minor updates

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: FieldSpec
 Type: Package
-Title: Functions useful for processing field spectroscopy data
+Title: Functions for processing field spectroscopy data
 Version: 0.89
-Date: 2013-09-17
+Date: 2013-09-18
 Author: Shawn P. Serbin
 Maintainer: Shawn P. Serbin <[email protected]>
 Description: A field spectroscopy package containing functions to process
     spectral files collected with an Analytical Spectral Devices (ASD) or
-    Spectral Evolution instrument. The goal is to stream line and standardize
-    spectral data processing for use in ecology, remote sensing, and plant
+    Spectral Evolution instrument. The goal is to streamline and standardize
+    spectral data processing for use in remote sensing, ecology, and plant
     ecophysiological research.
 Depends:
     XML,

R/read.asd.R

@@ -199,9 +199,7 @@ read.asd = function(file.dir=NULL, out.dir=NULL, start.wave=NULL, end.wave=NULL,
 
     ### Close progress bar
     close(pb)
-
-    ### Return spectra data object if requested i.e. spec.dataframe=TRUE
-
+
   } else {
     to.read <- file(file.dir, "rb")
 

inst/examples/process_spectra.r

@@ -27,9 +27,12 @@ settings <- settings('/Users/serbin/Data/Dropbox/SoyFACE/R_Spectra_Training/SoyF
 #--------------------------------------------------------------------------------------------------#
 # Run each function separately
 
+### Get metadata
+metadata <- extract.metadata(settings.file=settings,intern=TRUE)
+
 ### Import ASD binary files to ASCII format
-read.asd(settings.file=settings,spec.dataframe = FALSE)   # Using settings file
-spectra <- read.asd(settings.file=settings,spec.dataframe = TRUE) # output a dataframe with the spectra
+read.asd(settings.file=settings)   # Using settings file
+spectra <- read.asd(settings.file=settings) # output a dataframe with the spectra
 
 # Look at spectra
 plot(seq(350,2500,1),spectra[2,2:dim(spectra)[2]],type="l")

inst/extdata/settings.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <settings>
   <!-- Directory of ASD files or sub-directories to process -->
-  <asd.dir>PATH TO ASD FILES</asd.dir>
+  <spec.dir>PATH TO SPECTRA FILES</spec.dir>
   <!-- Main output directory -->
   <output.dir>PATH TO OUTPUT</output.dir>
   <instrument>