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    R and Python for Oceanographers: A Practical Guide with Applications
    R and Python for Oceanographers: A Practical Guide with Applications
    R and Python for Oceanographers: A Practical Guide with Applications
    Ebook274 pages1 hour

    R and Python for Oceanographers: A Practical Guide with Applications

    By Hakan Alyuruk

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    About this ebook

    R and Python for Oceanographers: A Practical Guide with Applications describes the uses of scientific Python packages and R in oceanographic data analysis, including both script codes and graphic outputs. Each chapter begins with theoretical background that is followed by step-by-step examples of software applications, including scripts, graphics, tables and practical exercises for better understanding of the subject. Examples include frequently used data analysis approaches in physical and chemical oceanography, but also contain topics on data import/export and GIS mapping. The examples seen in book provide uses of the latest versions of Python and R libraries.

    • Presents much needed oceanographic data analysis approaches to chemical and physical oceanography
    • Includes examples with software applications (based on Python and R), including free software for the analysis of oceanographic data
    • Provides guidance on how to get started, along with guidance on example code and output
    LanguageEnglish
    PublisherElsevier Science
    Release dateJun 9, 2019
    ISBN9780128134924
    R and Python for Oceanographers: A Practical Guide with Applications
    Author

    Hakan Alyuruk

    Hakan Alyuruk is a research assistant (PhD) at the Institute of Marine Sciences and Technology, Dokuz Eylül University. His doctoral studies centered on characterization and determination of dissolved organic matter in seawater samples. His current research interests are mainly based on the in-depth chemical analyses and biogeochemical cycles of organic matter in the water column.

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      Book preview

      R and Python for Oceanographers - Hakan Alyuruk

      India

      Chapter 1

      Introduction to R and Python

      Abstract

      R is a programming language and environment for statistical computing and graphics, while Python is an interpreted, general-purpose, object-oriented, and high-level programming language. Since R and Python are open source languages and freely distributed, usage of both languages in scientific computation and data analysis have substantially increased in the last decade. R and Python are widely used for academic and commercial purposes, and it is possible to find rich information on their usage through help documentations, user communities, internet resources, and books. In this chapter, a brief introduction to R and Python programming languages is given, including their developments, advantages over other languages, package systems and structural components, installation instructions, and editing tools.

      Keywords

      R; Python; Packages; Installation; IDE; Editor; Scientific computing

      1.1 Introduction to R

      R is a language and package-based software environment that provides a wide variety of functions for statistical computing and graphics. R is a project of GNU, and its root depends on S language with some differences. S language and environment was developed by John Chambers and his colleagues at Bell Laboratories (formerly AT&T and now Lucent Technologies). While S language provides programmable research tools for statistical analysis, R has evolved as an Open Source alternative of the S language. R was initially developed by Robert Gentleman and Ross Ihaka at the statistics department of the University of Auckland. Its name R comes from the first letters of its developers. Besides its statistical capabilities (such as linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, etc.), high-resolution publication-quality plots can be produced with full control of the users. R is distributed under the terms of Free Software Foundation's GNU GPL license. Thanks to terms of this license, source codes of both base distribution and external packages with GPL license can be accessed, modified, and re-distributed by the user. Therefore, data analysts can view and contribute to source codes of these packages by accessing the running algorithms and adding their specific functions. As a result, scientists and students at universities can use R freely and without a license fee. The use of free software in science encourages and improves worldwide collaboration on data-analysis approaches. Also, R is used in teaching statistics at undergraduate and graduate levels at universities since students can freely use these statistical tools [1, 2].

      The base distribution of R is maintained by the R Development Core Team since 1997. In addition, a huge group of volunteer developers contribute to the project by developing new packages or upgrading existing add-on packages to improve their functionalities. The project's website is the main official information source and can be reached from Fig. 1.1:

      Fig. 1.1 A view of official R-Project website.

      https://www.r-project.org

      1.2 R environment

      R statistical environment system is composed of two main parts: base-distribution system and add-on packages.

      1.2.1 Base system of R

      The base system consists of core functions required to run R language. Also, core statistical functions (stats package) and graphical tools (graphics package) are included as dependencies of other add-on packages. Core packages included in the installation media of base system cover standard statistical functions, such as statistical tests, linear models, non-linear models, data-handling functions, clustering functions, and survival-test functions. A list of packages within the base system (included in R version 3.4.0) is given below.

      A list of base distribution packages:

      1.2.2 Add-on packages

      Add-on packages are developed and maintained by the user community. These packages contain many advanced statistical, computational, and graphical functions. Some of the packages have dependencies on other packages.

      Examples of add-on packages:

      1.3 Installation of R

      1.3.1 Installation of R base software

      R is an open source software, and it can be downloaded and installed freely. Latest/older versions of R software for Windows, Linux, or Mac OSX operating systems could be downloaded and installed from http://cran.r-project.org/ (Fig.

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