[FULL] Primer 6 And Permanova User Manual (Latest)

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**ABBREVIATIONS:** **TESTS FOR PERMANOVA** {#Sec13} ------------------------ The permutational multivariate analysis of variance (PERMANOVA) or the pseudo-*F* statistics is an alternative to the traditional *F*-test (e.g., [@CR23]; [@CR8]) for testing multivariate homogeneity of group means (e.g., [@CR8]). PERMANOVA is a univariate test of a null hypothesis *H*~0~ of equal means across groups in the presence of random structure in the multivariate data sets. Like the traditional *F*-test, the test statistic is based on a permutation method but with a different normal approximation to the distribution of the test statistic. Unlike the *F*-test, PERMANOVA is not based on the assumption that the covariance matrices are equal (as with the traditional *F*-test), but is based on randomization. Instead, the test statistic is based on the sum of squares of distances between random multivariate vectors and the actual vectors of the data. The PERMANOVA test is available in PRIMER, version 6, and the software is available for Windows and Macintosh systems. At the start of the analysis, the software provides background information on the test procedure including a simple tutorial on multivariate analysis. If the program is launched from the menu bar, the welcome screen is automatically displayed (Fig. [1](#Fig1){ref-type="fig"}) with the following information: the sample size, number of samples, the number of groups, the number of variables, and the number of permutations. If the input is from the text file, the number of samples will be read by the program and the input for the number of variables and groups is entered by the user. The number of permutations is entered via a check box. After these settings are completed, the "Analysis" button is pressed (Fig. [1](#Fig1){ref-type="fig"}). Fig. 1The welcome screen of the *perMANOVA* function in PRIMER 6. **PERMANOVA PROCEDURE** {#Sec14} The user is first asked to pick the vector(s) of interest to be analyzed by the test (Fig. [2](#Fig2){ref-type="fig"}). This vector(s

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