practical phylogenetic comparative methods

[iadamo1]

@rvosa the tutorial for the phylogenetic comparative methods uses a data set (landplants) which was present in the older versions of the package ape. should the students just download the older version or it is better to look for another tutorial?

[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

[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.

[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]

Sorry for the late replay, no problem I will look at them!

Il giorno ven 13 ott 2017 alle 20:14 Rutger Vos notifications@github.com 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.

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[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 01658141b4348234db18c4e243e86cc88e67370f 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.