I'm trying to analyse some data I've gathered from some fossils. I have about 40 different specimens and for each specimen I've recorded the width of the body, and also the presence or absence of certain anatomical features. I want to determine if there is a relationship between the width of the body and the preservation of certain features, and also whether certain features are likely to be preserved together. There is also missing data for some specimens, for example where the head region is broken off from the slab, I cannot code whether the head is preserved or not.

I would like to apply some kind of multivariate analysis to these data, such as an MDS or PCA, is this possible, bearing in mind that I have some missing values? Can anyone suggest an appropriate approach?