Merge branch 'dev'

.Rbuildignore

@@ -1,2 +1,7 @@
-^.*\.Rproj$
-^\.Rproj\.user$
+^anap.txt$
+^anap_header.txt$
+^geoSpectral.Rproj
+^.*\.Rproj$         # Automatically added by RStudio,
+^\.Rproj\.user$     # used for temporary files. 
+^NEWS\.md$          # A news file written in Markdown
+^\.travis\.yml$     # Used for continuous integration testing with travis

DESCRIPTION

@@ -1,31 +1,46 @@
 Package: geoSpectral
 Type: Package
-Title: Classes and methods for spectral (optical) data
-Version: 0.11
-Date: 2012-07-02
+Title: Classes and Methods for Working with Spectral Data with Space-Time Attributes
+Version: 0.17.5
+Date: 2020-02-17
 Depends:
-    R (>= 2.10.0),
+    R (>= 2.10.0)
+Imports:
     methods,
-    rgdal,
+    dplyr,
     spacetime,
-    reshape2
-Author: Servet Cizmeli
-Maintainer: Servet Cizmeli <[email protected]>
-Description: This package provides S4 classes and basic manipulation methods
-    for datasets frequently used in remote sensing, bio-optical oceanography and
-    environmental and earth sciences. The package is based on the data type called
-    Spectra which extends the STIDF class of package spacetime. Spatial/temporal and
-    spectral aspects of Bio-Optical data that are regularly collected during Bio-
-    Optical oceanography campaigns can be easily represented with the Spectra class.
+    xts,
+    maps,
+    rgdal,
+    leaflet,
+    rbokeh,
+    plotly,
+    sp,
+    stats
+Author: Servet Ahmet Cizmeli [aut, cre] (<https://orcid.org/0000-0001-6694-9305>)
+Authors@R: 
+    person("Servet Ahmet", "Cizmeli", , "[email protected]", c("aut", "cre"), comment = c(ORCID = "0000-0001-6694-9305"))
+Maintainer: Servet Ahmet Cizmeli <[email protected]>
+URL: https://github.com/PranaGeo/geoSpectral
+BugReports: https://github.com/PranaGeo/geoSpectral/issues
+Description: Provides S4 classes and data import, preprocessing, graphing, 
+    manipulation and export methods for geo-Spectral datasets (datasets with space/time/spectral 
+    dimensions). These type of data are frequently collected within earth observation projects 
+    (remote sensing, spectroscopy, bio-optical oceanography, mining, agricultural, atmospheric, 
+    environmental or similar branch of science).
 License: GPL
 LazyLoad: yes
 Collate:
+    geoSpectral.R
     SpcHeader-Class.R
     SpcHeader-Methods.R
     Spectra-Class.R
     Spectra-Methods.R
     SpcList-Class.R
     SpcList-Methods.R
-    geoSpectral.R
-RoxygenNote: 6.0.1
-Suggests: testthat
+    Spectra-ImportFuns.R
+RoxygenNote: 7.0.2
+Suggests:
+    testthat,
+    xlsx,
+    geoSpectral

