This guide's walkthrough section includes summaries of analytical approaches used in numerous investigations. Each walkthrough includes a brief description of the analytical approaches used along with a graphical representation of the central workflow. Methodological details that are not related to statistical analyses are largely omitted and readers should consult the original article referenced in each walkthrough. These examples are useful in understanding how and under what circumstances methods described in this guide have been used by others in microbial ecology. A key of symbols used across our walkthrough graphics and a list of walkthroughs are provided below.
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Key
Index
Methods used
Data transformations
Analysis of similarity (ANOSIM)
Non-metric multidimensional scaling (NMDS)
Similarity percentages breakdown (SIMPER)
BIOENV
Spatial and Temporal Variation in a Caribbean Herbivorous Fish Assemblage
Methods used
Data transformations
Redundancy analysis
Principal components of neighbour matrices
Diversity and dynamics of rare and of resident bacterial populations in coastal sands
Methods used
Data transformations
Redundancy analysis
Forward variable selection
Variation partitioning
The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments
Methods used
Data transformations
Mantel testing
Redundancy analysis
Forward variable selection
Variation partitioning
Path analysis
The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics
Methods used
Data transformations
Correspondence analysis
Partial correspondence analysis
Analysis of similarity (ANOSIM)
Cluster analysis
PERMDISP2 (featuring principal coordinates analysis)
Procrustes analysis
Soil characteristics more strongly influence soil bacterial communities than land-use type
Methods used
Data transformations
Non-metric multidimensional scaling
Analysis of similarity (ANOSIM)
Canonical correspondence analysis