Hi I am working on qualitative data of 200 genotypes and 40 morphological traits. the morphological traits I have measured are coded (1 to 9).For example for petal color (1=red, 2=yellow, 3=other) and for fruit color (1=light red, 3=red, 5=dark red, 7=red-black). can anyone help me in analysing this data using R software, or introduce me the packages that are suitable for this?
Meanwhile, I have found "RQDA" and "vcd" packages for analysing on R, but I think these are not suitable for analysing my data or maybe I coul not work with them. among the analyzes I want to do are the following: PCA, loading for the factors of traits, eigenvectors for the variables of factors, dendrogram of grouping for genotypes, pearson correlation coefficient among traits.
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Most of the analyses you mentioned are available through basic R. You should start by learning R, if you'll have specific questions post them here and you'll get help.