User talk:Bobspielbauer/sandbox

Hi Bob--

The first thing I noticed about the article in your sandbox is that it has several "dead" links (negative evidence, morphological, lineage) that don't actually go to the pages you want them to link to. Definitely check those out before updating the molecular clock page. I really like your first paragraph about the molecular clock; I don't know much about it, but I felt like it was explanatory enough that I could get a grasp on what you were talking about and where you were going.

For node calibration, I would consider linking to an explanation of phylogenetic trees and nodes, just to give a layperson a chance to follow along with the terminology. If someone doesn't understand what a "node" is, then they won't be able to understand this paragraph of your section. Minor detail: should be "fossil-constrained nodes" instead of "fossil constrained nodes." Finishing up the section on tip calibration leaves me with one question, though. With the FBD models, are those a type of tip calibration? Or are they a combination of tip/node? Or are they something else entirely? That could be made more clear, because I was left uncertain about that. I like it overall! Like I said, this is a topic I was unfamiliar with, but it "felt" like a Wikipedia article should, and I can say that I understand the topic now.

Enwebb (talk) 05:50, 3 March 2017 (UTC)

Add Pictures of nodes, tips, and sampled ancestors? - Bob — Preceding unsigned comment added by Bobspielbauer (talk • contribs) 15:54, 3 March 2017 (UTC)

Feedback from Emily

Emilysessa (talk) 15:00, 13 April 2017 (UTC)

Very nice addition to this page, and improvement of the Calibration section. It's really nicely written, and well structured/organized.

This sentence needs a citation: Thus, calibration based solely on minimum clade ages will produce clade divergence dates that are more recent than reality.

Add a link to the page for prior probability: a prior probability of the divergence time is established

This sentence needs more explanation; it's very, very vague and general. What studies are you referring to? All molecular dating analyses??? Just studies of plants or some other organisms? I think you probably should remove it, or make it concrete in a way that a citation can be added. "In many cases, only one or two fossils are used to calibrate the time scale of the tree."

I think it would also be worth adding more information about priors and how they are modeled. That's a bit of a gap that I see in the node calibration section. You could add a sentence like: "Several different probability distributions are available for assigning the prior probability of a fossil to a node, these include lognormal, etc." and link to the wiki pages for those individual distributions.

I also notice that the Methods section on this page is super weak - that's not part of what you did, obviously, but if you want to do a community service you could write a few sentences to shore up that section, maybe mentioning and linking to the websites for BEAST and r8s, since those have been the two workhorses for these analyses, traditionally.

Great job!