NAMESPACE

@@ -1 +1,122 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export("spc.colnames<-")
+export("spc.setheader<-")
+export("spc.setinvalid.idx<-")
+export("spc.setselected.idx<-")
+export("spc.setwavelengths<-")
+export(SpcHeaderAdd)
+export(SpcList)
+export(Spectra)
+export(spc.Read_ASD)
+export(spc.Read_NOMAD_v2)
+export(spc.STI.stdistance)
+export(spc.bbox2lines)
+export(spc.cname.construct)
+export(spc.colMeans)
+export(spc.colnames)
+export(spc.data2header)
+export(spc.example_spectra)
+export(spc.export.text)
+export(spc.export.xlsx)
+export(spc.getheader)
+export(spc.getinvalid.idx)
+export(spc.getselected.idx)
+export(spc.getwavelengths)
+export(spc.header.infos)
+export(spc.header2data)
+export(spc.import.text)
+export(spc.interp.spectral)
+export(spc.invalid.detect)
+export(spc.lapply)
+export(spc.lines)
+export(spc.make.stindex)
+export(spc.makeSpcList)
+export(spc.plot)
+export(spc.plot.depth)
+export(spc.plot.depth.overlay)
+export(spc.plot.depth.plotly)
+export(spc.plot.grid)
+export(spc.plot.map.leaflet)
+export(spc.plot.map.plotly)
+export(spc.plot.map.rbokeh)
+export(spc.plot.overlay)
+export(spc.plot.plotly)
+export(spc.plot.time)
+export(spc.plot.time.plotly)
+export(spc.rbind)
+export(spc.select)
+export(spc.timeMatch)
+export(spc.updateheader)
+exportClasses(SpcHeader)
+exportClasses(SpcHeaderList)
+exportClasses(SpcList)
+exportClasses(Spectra)
+exportMethods("$")
+exportMethods("spc.setheader<-")
+exportMethods(dim)
+exportMethods(head)
+exportMethods(names)
+exportMethods(ncol)
+exportMethods(nrow)
+exportMethods(rep)
+exportMethods(show)
+exportMethods(sort)
+exportMethods(spc.data2header)
+exportMethods(spc.getheader)
+exportMethods(spc.header2data)
+exportMethods(spc.invalid.detect)
+exportMethods(spc.rbind)
+exportMethods(spc.updateheader)
+exportMethods(subset)
+import(maps)
+import(methods)
+import(rgdal)
+import(sp)
+import(spacetime)
+import(xts)
+importClassesFrom(spacetime,STIDF)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,everything)
+importFrom(dplyr,select)
+importFrom(grDevices,dev.new)
+importFrom(grDevices,rainbow)
+importFrom(graphics,abline)
+importFrom(graphics,axis)
+importFrom(graphics,box)
+importFrom(graphics,grid)
+importFrom(graphics,hist)
+importFrom(graphics,legend)
+importFrom(graphics,lines)
+importFrom(graphics,locator)
+importFrom(graphics,matlines)
+importFrom(graphics,matplot)
+importFrom(graphics,matpoints)
+importFrom(graphics,mtext)
+importFrom(graphics,par)
+importFrom(graphics,plot.new)
+importFrom(graphics,points)
+importFrom(graphics,title)
+importFrom(leaflet,"%>%")
+importFrom(leaflet,addCircles)
+importFrom(leaflet,addTiles)
+importFrom(leaflet,leaflet)
+importFrom(plotly,add_trace)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)
+importFrom(plotly,subplot)
+importFrom(plotly,toRGB)
+importFrom(rbokeh,"%>%")
+importFrom(rbokeh,figure)
+importFrom(rbokeh,ly_map)
+importFrom(rbokeh,ly_points)
+importFrom(sp,Line)
+importFrom(sp,Lines)
+importFrom(sp,SpatialPoints)
+importFrom(sp,coordinates)
+importFrom(sp,spDistsN1)
+importFrom(stats,approx)
+importFrom(stats,time)
+importFrom(utils,modifyList)
+importFrom(utils,read.table)
+importFrom(utils,write.table)

NEWS.md

@@ -0,0 +1,12 @@
+# geoSpectral 0.17.5 (2019-02-17)
+
+## Package check warnings
+
+* Fixed the warning during package check : `Documented arguments not in \usage in documentation object spc.setheader<-,list-method: ‘...’`    
+
+## Updated DESCRIPTION
+
+* Added Orcid info to field : Author
+* Added the field : Authors@R
+* Added the field : URL
+* Added the field : BugReports

R/SpcHeader-Class.R

@@ -1,11 +1,15 @@
-# TODO: Add comment
-# 
-# Author: acizmeli
-###############################################################################
 
 #########################################################################
 # Class : SpcHeader	
 #########################################################################
+#' \code{SpcHeader} class for header object storing metadata.
+#' @description Definition for \code{SpcHeader}. This class is required
+#' for the @header slot of \code{Spectra} object. This class directly inherits
+#' R lists, so there is no additional slots.
+#' 
+#' @examples 
+#' new("SpcHeader")
+#' @export
 setClass("SpcHeader", contains="list",
 		prototype=prototype(list(Station=NA,Cruise=NA,Latitude=NA,Longitude=NA)))
 setMethod("initialize",
@@ -27,6 +31,16 @@ setValidity("SpcHeader", function(object){
 #########################################################################
 # Class : SpcHeaderList	
 #########################################################################
+#'  \code{SpcHeaderList} class.
+#' @description Definition for \code{SpcHeaderList}. This class provides
+#' a collection of multiple \code{SpcHeader} objects inside a list.
+#' 
+#' @examples 
+#' h1 = new("SpcHeader")
+#' h2 = new("SpcHeader")
+#' as(list(h1, h2), "SpcHeaderList")
+#' new("SpcHeaderList") 
+#' @export
 setClass("SpcHeaderList", contains="list",
 		prototype=prototype(list(new("SpcHeader"))))
 

