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geoSpectral

geoSpectral is an R package providing a new data type for R that stores spectral, temporal and spatial attributes of measurement data as well as methods for accessing and manipulating the spectral (and non-spectral) data. Once spectral data is imported into geoSpectral, the statistical and data processing power of R is available for various kinds of scientific analyses.

It provides the S4 classes: Spectra (stores spatial/temporal/spectral aspects of data), SpcHeader (stores metadata in an R list object) and SpcList (makes a collection of Spectra objects in an R list) as well as basic data access and manipulation methods for importing, acessing and subsetting, converting into R objects, analyzing, plotting and exporting scientific earth observation data.

License

The package is issued with a GPLv3 license. Please consult the license documentation if you would like to use geoSpectral in your software projects.

Quick Installation

To install geoSpectral, try the following R commands :

#Stable Version from CRAN
install.packages("geoSpectral")

or

#Development Version from the dev branch of Github
devtools::install_github("PranaGeo/geoSpectral", ref="dev", dependencies=TRUE)

Usage

After installing the package, you can try from the R prompt : ?geoSpectral to consult the brief documentation of the package or ?Spectra to see the help of the constructor function the main class, Spectra().

Contributions

Your comments,suggestions and contributions are very welcome. Please feel free to open issues here.

Help the development

If you would like to contribute to the development, get a GitHub account, fork the dev branch of this project to your GitHub account, clone it to your local machine, work on it, commit your changes, push your changes to your GitHub fork and send us a pull request and we will discuss. For more information, visit the fork & pull development model page.

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Version

Install

install.packages('geoSpectral')

Monthly Downloads

18

Version

0.17.5

License

GPL

Issues

Pull Requests

Stars

Forks

Maintainer

Servet Cizmeli

Last Published

February 20th, 2020

Functions in geoSpectral (0.17.5)

geoSpectral

Classes and Methods for Working with Spectral Data with Space-Time Attributes
head,Spectra-method

Return the first or last part of a Spectra object
$,SpcList-method

Extract or replace parts of a SpcList object
spc.getheader

Extract a field of the @header slot of a Spectra object
spc.bbox2lines

Constructs a rectangle with a Spectra object
spc.interp.spectral

Interpolate spectral values
spc.getheader,list-method

Extract a field of the @header slot of a SpcList object
rep,Spectra-method

Replicate rows of Spectra object
spc.STI.stdistance

Report the space and time distance of each row of an STI-inherited object
spc.header2data

Copy header data into the @data slot
names,SpcList-method

names of SpcList object
SpcList-class

SpcList class definition
spc.cname.construct

Generating column names for a Spectra object
show,SpcHeader-method

Show a SpcHeader object
names,Spectra-method

The Names of a Spectra object
spc.select

Selecting rows of a Spectra object with the mouse
spc.rbind

Combine Spectra Objects by Rows
spc.plot.grid

Plotting SpcList object in a grid
spc.plot.depth.plotly

Display a Spectra object
spc.plot.map.leaflet

Display a Spectra object
spc.colnames

Column names of Spectra object
spc.colMeans

Computes the mean along the rows of a Spectra object
show,SpcList-method

Show a SpcList object
show,Spectra-method

Show a Spectra object
ncol,Spectra-method

The Number of Columns of a Spectra object
spc.lapply

Apply a function over a Spclist
spc.invalid.detect

Determinate invalid rows of a Spectra object
spc.getinvalid.idx

Get index of Spectra rows marked as invalid
spc.plot.time.plotly

Plot a Spectra object data with respect to time
spc.getselected.idx

Extract index inside of a Spectra object
spc.example_spectra

Create example of Spectral object
spc.plot.plotly

Plot a Spectra object data
spc.rbind,STIDF-method

Combine STIDF objects by Rows
spc.plot.time

Plotting Spectra object
subset,Spectra-method

Subsetting for a Spectra and spcList classes
spc.data2header,list-method

Populate fields of header slot using data from data slot
spc.plot.map.plotly

Display a Spectra object
spc.plot.depth.overlay

Plotting SpcList object
spc.export.text

Exporting into text format
sort,Spectra-method

Sort a Spectra object
spc.plot

Plotting Spectra object
dim,Spectra-method

Dimensions of a Spectra object.
spc.makeSpcList

Conversion from Spectra to Spclist
spc.export.xlsx

Exports a Spectra object into Excel format.
sort,SpcList-method

Sort a SpcList object
nrow,Spectra-method

The Number of rows of a Spectra object
spc.getwavelengths

Extract wave lenghts of a Spectra object
spc.header.infos

Getting as input the Spectra heade
spc.data2header

Populate fields of header slot using data from data slot
spc.plot.depth

Plotting Spectra object
spc.setwavelengths<-

Setting wavelengths in a Spectra object
spc.Read_ASD

Read the ASD Spectra from text file
spc.timeMatch

Match two time sequences
spc.setheader<-

Set a field of the @header slot of a Spectra object
spc.setheader<-,list-method

Set a field of the @header slot of a SpcList object
spc.make.stindex

Create a spatio-temporal index based on a list of Spectra objects
spc.Read_NOMAD_v2

Read the NOMAD v2 bio-optical database
spc.plot.map.rbokeh

Display a Spectra object
spc.plot.overlay

Plotting multiple Spectra objects inside a SpcList
spc.updateheader

Update a field of the @header slot of a Spectra object
spc.setselected.idx<-

Set index to a Spectra object
spc.lines

Add spectra to an existing plot
spc.setinvalid.idx<-

Set rows of Spectra as invalid
subset,SpcList-method

Subsetting for a spcList and Spectra classes
Spectra-coerce

Conversion between Spectra and data.frame objects
Arith,Spectra,Spectra-method

Apply arithmetic operations on and between Spectra objects.
SpcHeaderList-class

SpcHeaderList class.
Spectra-class

Spectra class definition
SpcHeaderAdd

Set a field of the @header slot of a SpcHeader class object
SpcList

Constructor function for the SpcList class.
SpcHeader-class

SpcHeader class for header object storing metadata.
$,Spectra-method

Extract or replace parts of a Spectra object
Spectra

Constructor function for the class Spectra.