Package: spaa 0.5.3

1. The installation | 2. Functions and datasets in spaa | 2.1 Main Functions | 2.2 Embedded datasets | 3. Calculating niche width | 3.1 Converting community data into a matrix | 3.1.2 Individual-based Field Record Sheet | 3.1.2 Plot-based Record Sheet | 3.2 Calculating species associations | 3.2.1 Species association of the community as a whole | 1. Variance of species relative frequency (Equation 1) sigmaTsq: | 2. Variance of the number of species (Equation 2) STsq | 3. Species' relative frequency (Equation 3) pi | 4. Variance ratio (Equation 4) var.ratio | 5. The W statistic (Equation 5) | 3.2.2 Significance test of inters-pecific associations | 1. Yates-corrected chi-square test for significance (Equation 6), see chisq and chisqass | 2. V ratio (Equation 7) V | 3. Jaccard's index (Equation 8) Jaccard: | 4. Ochiai index (Equation 9) Ochiai: | 5. Dice Index (Equation 10) Dice: | 6. PCC: Point Correlation Coefficient PCC (Equation 11) | 7. AC Association coefficient (Equation 12) AC | 8. Spearman's rank correlation coefficient Spearman (Equation 15) | 9. Pearson's correlation coefficient Pearson (Equation 16) | 3.3 Calculating niche width | 1. Levins niche width index (Equation 17) | 2. Shannon's niche width index (Equation 18) | 3.4 Niche overlap | 1. Levin's niche overlap index (Equation 19) | 2. Schoener's niche overlap index (Equation 20) | 3. Petraitis's niche overlap index (Equation 21) | 4. Pianka's niche overlap index (Equation 22) | 5. Czechanowski's niche overlap index (Equation 23) | 6. the simplified Morisita index (Equation 24) | Example: | 3.5 Bootstrap of the confidence intervals for niche width | 3.6 Visualisation | 3.6.1 Semi-matrix plots | 3.6.2 Species association network | 3.7 Other functions | 3.7.1 Obtain the most frequently occurred species in the community matrix | 3.7.2 Other useful functions | Acknowledgements | References