**XYOM ANALYZES, CLASSIFICATION **

**Input:**

A single file containing data which may be:

- Global size (one column matrix)
- DISTANCES (square matrix),
- Mahalanobis distances (i.e., Euclidean distances between …_DF.txt)
- Euclidean distances between …_PC.txt

- PRINCIPAL COMPONENTS (rectangular matrix)
- TABLE (rectangular matrix)
- matrix of traditional measurements,
- matrix of shape variables (…_NEF,matrix of …_ORP, etc…)

**Analyses:**

- if input data are labelled as
**TABLE****Between group****PCA**(**gPCA**) see: Mitteroecker, P., Bookstein, F., 2011. Linear Discrimination, Ordination, and the Visualization of Selection Gradients in Modern Morphometrics. Evol Biol. 38,100-114. doi:10.1007/s11692-011-9109-8.- Validated classification based on
**Maximum likelihood method**(**CCCMLi**) see: Dujardin, J.P., Dujardin, S., Kaba, D., Santillán-Guayasamín, S., Villacís, A. G., Piyaselakul, S., Sumruayphol, S., Samung, Y., Morales-Vargas, R., 2017. The maximum likelihood identification method applied to insect morphometric data. Zoological Systematics, 42(1), 46-58. - Validated classification based on
**Mahalanobis distance method**(**CCCMaha**). Be careful about statistical assumptions. See: Kovarovic, K., Aiello, L. C., Cardini, A., Lockwood, C. A. 2011. Discriminant function analyses in archaeology: are classification rates too good to be true? Journal of Archaeological Science, 38: 3006-3018 **PCA****(Principal Component Analysis**)

- if input data are labelled as
**PC****DA**(**Discriminant analysis**), with XYOM, a DA always assumes the entry data are PC; it cuts the number of the first PCs to the number of individuals in the smallest group, minus one.- Validated classification based on
**Maximum likelihood method**(**CCCMLi**) - Validated classification based on
**Mahalanobis distance method**(**CCCMaha**) **HC****BOOTSTRAP**(**hierarchical clustering**): single linkage algorithm, bootstraps of input data and resulting trees. See: Couette, S., G. Escarguel, and S. Montuire. 2005. Constructing, bootstrapping, and comparing morphometric and phylogenetic trees: A case study of new world monkeys (Platyrrhini, Primates). Journal of Mammalogy, vol. 86, no. 4, pp. 773 – 781. See also: Morales Vargas, R. E., N. Phumala-Morales, T. Tsunoda, C. Apiwathnasorn, and J.-P. Dujardin, 2013. The phenetic structure of*Aedes albopictus*. Infection, Genetics and Evolution, vol. 13, no.1, pp. 242–251.

No graphical output.

- if input data are labelled as
**DISTANCES (Mahalanobis, Euclidean)****HC**(**hierarchical clustering**): single linkage algorithm with**graphical output.**

- if input data are labelled as
**Global size**- Validated classification based on
**Maximum likelihood method**(**CCCMLi**) **Oneway ANOVA**Parametric ANOVA output, and**non-parametric estimation****of statistical significance**.

- Validated classification based on

**Output:**

- Report:
- HC:
**Newick**format with**bootstrap if input are PC.** - Validated classification: scores of correct assignments
- For gPCA, a detailed report about wrong assignations of group origin

- HC:
- Graphic :
- HC:
**Tree**. Single linkage dendrogram**if input are DISTANCES**, - PCA, gPCA, DA:
**factor map**of first two multivariate factors - Oneway ANOVA:
**quantile boxes**

- HC: