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Chapter 17 : Issues of Study Design and Statistical Analysis for Environmental Microbiology
Authors:
Kenneth M. Portier,
Ronald Corstanje
Content Type: Reference
Publication Year:
2007
Category: Environmental Microbiology
Book DOI:
10.1128/9781555815882
Chapter DOI:
10.1128/9781555815882.ch17
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Abstract:
The practice of good science requires a concise description of study objectives and a study design that matches its objectives. A good study design requires (i) definition of the population or factors of interest in the study, (ii) identification of study units, (iii) collection of representative measurements, and (iv) a statistical analysis matched to study objectives and data characteristics. The goal of this chapter is to help one see the statistical issues involved in study design and data analysis. The majority of studies in environmental microbiology involve some form of comparisons since it is through comparisons that we learn where differences exist and/or what factors can influence microbial populations. Experimental designs specify the nature and extent of comparisons that are of interest in a particular study. The goal of data collection, be it in a sampling study or an experimental design, is to obtain a set of measures from a population to gain insight into how values for a particular population characteristic vary from sample unit to sample unit. In this chapter the authors have attempted to raise readers awareness of the role and function of statistics at both the study design and the data analysis steps of environmental microbiological studies.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
Figures
Issues of Study Design and Statistical Analysis for Environmental Microbiology
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Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig01
FIGURE 1
Spatial sampling plans, each containing 40 locations. (a) Simple random locations; (b) random locations within cells of a systematic grid (spatial stratification); (c) systematic locations with a random starting point and fixed between-sample distance, δ; and (d) overlapping grid samples of equal between-sample distance and two random starting points.
10.1128/9781555815882/f0201-01_thmb.gif
10.1128/9781555815882/f0201-01.gif
FIGURE 1
Spatial sampling plans, each containing 40 locations. (a) Simple random locations; (b) random locations within cells of a systematic grid (spatial stratification); (c) systematic locations with a random starting point and fixed between-sample distance, δ; and (d) overlapping grid samples of equal between-sample distance and two random starting points.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig02
FIGURE 2
Typical shapes for common discrete statistical distributions. Distribution parameters: n, number of experiments, ranging from 2 to infinity; π, probability of success, ranging between 0 and 1; λ > 0, Poisson mean.
10.1128/9781555815882/f0205-01_thmb.gif
10.1128/9781555815882/f0205-01.gif
FIGURE 2
Typical shapes for common discrete statistical distributions. Distribution parameters: n, number of experiments, ranging from 2 to infinity; π, probability of success, ranging between 0 and 1; λ > 0, Poisson mean.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig03
FIGURE 3
Typical shapes for common continuous statistical distributions. Distribution parameters are displayed as Greek letters. For the normal and lognormal distributions, µ and σ are the mean and standard deviation controlling the center and spread, respectively. The Weilbull distribution is controlled by a shape and a scale parameter. The Student t, F, and chi-square distributions are controlled by one or two parameters referred to as the degrees of freedom, 1 ≤ df, df1, df2 < infinity. For these distributions, changing the degrees of freedom changes both the shape and spread of the distribution as demonstrated by the dotted lines.
10.1128/9781555815882/f0206-01_thmb.gif
10.1128/9781555815882/f0206-01.gif
FIGURE 3
Typical shapes for common continuous statistical distributions. Distribution parameters are displayed as Greek letters. For the normal and lognormal distributions, µ and σ are the mean and standard deviation controlling the center and spread, respectively. The Weilbull distribution is controlled by a shape and a scale parameter. The Student t, F, and chi-square distributions are controlled by one or two parameters referred to as the degrees of freedom, 1 ≤ df, df1, df2 < infinity. For these distributions, changing the degrees of freedom changes both the shape and spread of the distribution as demonstrated by the dotted lines.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig04
FIGURE 4
Examples of normal quantile plots. Closeness to the straight line is a measure of the normality of the sample data.
10.1128/9781555815882/f0207-01_thmb.gif
10.1128/9781555815882/f0207-01.gif
FIGURE 4
Examples of normal quantile plots. Closeness to the straight line is a measure of the normality of the sample data.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17eq01
Untitled
10.1128/9781555815882/f0207-02_thmb.gif
10.1128/9781555815882/f0207-02.gif
Untitled
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig05
FIGURE 5
Frequency and density histograms for normally distributed data. Note that the shapes of the distribution are similar and only the vertical axis scale is changed.
10.1128/9781555815882/f0207-03_thmb.gif
10.1128/9781555815882/f0207-03.gif
FIGURE 5
Frequency and density histograms for normally distributed data. Note that the shapes of the distribution are similar and only the vertical axis scale is changed.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig06
FIGURE 6
Comparative box plots indicating the median (middle of notch), upper and lower quartiles (solid box top and bottom), interquartile range (IQR = height of box), upper and lower fence values (line terminators = median ± 3 IQR), and potential outliers (circle dots).
10.1128/9781555815882/f0208-01_thmb.gif
10.1128/9781555815882/f0208-01.gif
FIGURE 6
Comparative box plots indicating the median (middle of notch), upper and lower quartiles (solid box top and bottom), interquartile range (IQR = height of box), upper and lower fence values (line terminators = median ± 3 IQR), and potential outliers (circle dots).
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17fig07
FIGURE 7
Biplot of the first two principal components of a 4-variate analysis which is known to have three groups, identified as A, B, and C.
10.1128/9781555815882/f0209-01_thmb.gif
10.1128/9781555815882/f0209-01.gif
FIGURE 7
Biplot of the first two principal components of a 4-variate analysis which is known to have three groups, identified as A, B, and C.
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
/content/10.1128/9781555815882.ch17.ch17eq02
Untitled
10.1128/9781555815882/f0212-01_thmb.gif
10.1128/9781555815882/f0212-01.gif
Untitled
Citation:
Portier K, Corstanje R.
2007.
Issues of Study Design and Statistical Analysis for Environmental Microbiology,
p 199-215.
In
Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed),
Manual of Environmental Microbiology, Third Edition.
ASM Press, Washington, DC.
doi: 10.1128/9781555815882.ch17
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/content/book/10.1128/9781555815882.ch17
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