lunasare/datelifems1

Hi there 👋

Welcome to my GitHub profile!

You can visit my academic website at https://lunasare.com

datelifems1's Issues

Final decision: Fix Fig 2 & 3

AE: "In Fig. 2 and 3 It looks like the Paleogene starts 45 Ma. I would use equally spaced numbers e.g. 0, 10, 20, … instead of showing boundary ages (as 45 is not one)."

https://github.com/LunaSare/datelifeMS1/blob/main/submission/Figure_2.pdf
https://github.com/LunaSare/datelifeMS1/blob/main/submission/Figure_3.pdf

I think we can use inkscape magic to address this fix, too.
It might be good to create a graph that uses 0,10,20... so that we know where the numbers should go on the axis and then use the same axis for all.

todo

• 1. Create summary ages table for table 2
• 2. Update tables of figure of all Fringillidae, add to Supplementary data
• 3. update figure 5, especially points of source ages, identify which ones were used and which ones were excluded.
• 4. Choose one figure to showcase results of cross validation analyses
• 5. Add other cross validation figures to supplements
• 6. Check that cross validation is run without chronograms from the same study, especially for study from Price etal. 2014, chronogram 2
• 7. Address remaining comments
• 8. Submit!!!

merge redundant functions

Possibly redundant pairs:

• extract_calibrations and get_calibrations
• match_all_calibrations and mrca_calibrations

For each pair, check:

• do they give the same output?
• if yes, which one is faster
• keep the fastest one

Geiger citation

Should be Pennell, M.W., J.M. Eastman, G.J. Slater, J.W. Brown, J.C. Uyeda, R.G. FitzJohn, M.E. Alfaro, and L.J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 30:2216-2218.

Final decision: Fix Fig 1

https://github.com/LunaSare/datelifeMS1/blob/main/submission/Figure_1.svg

AE: "In Fig. 1 the labels if the x-axis appear to be slightly shifted to the right"

Maybe you can work your inkscape magic @snacktavish on this Figure and move the labels to the left so they align with the ticks on the x axis?