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.
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.