R/SpcHeader-Methods.R

@@ -1,53 +1,28 @@
-#########################################################################
-# Method : spc.ScanFileName  
-#########################################################################
-#Uses FileNameScanTemplate
-#If there is Skip in the field name, it will be skipped
-#Scan : A string, can be either of "DirName" or "FileName".
-spc.ScanFileName = function(template, in.listnames,Scan) {
-  #Take the first instrument
-  out = SpcHeaderAdd(template, "InBaseName", basename(in.listnames))
-  out = SpcHeaderAdd(out, "InDirName", dirname(in.listnames))
-
-  mytemplate = switch(Scan,
-         DirName = "DirNameScanTemplate",
-         FileName = "FileNameScanTemplate")
-
-  if (is.character(template[[mytemplate]])){		
-    for (I in 1:length(template[[mytemplate]])){
-
-      if(!grepl(template[[mytemplate]][I],"Skip", ignore.case=T)) {
-        if (class(out)=="SpcHeader")
-          EXT = out$extension
-        if (class(out)=="SpcHeaderList")
-          EXT = out[[1]]$extension
-        #Choose the directory name in the hierarchy that contains the tags
-        try(tags<- ExtractTagFromFilename(in.listnames, REV_TAGNO=template$ReverseDirTagNo, SEP="/"),silent=T)
-        if (!exists("tags") || is.null(tags))
-          tags = ExtractTagFromFilename(in.listnames, REV_TAGNO=1, SEP="/")
-
-        #Determine the tags in the input directory name
-        tags = ExtractTagFromFilename(tags, TAGNO=I, SEP="_",  EXT)
-
-        #If it is the Date field, use DatesFromFilename() to convert it to an xts object
-        if(template[[mytemplate]][I]=="Date"){
-          temp = DatesFromFilename(tags, "Date", SORT=FALSE)
-          tags = temp$StartDate
-        }
-        tags = gsub(template[[mytemplate]][I],"",tags)
-        out = SpcHeaderAdd(out, template[[mytemplate]][I], tags)
-        rm(tags)
-      }
-    }
-  }
-  return(out)
-}
 
 #########################################################################
 # Method : SpcHeaderAdd	
 #########################################################################
+#'  Set a field of the @header slot of a \code{SpcHeader} class object
+#' @description Function add the value of a field in the header slot of \code{SpcHeader} class object
+#'
+#' @usage 
+#' SpcHeaderAdd (object,Name,Value,...)
+#' 
+#' @param object of class SpcHeader
+#' @param Name a character variable  
+#' @param Value a numeric variable
+#' @param ... arguments to be passed to or from other methods
+#' @examples 
+#' sp=spc.example_spectra()
+#' sp@header
+#' sp@ShortName
+#' sp@header=SpcHeaderAdd(sp@header,sp@ShortName,10)
+#' sp@header
+#' @rdname SpcHeaderAdd
+#' @export
 setGeneric("SpcHeaderAdd",function(object,Name,Value,...)
 		{standardGeneric("SpcHeaderAdd")})
+#' @rdname SpcHeaderAdd
 setMethod("SpcHeaderAdd", signature="SpcHeader", function(object,Name,Value){	
 			templist = list()
 			if (length(Value)>1){
@@ -69,18 +44,33 @@ setMethod("SpcHeaderAdd", signature="SpcHeader", function(object,Name,Value){
 #' Show a SpcHeader object
 #' @description Display a SpcHeader object
 #'
-#' @usage 
-#' show(object)
-#' 
 #' @param object of class SpcHeader
 #' @seealso \code{\link{show}}
 #' 
 #' @examples 
 #' x=spc.example_spectra()
 #' show(x@header)
 #' 
+#' @export
 setMethod("show", signature="SpcHeader", function(object){
 			fieldnames = names(object)
 			sapply(1:length(fieldnames), function(x) cat(paste(fieldnames[x], " : ", 
 										object[fieldnames[x]], "\n")))
-		})
+		})
+setGeneric(name="spc.export.text",
+           def=function(input,filename,writeheader=TRUE,sep=";",...) {standardGeneric("spc.export.text")})
+setMethod("spc.export.text", signature="SpcHeader", definition=function(input,filename,append=F,sep=";",...){
+  nms = names(input)
+  nms = paste("Spectra|header",sep,nms,sep="")
+  browser()
+  out1 = lapply(input,function(x){
+    #If the separator character exists in the header, then eliminate it 
+    x<-gsub(sep,"",x)
+    if(length(x)>1)
+      x<-paste(x,collapse=sep)
+    else
+      x<-as.character(x)
+  })
+  out1 = cbind(nms,out1)
+  write.table(out1,filename,row.names=F,col.names=F,append=append,quote=F,sep=sep)
+})

R/SpcList-Class.R

@@ -1,6 +1,14 @@
 #########################################################################
 # Class : SpcList
 #########################################################################
+#' SpcList class definition
+#' @description Definition for \code{SpcList}, a class to store multiple \code{Spectra}
+#' objects inside a list-like object. See the help of the constructor function \code{\link{SpcList}}.
+#' @slot .Data list, Inherited R list object
+#' @slot by character, Determines the header field in the Spectra objects
+
+#' within the SpcList that describes how they are different one from the other.
+#' @export
 setClass("SpcList",contains="list",
 		representation=representation(by="character"), 
 		prototype=prototype(by="VariousVariables")