Dear Adrian, Your approach seems correct to me. Your disease severity variable is not categorical but ordinal (semi-quantitative) and you can perform PCA (on the covariance matrix: scale.unit = FALSE) and HCPC on the mean scores as suggested. You can also directly perform a hierarchical clustering of the 109 isolates by applying hclust() to the Euclidean distance matrix.
Best wishes, François ------------------------------------------------------------------------------- François Gillet , Emeritus Professor Université Bourgogne Franche-Comté - CNRS UMR 6249 Chrono-environnement UFR Sciences et Techniques 16, Route de Gray F-25030 Besançon cedex France [ http://chrono-environnement.univ-fcomte.fr/ | http://chrono-environnement.univ-fcomte.fr/ ] Phone: +33 (0)3 81 66 62 81 iPhone: +33 (0)7 88 37 07 76 Location: La Bouloie, Bât. Propédeutique, -114L ------------------------------------------------------------------------------- Associate Editor of Plant Ecology and Evolution [ http://www.plecevo.eu/ | http://www.plecevo.eu ] ------------------------------------------------------------------------------- Homepage: [ https://chrono-environnement.univ-fcomte.fr/spip.php?page=perso&nom=GILLET&prenom=Fran%C3%A7ois&lang=en | https://chrono-environnement.univ-fcomte.fr/spip.php?page=perso&nom=GILLET&prenom=Fran%C3%A7ois&lang=en ] ResearchID : [ http://www.researcherid.com/rid/B-6160-2008 | https://publons.com/researcher/1228828/francois-gillet/ ] ORCID ID: [ http://orcid.org/0000-0002-3334-1069 | http://orcid.org/0000-0002-3334-1069 ] Google Scholar : [ http://scholar.google.com.au/citations?user=a5xiIfQAAAAJ | http://scholar.google.com.au/citations?user=a5xiIfQAAAAJ ] ------------------------------------------------------------------------------- While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside of yours. Il se peut que j'envoie ce courriel en dehors de mes heures de travail normales, je ne m'attends pas à recevoir une réponse en dehors des vôtres. ------------------------------------------------------------------------------- ----- Mail original ----- De: "Adnan Sisic" <adnan_si...@live.com> À: "R-sig-ecology@r-project.org" <r-sig-ecology@r-project.org> Envoyé: Vendredi 15 Juillet 2022 12:32:40 Objet: [R-sig-eco] Question: Is it correct to use HCPC analysis (FactoMineR package) on categorical data Dear Sig. Ecology members, I have categorical disease severity data, disease scale - scores from 1 (healthy plant) to 10 (heavily diseased/dying plant). In total I have 109 isolates tested, each in 3 replicates. Is it correct to use mean score of 3 replicates for each isolate as inputs, calculate Euclidean distances between isolates and perform Hierarchical Clustering on Principal Components (HCPC) in FactoMineR package? Thanks and best regards, ---- FG �kologischer Pflanzenschutz Universit�t Kassel Nordbahnhofstr. 1a D-37213 Witzenhausen Deutschland Dept. of Ecological Plant Protection University of Kassel Nordbahnhofstr. 1a D-37213 Witzenhausen Germany Tel. 05542 98 1569 Fax. 05542 98 1564 www.uni-kassel.de/go/fb11-oekologischer-pflanzenschutz [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
