Preface Remote sensing and GIS are undeniably important methodological tools for studies related to inventory, surveying, and monitoring of natural resources. However, the highly priced proprietary softwares and unavailability of public satellite data are barriers to their use by broader community, particularly in developing countries. To maximize the scientific and societal benefits of the spatial data, open data and softwares are being promoted. Several satellite data from different sources with a wide array of spatial, spectral, temporal, and radiometric resolutions are now being made available free to all categories of users. To analyze the satellite data of widely differing characteristics and other spatial and non-spatial data from different sources, rapid advancements have been observed in free/open-source software (FOSS) GIS. R has become the world-wide language for statistics, predictive analytics, and data visualization. Not only statistics, it has a wide range of tools for spatial analysis as well as digital image analysis and can handle any process needed for image analysis with more flexibilities. It offers the widest range available of methodologies available for digital image processing, from the most basic to the most complex. As an open source project, it’s freely available for a range of platforms, including Windows, Mac OS X, and Linux. It’s under constant development, with new procedures added daily. Additionally, R is supported by a large and diverse community of data scientists and programmers who gladly offer their help and advice to users. Further, some of its most powerful features come from the thousands of extensions (packages) provided by contributing authors. It can be hard for new users to get a handle on what R is and what it can do. Although the codes for different digital image analysis procedures are available on the web, the new users will find it difficult to work with all the analysis as codes for all type of image analysis is not available at one place. Remote Sensing Data Analysis in R is a guide book containing codes for most of the operations which are being performed for analysing any satellite data for deriving meaningful information. The goal of this book is to provide hands on experience in performing all the activities from the loading of raster and vector data, mapping or visualisation of data, pre-processing, calculation of indices, classification and advanced machine learning algorithms on remote sensing data in R. The reader will be able to acquire skills to carry out most of the operations of raster data analysis – more flexibly - in open-source freely available software i.e. R which are generally available in the paid digital image processing softwares.

1.1 R and R studio R has become the world-wide language for statistics, predictive analytics, and data visualization. R is not limited to statistics; it has a wide range of tools for spatial analysis and digital image analysis and can handle any process needed for image analysis flexibly. It offers a wide range of methodologies for digital image processing, from the most basic to the most complex. As an open source project, it’s freely available for a range of platforms, including Windows, Mac OS X, and Linux. An integrated development environment (IDE) for R, R Studio, allows interactive execution of R functions with user interface. RStudio is available in two formats - RStudio Desktop and RStudio Server - both available in free and fee-based (commercial) editions. 1.1.1. Download and install R The R software setup files can be downloaded from any of the widely distributed Comprehensive R Archive Network (CRAN). To download R, please choose your preferred CRAN mirror, a location close to you. Follow the following steps:

2.1. Open source satellite data The satellite images have been invaluable information sources for Natural Resource Management. They provide synoptic view of the Earth periodically helping in inventory, surveying, and monitoring in agriculture, hydrology, geology, mineralogy, land cover, land use and environment. Free global satellite image data of spatial resolutions of 1m to 1 km and spectral resolution of single band to hyperspectral are available from an increasing number of sources (Table 2.1).

The satellite data is available in raster format. Raster data consists of two – dimensional array of pixels or grids which stores the values representing features. All the pixels are of same size and shape with their particular coordinate location. A raster data format is shown below.

Sensors onboard the satellite records the intensity of emitted or reflected electromagnetic radiations in the form of digital number (DN) for each pixel. These digital numbers can be transformed to more meaningful intensity units like radiance or reflectance. This process of conversion of digital numbers to radiance or reflectance is known as radiometric calibration. Sensor specific information is required to conduct radiometric calibration.

Vector data consists of points, lines and polygons with x, y coordinates known as vertices representing the geographic location i.e. latitude and longitude. Vector data depicts the shape of the spatial feature. Points consist of single x, y locations. Examples of points are tower location, sampling location, etc. Lines represent 1 – dimensional features like roads, streams, etc., and are composed of many or at least two connected points or vertices. Polygons denote 2 – dimensional features like boundaries with three or more vertices that are connected and closed. The vector data are represented in the following figure (fig. 5.1).

Coordinate Reference System (CRS) is a framework of coordinate based local, regional or global reference system used to represent the locations of geographic features. Coordinate Reference Systems (CRS) provide a standardized way to define the real-world geographic locations which further enable us to use common locations of geographic datasets for integration. The datasets from different sources and CRS are transformed to a common CRS in order to perform various integrated analytical operations like overlaying of data layers. Coordinate Reference Systems are mainly of two types: Geographic Coordinate System: This is global or spherical coordinate system in which locations of features on earth are defined in terms of latitude and longitude values. Latitude and longitude are angles based on a point at the centre of the earth. In this system, locations are defined by degrees, therefore, distances cannot be measured accurately. The most common geographic coordinate system is the World Geodetic System 84 (WGS84). Projected Coordinate System: In this system, locations of features are defined using cartesian x, y coordinates on a flat, two – dimensional surface. This system is based on sphere or ellipsoid projected on flat surface. Projected Coordinate System are generally referred as projec- tion. It is required for preparing maps on paper or computer screen. Un- like Geographic Coordinate System, projected coordinate system has ac- curate measurements of distance, angles and areas across the two dimen- sions. However, there is alwaystrade-offs between area, direction, shape, and distance in this system due to distortions created while representing ellipsoid or spheroid on a flat map. So, the projection type is selected based on its application. Most common projections are Universal Trans- verse Mercator (UTM), Lambert Conformal Conic and Albers Equal Area.

Raster sub-setting is done to select the desired area or bands of the raster image on which the user wants to perform analysis. Raster sub-setting is done in two ways: Spectral subset: Spectral sub-setting is done to extract few desired bands from the multiband raster image which are required for analysis. Spatial subset: Spatial sub-setting is done to minimize the area or extent of raster image to the desired area or extent for further analysis. Raster sub-setting in R is done by functions available in the ‘raster’ package. The following packages are required in this chapter:

Vector data analysis is performed to convert raw input vector data to output that provides new and meaningful information which ultimately supports decision making and disclose hidden patterns. There are various techniques to analyse vector data like buffering, intersect, union, and so on. Some of the most commonly used techniques with their R-code examples are explained in this chapter. First of all, you need to import all the packages which are required for performing this exercise. These packages include rgdal and sp for importing and re-projecting vector data as well as raster and rgeos for performing vector analysis operations.

Mosaic is the combination of two or more raster images into single image. Sometimes, single image captured by remote sensing satellite doesn’t completely covers the desired study area mostly. Therefore, users resort for mosaicking two or more images captured by satellite sensors from different paths so that the whole study area is merged into a single raster image to facilitate the image processing and analysis. The pixel size of the raster images should be same for mosaicking. In most of the cases, there is spatial overlapping among the raster images from which we want to create mosaic. These overlapping areas are handled in multiple ways which is being discussed further using R – code example. For mosaicking raster images in R, mosaic function of the raster package is used.

Many times, users have to work with raster datasets of different spatial and radiometric resolutions. So, there is requirement of bringing their resolutions to the same resolution in order to facilitate their processing. Resampling is the process of deriving pixel values from the existing image to the new raster image of different pixel size. Resampling is most common pre-processing step in remote sensing. It is done both at spatial and radiometric scale. At spatial scale, resampling is done either to increase the spatial resolution i.e. decrease pixel size known as Upsampling or to decrease the spatial resolution i.e. increase pixel size known as Downsampling. Radiometric resampling is performed to increase or decrease the radiometric resolution of the image. In R, resampling of raster image is performed by raster package. The details of the resampling methods and their respective R – code with examples are discussed in this chapter. First of all, we need to import the raster image on which we wish to perform resampling operations by using following R – code. In R, resampling is feasible on one band only. So, we will import single band raster image.

The calculation of raster data statistics is very essential before performing some geoprocessing operations. Raster data statistics involve knowing the distribution of pixel values in a band, comparing the pixel values of two bands, extracting values of all bands for a particular geographical location or point, and computing statistics like mean, median, standard deviation, etc. at pixel level across all bands of raster dataset. In R, codes to perform raster data statistics are present in raster package. The visualisation of raster data statistics can be done by rasterVis package. So, we need to import these packages in R in order to perform this exercise.

The sensors present over remote sensing satellites are designed to collect energy or radiance from the varied surface features having wide range of radiance i.e. from features like water bodies having very low radiance to features like sand or snow having very high radiance. But, most of the time, the study area may not have all these features; therefore, radiance values may remain confined to a narrow range. This reduces the contrast of the image, thereby decreases its visual quality. In this context, image contrast enhancement techniques are used for effective visualization and display of remote sensing image on computer screens or hard copy so that maximum amount of information can be derived through its visual interpretation. Contrast enhancement of a digital image is a technique to modify the original grey levels of input image to the entire available range of the grey levels. This increases the contrast between various features in the image which improves the visual quality of original image. Contrast enhancement can be done by both linear and non-linear methods. Some of the commonly used contrast enhancement techniques with their implementation in R software are discussed in this chapter. We need following packages for performing this exercise in R. raster package is required for importing of raster image and for performing contrast enhancement. RStoolbox package is also required for contrast enhancement as well as for visualization of raster data with ggplot2 package. rasterVis package is mainly used in this exercise for plotting histogram of the raster data.

