectra", 
           def = function (source1,target_lbd,show.plot=FALSE){
             if(missing(target_lbd))