practical phylogenetic comparative methods about mebioda

[iadamo1]

I have already checked the phylogenetic signal and diversification practicals and I had to make a couple of changes only on the diversification one. The main issue is that the package LASER was removed from the CRAN repository so I downloaded it from the archive and everything worked fine. They are shorter than the other ones so I think they can be done in one day.
Thanks, I will do the RBIEN/SALVIAS tutorials today.

[iadamo1]

Sorry for the late replay, no problem I will look at them! Il giorno ven 13 ott 2017 alle 20:14 Rutger Vos <[email protected]> ha scritto:

…

Can you have a look at the paper and the Dryad supplementary materials I am considering for the Tuesday? https://github.com/naturalis/mebioda/blob/master/doc/week3/README.md#day-2---topological-analysis It's a simulation paper about tree shape and how extinction events can get swamped/erased over time. I sort of know some of the authors so we can bug them with questions. I am hoping we can turn the scripts from the supplementary materials into some *.rmd files in which we can replay some of the analyses as a practical. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#20 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AX5UH0jBsRjUJNl--SodTTpurUaYds8Yks5sr6hQgaJpZM4PtfJK> .

[rvosa]

If you paste the newick string here we'll keep track of it and make sure it ends up in the teaching materials.

[iadamo1]

here is the string for the landplant data that was in the ape packege;
(Marchantia:0.033817,(Lycopodium:0.040281,((Equisetum:0.048533,Osmunda:0.033640,Asplenium:0.036526):0.011806,(((Cycas:0.009460,Zamia:0.018847):0.005021,Ginkgo:0.014702,((Pinus:0.021500,(Podocarpac:0.015649,Taxus:0.021081):0.006473):0.002448,(Ephedra:0.029965,(Welwitsch:0.011298,Gnetum:0.014165):0.006883):0.016663):0.006309):0.010855,(Nymphaea:0.016835,(Saururus:0.019902,Chloranth:0.020151,((Araceae:0.020003,(Palmae:0.006005,Oryza:0.031555):0.002933):0.007654,Acorus:0.038488):0.007844,(Calycanth:0.013524,Lauraceae:0.035902):0.004656,((Magnolia:0.015119,Drimys:0.010172):0.005117,(Ranunculus:0.029027,(Nelumbo:0.006180,Platanus:0.002347):0.003958,(Buxaceae:0.013294,(Pisum:0.035675,(Fagus:0.009848,Carya:0.008236):0.001459):0.001994,(Ericaceae:0.019136,Solanaceae:0.041396):0.002619):0.004803):0.006457):0.002918):0.007348,Austrobail:0.019265,Amborella:0.019263):0.003527):0.021625):0.012469):0.019372);

[rvosa]

Can you also check phylogenetic signal and diversification?

[rvosa]

And the RBIEN/SALVIAS tutorials: https://github.com/naturalis/RBIEN/tree/master/tutorials

[rvosa]

Can you have a look at the paper and the Dryad supplementary materials I am considering for the Tuesday? https://github.com/naturalis/mebioda/blob/master/doc/week3/README.md#day-2---topological-analysis

It's a simulation paper about tree shape and how extinction events can get swamped/erased over time. I sort of know some of the authors so we can bug them with questions. I am hoping we can turn the scripts from the supplementary materials into some *.rmd files in which we can replay some of the analyses as a practical.

[iadamo1]

paper and data, tree balance:
while going over the scripts there are some table txt files (folder R_files_for_Dryad) e.g. mesa_seed_list or CRS_times, that are imported but were not generated within the scripts. I am not sure I am looking at this correctly, it seems strange that someone should be able to repeat the analyses but there are some data missing. I will make a list tomorrow morning of the question that maybe the authors can answer.

[iadamo1]

so my doubts are:
is the MESA_seed_list.txt file used in the collectKey().r scripts simply a list of the seed numbers of the MESA output files? is it possible to get the file CSR_times.txt and CRS_relative_points.txt?
how were the txt input files generated used for the two-way Anova and Dunnett contrasts generated?
they may be very basic doubts but if I understand the content of the seed list file and the one relative to the CRS times, I can make the scripts run and then the steps will be clearer.

[rvosa]

I have sent a mail to Gabe with your questions (you're on the CC). Hopefully we get some answers.

[rvosa]

I have received files (added as commit 0165814 to folder week3/w3p2) as well as the following response:

is the MESA_seed_list.txt file used in the collectKey().r scripts simply a list of the seed numbers of the MESA output files?

Yes, but it's not a fully consecutive number sequence. Some seeds resulted in trees that died before reaching equilibrium/carrying capacity so the file contains only those seeds that produced a full sim run.

would it be possible to get the file CSR_times.txt and CRS_relative_points.txt?
how were the txt input files generated that were used for the two-way Anova and Dunnett contrasts?

Basically, I put the data together "by hand" in Excel and exported them to these text files that were then imported into R.

[iadamo1]

perfect, thanks a lot! I m looking at the data the Jòzsef provided and at the tools today, I think I will have to ask him which primers he used in order to trim them.
Have a nice week end.

[rvosa]

Great, you have a nice weekend too!

[iadamo1]

1.I have added the txt files for the statistical analyses, I found on dryad the excel file with the summary of the data that they used so I put them separately to export the txt version, I was only missing two files from this excel file, which I tried to generate following what they did for other files. Still, I would like to ask the authors a confirmation.
2. I still have a doubt on the 2-way anova, but tomorrow morning I will check again and if I did not solve it we could send them and email with both the questions.

[rvosa]

I am just updating this issue with the request to make sure that the README file within the practical folder ends up having useful information in it: right now it is empty, whereas it should record the steps to take to recreate the results in the paper.