Short remarks after checking the project:

1) Learn how to write emails:

E.g.: https://englishlive.ef.com/blog/career-english/write-perfect-professional-email-english-5-steps/

Thus, when you are writing semi-formal email you start with "Dear Mr/Dr/Prof Name Surname" and you end with "Best regards/Sincerely".

You do not write e.g "Witaj", "Witam", "Dear Mr Lukaskoz", "Hello", "Hi", etc.

It is also polite (and useful - think about SPAM filters) to include the body of the email (not the attachment and the subject only).

Additionally, if you are asked to add attachment do so (no dropbox or external services should be used, in our case the result should fit into few MB thus it is not justified to use external services).

Use spell checker.

2) Timing
When you have to deliver something until specific time you need to do it (in many cases the automatic system will close down the possibility to send the application/project/stipend after specified time).

3) Assessment:
There should be 22 persons (USOS data)

                        Date    Mark    Details
1. Mikolaj Arciszewski    25.11    redo    Lack of the alignments, rooted trees, bootstrap. Lacks of the conclusions in the summary.pdf
2. Ismail Lachheb         27.11    redo    Lack of the unrooted trees, ml & bootstrap. Extend conclusions also for biological meaning.
3. Radoslaw Bielecki      27.11    redo    Lack of the structure in tar.gz (one directory with 100 files). No R scripts. No bootstaping. The file "Rados_awBielecki_raport.pdf" briefly describes what has been done, but it does not include the results. The raport should be in English. 
=======
4. Kamil Lopuszanski      28.11    pass    One of the best projects reports (see Report.pdf)
5. Ethan Kang             28.11    pass    Do not use dropbox (or any other service which need to log in). 
6. Paulina Duda           28.11    redo    The subject of the email and the tarball not named correctly. Only cleaning the data has been done. No phylogenetic analysis.
7. Paulina Knut           28.11    redo    Make it possible to compress the files to tar.gz. Trees can not be read. Fix it. Should be in English.
8. Michal Kukielka        28.11    redo    Raport.html (should be pdf by the way) do not contain single figure (no alignments, trees, summary tables with scores). You showed the code for some parts of the analysis, but this is not result raport. Using jupyter is no excuse for not including figures. Will you write such thing in your master thesis?
9. Jakub Poziemski        28.11    redo    Do not send unfinished project. Either you did something or not. You even did not add pdf file (just the jupyter notebook). Add all missing parts.
10.Marlena Osipowicz      29.11    redo    Compress to tar.gz format. Make pdf. Your raport should not have 66 pages (e.g. pages 16-41 are not needed). Trees cannot be read. 
11.Igor Filipiuk          29.11    redo    The subject of the email not correct. IgorFilipiuk_SAD2_report.pdf do not contain the results (no figures, no alignments, trees, summary tables with scores, some conclusions are presented but there are no data in pdf file which supports them).
12.Rufin Latawiec         29.11    redo    No pdf with the results. Html also with some problems: no alignments, no bootstrap, trees cannot be read. lack of the aim and the conclusions of the project.
13.Stanislaw Massalski    29.11    redo    No pdf with the results. Html also with some problems: add introduction, focus on the results, rather than the code. More structure (add headlines, figure descriptions, etc.). Should be in English. Almost pass.
14.Alicja Nowakowska      29.11    redo    No pdf and in Polish. Add introduction (the purpose of the project). Almost pass.
15.Mikolaj Blaz           29.11    redo    Pdf file "Phylogenetic analysis.pdf" do not contain figures (alignment, trees, etc.) and tables to support the claims. Do not use external services to attach the project files (especially the ones which will make attachment not valid after some time).

Missing:
Katarzyna Bednarska
Aleksander Radolak
Shadi Darvish Shafighi
Katarzyna Dziopa
Magda Grynkiewicz
Michal Lemanczyk
Jakub Sieron


4) Conclusions:
    a) All who did not pass are asked to fix their projects and send it until 05.12.2018.
    b) To practise more all those aspects a new project will be announced next week.

5) Use this laboratories to start fixing the project 1. 

All who "passed" (all other at home):

a) Refresh your knowledge about some distributions such as Gamma, Beta, Bin

a) Metropolis-Hastings algorithm. Read:
- https://theoreticalecology.wordpress.com/2010/09/17/metropolis-hastings-mcmc-in-r/)
- https://stephens999.github.io/fiveMinuteStats/MH-examples1.html

b) the Gibbs sampler
- https://stephens999.github.io/fiveMinuteStats/gibbs1.html
- https://stephens999.github.io/fiveMinuteStats/gibbs2.html
- https://stephens999.github.io/fiveMinuteStats/gibbs_structure_simple.html

c) Monte Carlo and STAN (packages in R: 'coda' and 'rstan'), 

In next laboratories we will use all those informations.