Icon1 Introduction to CAP
Icon1.1 Improvements implemented in CAP 5.0
Icon1.1.1 Improvements to previous versions of CAP
Icon1.2 Methods offered by CAP
Icon1.3 Installation and System Requirements
Icon1.4 General instructions
Icon1.5 User preferences
Icon1.6 Quick guide to running a data set
Icon1.7 Video guides
Icon1.8 Choose demo data set
Icon1.9 Large data files
Icon1.10 Maximum size of the data set and computation speed
Icon1.11 Common errors and problems
Icon2 Comparing and classifying communities
Icon2.1 Searching for similarity
Icon2.2 Cluster analysis
Icon2.3 Multivariate analysis
Icon2.5 Principal Component Analysis (PCA)
Icon2.6 Reciprocal averaging (RA)
Icon2.7 Discriminant Analysis
Icon3 Demonstration data sets
Icon3.1 Worked Example - Stream Invertebrates
Icon3.2 Worked Example - Japanese Pottery
Icon3.3 Worked Example - Martinsville Igneous
Icon3.4 Worked Example - Cicada Song
Icon4 Raw Data
Icon4.1 Creating and editing a data set
Icon4.1.1 Organising your data for analysis
Icon4.1.2 Preparing large data sets in a spreadsheet program
Icon4.1.3 Import from Excel
Icon4.1.4 Data entry from within CAP
Icon4.1.4.1 Creating a data grid of a certain size
Icon4.1.5 Copying and pasting data
Icon4.1.6 Editing existing data
Icon4.1.7 Saving new or edited data
Icon5 Working Data
Icon5.1 Data transformations
Icon5.2 Relativisations
Icon5.3 Dealing with zeros or sparse data
Icon5.4 Transposing data
Icon6 Grouping
Icon6.1 Changing group properties
Icon7 Summary tab
Icon7.1 Data set statistics
Icon8 Ordination
Icon8.1 Principal Component Analysis - PCA
Icon8.1.1 Variance
Icon8.1.2 Scores
Icon8.1.3 Eigenvectors
Icon8.1.4 Viewing the correlation between variables (species)
Icon8.1.5 Cross products
Icon8.1.6 PCA plot
Icon8.1.7 Principal Axis vs Variable Plot
Icon8.1.8 Scree Plot
Icon8.2 Detrended Correspondence Analysis - DECORANA
Icon8.2.1 Computations - DECORANA
Icon8.2.2 Species Scores - DECORANA
Icon8.2.3 Sample Scores - DECORANA
Icon8.2.4 DECORANA plot
Icon8.3 Non-metric Multi-Dimensional Scaling
Icon8.3.1 Starting Configuration - MDS
Icon8.3.2 Site coordinates
Icon8.3.3 Stress
Icon8.3.4 MDS plots
Icon8.4 Reciprocal Averaging - RA
Icon8.4.1 Computations - Reciprocal Averaging
Icon8.4.2 Species Scores - Reciprocal Averaging
Icon8.4.3 Sample Scores - Reciprocal Averaging
Icon8.4.4 RA plot
Icon9.1 Setup window - TWINSPAN
Icon9.2 TWINSPAN Text
Icon9.3 Site summary
Icon9.4 Variables summary
Icon9.5 Dendrogram sites
Icon9.6 Dendrogram species
Icon9.7 Editing TWINSPAN Dendrograms
Icon9.8 TWINSPAN Out
Icon10 Clustering
Icon10.1 Agglomerative cluster analysis
Icon10.1.1 Ward’s
Icon10.1.2 Single linkage
Icon10.1.3 Complete linkage
Icon10.1.4 Average linkage
Icon10.1.5 McQuitty’s
Icon10.1.6 Gower’s
Icon10.1.7 Centroid
Icon10.1.8 Cluster groups
Icon10.1.9 Dendrogram - Cluster analysis
Icon10.1.9.1 Edit Dendrogram
Icon10.1.10 Cluster summary
Icon10.2 Divisive cluster analysis
Icon10.2.1 Plot Clusters
Icon10.2.2 Cluster Groups
Icon10.2.3 Cluster Summary
Icon11 Similarity and Distance Measures
Icon11.1 Simple matching
Icon11.2 S3
Icon11.3 Rogers_Tanimoto
Icon11.4 S4
Icon11.5 S5
Icon11.6 S6
Icon11.7 Jaccards
Icon11.8 Sorensen
Icon11.9 S9
Icon11.10 S10
Icon11.11 Russell & Rao
Icon11.12 Kulczynski
Icon11.13 S13
Icon11.14 Ochiai
Icon11.15 Q1
Icon11.16 Q2
Icon11.17 Kulczynski-Quantitative
Icon11.18 Steinhaus
Icon11.19 Euclidean
Icon11.20 Average
Icon11.21 Chord
Icon11.22 Geodesic
Icon11.23 Manhattan
Icon11.24 Mean Character Difference (Czekanowski)
Icon11.25 Whittaker
Icon11.26 Canberra
Icon11.27 Bray-Curtis
Icon11.28 Squared Chord Distance
Icon11.29 Mahalanobis distance
Icon11.30 Renkonen
Icon12 Association analysis
Icon13 Group Tests
Icon13.1 Analysis of Similarity (ANOSIM)
Icon13.2 Similarity Percentages (SIMPER)
Icon13.3 Discriminant Analysis
Icon13.3.1 Eigenvalues - DA
Icon13.3.2 Discriminant Function Coefficients
Icon13.3.3 Fisher's Discriminant Functions
Icon13.3.4 Group Centroids - DA
Icon13.3.5 Significance tests - DA
Icon13.3.6 Discriminant analysis plot
Icon13.3.7 Dispersion matrices - DA
Icon13.3.8 Site Coordinates - DA
Icon13.3.9 Predictive Validation
Icon14 Variable Filtering
Icon14.1 Variable Filtering - Setup
Icon15 Compare
Icon15.1 Compare samples
Icon15.2 Profile Plot
Icon15.3 Scatter Plot
Icon15.4 Matrix Plot
Icon16 Printing, editing and saving results
Icon16.1 Exporting and copying charts
Icon16.2 Exporting dendrograms
Icon16.3 Printing charts and dendrograms
Icon16.4 Editing charts
Icon16.4.1 Zooming on charts
Icon16.4.2 The Editing Chart dialog
Icon16.4.3 Drawing a perimeter
Icon16.4.4 Preparing charts for output - Chart Tools
Icon16.4.5 Themes for charts
Icon16.5 Printing and exporting grid and text output
Icon17 Obtaining help
Icon17.1 References
Icon17.2 Citation

Copyright 2014, PISCES Conservation Ltd