Remote sensing images have an important characteristic known as spatial frequency. Spatial frequency is defined as the number of changes in pixel value per unit distance. Few changes in pixel or brightness value over an area in an image are known as low spatial frequency area like agricultural fields, forests, water bodies, etc. If the changes are large, then it is known as high frequency area like roads, built up areas, etc. Spatial filtering is an approach for extracting quantitative spatial information by taking into account the neighbouring pixel values along with the independent pixel value. Therefore, filtering is a technique for modifying or enhancing an image. Filtering is done to improve the interpretability of raster image or to extract certain information from them. It is a neighbourhood operation because the value of any pixel in the output image is determined by applying certain algorithm on the neighbourhood pixels of the corresponding input pixel. The nature of algorithm to be applied depends upon the information which user wants to derive from the raster image. Filtering operations are mainly done for smoothening, sharpening, noise removal and edge enhancement. A filter is a kernel of small array which is applied to input pixel and its neighbouring pixels in the raster. There are many types of filters which can be applied to a raster image in R. These types with their respective R – code examples are explained further.

Raster transformations involve mathematical manipulation of raster layers to generate new raster images. These transformed raster images either contain the information of interest or highlight the features which are not discernible in the original image. Transformations are also performed to preserve the essential information in reduced number of dimensions or layers. In this chapter, we are going to discuss few most commonly used transformation tools listed below:

Unsupervised classification is the technique of classification of raster data in which no prior information is provided by the user. Raster data is classified based on their spectral characteristics such that the pixels having similar spectral properties in the multispectral feature space are grouped together in one class. Unsupervised classification is mainly performed by clustering algorithms. The purpose of these algorithms is to minimize within cluster variability and maximize between clusters variability. The user must interpret and label the classes after performing unsupervised classification. This method of classification requires minimum data which makes it easy and quick, but user has toput efforts in identification of the classes. This method could be useful when user doesn’t have any prior knowledge about the study area. This method removes subjectivity and enables us to get the unique classes which might be unrecognized by the user. K-means is the most commonly used method for performing unsupervised classification. In this chapter, we have discussed K- means, CLARA and unsupervised random forest method for classification of raster data in R.

Supervised classification is the technique to classify raster image in which prior information about the classes in the form of training sites is provided by the user. Training site represents a homogeneous area in a particular class. The spectral response pattern of training sites is used to classify the raster image.The pixels of raster imagewhich have spectral response pattern similar to that of training sites of a particular class are grouped in that class. As there is some variability in the spectral response pattern of a particular class, therefore, multiple training sites per class are taken for supervised classification. Supervised classification of raster images can be performed by various methods. Conventional methods include maximum likelihood classifier, minimum distance to mean classifier, and parallelepiped classifier. Now a days, machine learning algorithms are also gaining importance in this context. These classifying algorithms are first trained or calibrated using the data of training sites.This trained model is then validated on the independent datasets for accuracy assessment. If the accuracy of the developed model is of acceptable level, then that model is used for the classification of raster data. In this chapter, we are going to discuss the execution of maximum likelihood classifier and few machine learning techniques for supervised classification of raster image in R software. The training sites used in this exercise are in the form of points shapefile. The raster image is classified into six classesi.e. built- up, fallow soil, riverine sand, salt-affected soil, vegetation, and water. For performing this exercise, first of all,set the working directory and import the required packages.

Elevation or height data of land surface above a defined vertical datum is stored in the form of raster grids which is known as Digital Elevation Model (DEM). The DEM data can be processed to derive many useful parameters like slope, aspect, curvature, roughness, etc. This process of quantitatively describing terrain obtained from DEM data through computation of many variables is known as Digital Terrain Analysis. Digital terrain analysis has applications in the various fields like hydrology, ecology, geomorphology, etc. DEM data for digital terrain analysis are available from the satellites like ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer), Cartosat, ALOS (Advanced Land Observation Satellite), and SRTM (Shuttle Radar Topography Mission). In this exercise, we are going to discuss the derivation of some primary and secondary terrain attributes from DEM data in R software. For performing digital terrain analysis in R, following packages are required.

Maps make it easier to interpret and communicate the results of any GIS analysis. R has a large number of packages for making thematic maps. Static mapping is straightforward with plot()methods provided by core spatial packages sf and raster. The use of plot() function have been discussed in the previous chapters. Another package for mapping isspwithspplot() having enough options for producing good quality thematic maps.It is also possible to create advanced maps using ggplot2. This chapter discusses, separately, preparing thematic maps from vectors and rasters with the above mentioned packages. A dedicated map-making package tmaphas been given special focus in this chapter.

Bibliography