Permutational multivariate analysis of variance (PERMANOVA), [1] is a non-parametric multivariate statistical permutation test. PERMANOVA is used to compare groups of objects and test the null hypothesis that the centroids and dispersion of the groups as defined by measure space are equivalent for all groups. A rejection of the null hypothesis means that either the centroid and/or the spread of the objects is different between the groups. Hence the test is based on the prior calculation of the distance between any two objects included in the experiment. PERMANOVA shares some resemblance to ANOVA where they both measure the sum-of-squares within and between groups, and make use of F test to compare within-group to between-group variance. However, while ANOVA bases the significance of the result on assumption of normality, PERMANOVA draws tests for significance by comparing the actual F test result to that gained from random permutations of the objects between the groups. Moreover, whilst PERMANOVA tests for similarity based on a chosen distance measure, ANOVA tests for similarity of the group averages.
In the simple case of a single factor with p groups and n objects in each group, the total sum-of-squares is determined as:
where is the total number of objects, and is the squared distance between objects i and j.
Similarly, the within groups sum-of-squares is determined as:
where is 1 if the observations i and j belong to the same group, and 0 otherwise. Then, the between groups sum-of-squares () can be calculated as the difference between the overall and the within groups sum-of-squares:
Finally, a pseudo F-statistic is calculated:
where p is the number of groups.
Finally, the PERMANOVA procedure draws significance for the actual F statistic by performing multiple permutations of the data. In each permutation the items are shuffled between groups, and the F-ratio is calculated for it, . The P-value is then calculated by:
PERMANOVA is widely used in the field of ecology and is implemented in several software packages including the PERMANOVA [2] software, PRIMER and R (programming language) Vegan, lmPerm [3] and Python (programming language) skbio [4] packages.
Analysis of variance (ANOVA) is a collection of statistical models and their associated estimation procedures used to analyze the differences among means. ANOVA was developed by the statistician Ronald Fisher. ANOVA is based on the law of total variance, where the observed variance in a particular variable is partitioned into components attributable to different sources of variation. In its simplest form, ANOVA provides a statistical test of whether two or more population means are equal, and therefore generalizes the t-test beyond two means. In other words, the ANOVA is used to test the difference between two or more means.
In probability theory and statistics, a normal distribution or Gaussian distribution is a type of continuous probability distribution for a real-valued random variable. The general form of its probability density function is The parameter is the mean or expectation of the distribution, while the parameter is the variance. The standard deviation of the distribution is (sigma). A random variable with a Gaussian distribution is said to be normally distributed, and is called a normal deviate.
In probability theory and statistics, variance is the expected value of the squared deviation from the mean of a random variable. The standard deviation (SD) is obtained as the square root of the variance. Variance is a measure of dispersion, meaning it is a measure of how far a set of numbers is spread out from their average value. It is the second central moment of a distribution, and the covariance of the random variable with itself, and it is often represented by , , , , or .
The weighted arithmetic mean is similar to an ordinary arithmetic mean, except that instead of each of the data points contributing equally to the final average, some data points contribute more than others. The notion of weighted mean plays a role in descriptive statistics and also occurs in a more general form in several other areas of mathematics.
In statistics, the Pearson correlation coefficient (PCC) is a correlation coefficient that measures linear correlation between two sets of data. It is the ratio between the covariance of two variables and the product of their standard deviations; thus, it is essentially a normalized measurement of the covariance, such that the result always has a value between −1 and 1. As with covariance itself, the measure can only reflect a linear correlation of variables, and ignores many other types of relationships or correlations. As a simple example, one would expect the age and height of a sample of children from a primary school to have a Pearson correlation coefficient significantly greater than 0, but less than 1.
An F-test is any statistical test used to compare the variances of two samples or the ratio of variances between multiple samples. The test statistic, random variable F, is used to determine if the tested data has an F-distribution under the true null hypothesis, and true customary assumptions about the error term (ε). It is most often used when comparing statistical models that have been fitted to a data set, in order to identify the model that best fits the population from which the data were sampled. Exact "F-tests" mainly arise when the models have been fitted to the data using least squares. The name was coined by George W. Snedecor, in honour of Ronald Fisher. Fisher initially developed the statistic as the variance ratio in the 1920s.
Analysis of covariance (ANCOVA) is a general linear model that blends ANOVA and regression. ANCOVA evaluates whether the means of a dependent variable (DV) are equal across levels of one or more categorical independent variables (IV) and across one or more continuous variables. For example, the categorical variable(s) might describe treatment and the continuous variable(s) might be covariates (CV)'s, typically nuisance variables; or vice versa. Mathematically, ANCOVA decomposes the variance in the DV into variance explained by the CV(s), variance explained by the categorical IV, and residual variance. Intuitively, ANCOVA can be thought of as 'adjusting' the DV by the group means of the CV(s).
