Computer Programming in Quantitative Biology

1st Edition - November 1, 1971
Author: R.G. Davies
Language: English
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 1 4 7 8 7 - 3

Computer Programming in Quantitative Biology covers the general background of Fortran coding and the more sophisticated computer programs likely to be encountered in quantitative… Read more

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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.

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 IV

Fortran characters

Statements and lay-out

Constants

Variables

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

Conclusion

References

Author Index

Subject Index