Computer Programming in Quantitative Biology

Computer Programming in Quantitative Biology

1st Edition - November 1, 1971

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  • Author: R.G. Davies
  • eBook ISBN: 9780323147873

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Computer Programming in Quantitative Biology covers the general background of Fortran coding and the more sophisticated computer programs likely to be encountered in quantitative biology. It discusses the application of over 40 appropriate and easily adaptable programming techniques to problems of major biological interest. Organized into 15 chapters, the book starts by providing an introductory outline of computer structure and function needed to appreciate many basic programming procedures. A chapter discusses some general principles underlying Fortran coding and the use of digital computers, with emphasis on major features of Fortran IV. Other chapters present short introduction to the statistical or mathematical techniques in each of the main sections under which program are described. These chapters also provide some aspects of matrix algebra that are essential for serious statistical programming and offer a general guide to efficiency in programming. All complete programs are accompanied by a flowchart and a detailed discussion. This book is a valuable source of information for biologists, computational biologists, research biologists, undergraduate students, and advanced or specialized students of biology.

Table of Contents

  • Preface

    Chapter 1: Introduction

    Chapter 2: Electronic Digital Computers

    Number Systems

    Decimal notation

    Binary notation

    Octal notation

    Interconversion of number systems

    Binary coded decimal

    Computer Structure and Function

    Input devices

    Computer storage

    Arithmetic unit

    Output devices

    Control unit

    Programming Languages

    Chapter 3: Synopsis of Fortran Programming

    Planning a Program


    Fortran characters

    Statements and lay-out



    Arithmetic expressions

    Mathematical functions

    Other supplied functions

    Arithmetic statements

    STOP, PAUSE and END statements

    Input—Output statements

    Further FORMAT specifications

    Transfer statements

    Subscripted variables and the DIMENSION statement

    The DO statement

    Arithmetic statement functions

    Function subprograms

    Subroutine subprograms

    Non-executable statements

    Running a Program

    Chapter 4: Three Simple Statistical Programs

    Program 1: Computation of mean, variance, standard deviation and other statistics of a sample

    Program 2: Correlation and regression

    Program 3: Comparison of means of two samples

    Chapter 5: Sorting, Tabulating and Summarising Data

    Program 4: Sorting an array in ascending and/or descending order

    Program 5: Ranking an array of numbers

    Program 6: Tabulation of frequency tables

    Program 7: Construction of two-way contingency tables

    Program 8: Data-summarising Program 1

    Program 9: Data-summarising Program 2

    Program 10: Data-summarising Program 3

    Program 11: Calculation of running means

    Chapter 6: Analysis of Variance

    Program 12: Two-factor analysis of variance without replication

    Program 13: Incomplete three-factor analysis of variance (two factors with replication)

    Program 14: Three-factor analysis of variance without replication

    Program 15: Analysis of variance: Latin square design

    Program 16: Analysis of variance: balanced incomplete block design

    Chapter 7: Correlation and Regression Analysis

    Program 17: Correlation and regression of data arranged in grouped frequency table

    Program 18: Regression with tests of significance and linearity by analysis of variance

    Program 19: Comparison of two regression lines by analysis of variance

    Program 20: Autocorrelations in time-series

    Program 21: Cross-correlations in time-series

    Program 22: Best-fit linear functional relationship between two variables, each subject to error

    Chapter 8: Matrix Methods

    Program 23: Dispersion and correlation matrices

    Chapter 9: Further Matrix Method

    Program 24: Determinant of a matrix

    Matrix Inversion

    Program 25: Matrix inversion

    Latent Roots and Vectors

    Program 26: Latent roots and vectors of a real symmetric matrix

    Program 27: Latent roots and vectors of a real non-symmetric matrix

    Chapter 10: Multiple Regression and Multivariate Analysis

    Program 28: Multiple linear regression analysis

    Program 29: Hotelling's T2 and discriminant function for two groups

    Program 30: Principal component analysis

    Program 31: Multiple discriminant analysis

    Chapter 11: Nonparametric Statistics

    Program 32: Chi-squared test of association in two-way contingency tables

    Program 33: Chi-squared test for goodness of fit

    Program 34: Spearman's rank correlation coefficient

    Program 35: Wilcoxon's signed ranks test

    Program 36: Mann-Whitney test for two independent samples

    Program 37: Kruskal-Wallis test for several independent samples

    Chapter 12: Fitting Theoretical Distributions to Data

    Program 38: Fitting a normal distribution and testing goodness of fit

    Program 39: Fitting a Poisson distribution and testing goodness of fit

    Program 40: Fitting a binomial distribution and testing goodness of fit

    Program 41: Fitting a negative binomial distribution and testing goodness of fit

    Chapter 13: Models and Simulation

    Program 42: Numerical integration by Simpson's rule

    Program 43: Solution of first-order ordinary differential equations by a Runge-Kutta method

    Subroutines RAND1 to RAND7

    Calculation of Probabilities from Statistic Distributions

    Program 44: Computation of probabilities corresponding to the test-statistics x2t, z and F

    Chapter 14: Three Special-Purpose Programs

    Program 45: Probit analysis

    Program 46: Single linkage cluster analysis

    Program 47: Estimation of population-size by marking and recapture

    Chapter 15: Efficiency in Programming

    Choice of Efficient Algorithms

    Economy in Computer Time

    Conservation of Core Storage

    Program 48: Dispersion and correlation matrices with compressed vector storage

    Accuracy Considerations

    Testing of Programs

    Use of Available Package Programs or Subroutines



    Author Index

    Subject Index

Product details

  • No. of pages: 504
  • Language: English
  • Copyright: © Academic Press 1972
  • Published: November 1, 1971
  • Imprint: Academic Press
  • eBook ISBN: 9780323147873

About the Author

R.G. Davies

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