In statistics, an effect size is a value measuring the strength of the relationship between two variables in a population, or a sample-based estimate of that quantity. It can refer to the value of a statistic calculated from a sample of data, the value of a parameter for a hypothetical population, or to the equation that operationalizes how statistics or parameters lead to the effect size value. Examples of effect sizes include the correlation between two variables, the regression coefficient in a regression, the mean difference, or the risk of a particular event happening. Effect sizes are a complement tool for statistical hypothesis testing, and play an important role in power analyses to assess the sample size required for new experiments. Effect size are fundamental in meta-analyses which aim to provide the combined effect size based on data from multiple studies. The cluster of data-analysis methods concerning effect sizes is referred to as estimation statistics.
In statistics, multivariate analysis of variance (MANOVA) is a procedure for comparing multivariate sample means. As a multivariate procedure, it is used when there are two or more dependent variables, and is often followed by significance tests involving individual dependent variables separately.
The Friedman test is a non-parametric statistical test developed by Milton Friedman. Similar to the parametric repeated measures ANOVA, it is used to detect differences in treatments across multiple test attempts. The procedure involves ranking each row together, then considering the values of ranks by columns. Applicable to complete block designs, it is thus a special case of the Durbin test.
ANOVA gage repeatability and reproducibility is a measurement systems analysis technique that uses an analysis of variance (ANOVA) random effects model to assess a measurement system.
In statistics, Levene's test is an inferential statistic used to assess the equality of variances for a variable calculated for two or more groups. This test is used because some common statistical procedures assume that variances of the populations from which different samples are drawn are equal. Levene's test assesses this assumption. It tests the null hypothesis that the population variances are equal. If the resulting p-value of Levene's test is less than some significance level (typically 0.05), the obtained differences in sample variances are unlikely to have occurred based on random sampling from a population with equal variances. Thus, the null hypothesis of equal variances is rejected and it is concluded that there is a difference between the variances in the population.
Kendall's W is a non-parametric statistic for rank correlation. It is a normalization of the statistic of the Friedman test, and can be used for assessing agreement among raters and in particular inter-rater reliability. Kendall's W ranges from 0 to 1.
In statistics, one-way analysis of variance is a technique to compare whether two or more samples' means are significantly different. This analysis of variance technique requires a numeric response variable "Y" and a single explanatory variable "X", hence "one-way".
The Brown–Forsythe test is a statistical test for the equality of group variances based on performing an Analysis of Variance (ANOVA) on a transformation of the response variable. When a one-way ANOVA is performed, samples are assumed to have been drawn from distributions with equal variance. If this assumption is not valid, the resulting F-test is invalid. The Brown–Forsythe test statistic is the F statistic resulting from an ordinary one-way analysis of variance on the absolute deviations of the groups or treatments data from their individual medians.
Named after the Dutch mathematician Bartel Leendert van der Waerden, the Van der Waerden test is a statistical test that k population distribution functions are equal. The Van der Waerden test converts the ranks from a standard Kruskal-Wallis test to quantiles of the standard normal distribution. These are called normal scores and the test is computed from these normal scores.
In statistics, Tukey's test of additivity, named for John Tukey, is an approach used in two-way ANOVA to assess whether the factor variables are additively related to the expected value of the response variable. It can be applied when there are no replicated values in the data set, a situation in which it is impossible to directly estimate a fully general non-additive regression structure and still have information left to estimate the error variance. The test statistic proposed by Tukey has one degree of freedom under the null hypothesis, hence this is often called "Tukey's one-degree-of-freedom test."
Fourier amplitude sensitivity testing (FAST) is a variance-based global sensitivity analysis method. The sensitivity value is defined based on conditional variances which indicate the individual or joint effects of the uncertain inputs on the output.
In statistics, the two-way analysis of variance (ANOVA) is an extension of the one-way ANOVA that examines the influence of two different categorical independent variables on one continuous dependent variable. The two-way ANOVA not only aims at assessing the main effect of each independent variable but also if there is any interaction between them.
In statistics, expected mean squares (EMS) are the expected values of certain statistics arising in partitions of sums of squares in the analysis of variance (ANOVA). They can be used for ascertaining which statistic should appear in the denominator in an F-test for testing a null hypothesis that a particular effect is absent.