Geostatistics SoSe 2015

Remember I mentioned homeworks?

Yes, they exist! How are they going to work? I am going to try to explain now.

Very likely you remember, the course has 2 hours of preparation and 2 hours of post-lecture homework. You have to earn you credits. So I am giving homework and I am making you learn other things along the way; otherwise you are not going to be able to download the data or submit your homework ;-). Say I am pushing your limits to make you learn Latex, Git, R, etc. during your “free” time.

Ok, but how this is going to work?

I downloaded data from different papers and I am going to ask you to analyze these data and write the following two paragraphs:

  • A Materials and Methods paragraph describing what you did.

  • A Results paragraph describing what you found.

You are going to write that using Latex and I am going to compile the .tex files you are going to upload to the Geostatistics repository using Git.

This means that you need to install and get familiar with these two systems.

So I am going to give you a brief intro to them and point you to material you will have to read to actually get things going (this is part of your pre-lecture preparation duties). This should not take you more than two hours, so don’t worry.

How to Latex

Latex is a typesetting system. Is not a What You See is What You Get (WYSWYG) text processor but a system designed to produced publication ready documents from plain text files. Is a markup language, which means that it looks strange at the beginning but it produces very nice results with relatively little effort.

A Latex file looks something like this (modified from here): \documentclass{article} \title{Geostatistics homework 1} \author{Sergio Vargas} \date{April 2015} \begin{document} \maketitle %this will print the title here, and comments start with % Oh God! we get to use latex in this course! \end{document}

When you compile this text file using Latex a .dvi file will be produced and you can convert this to .pdf or .ps. You can create pdfs directly using pdftex. Anyway, there are lots of things you can do with latex.

Quoting the latex website: “LaTeX is the de facto standard for the communication and publication of scientific documents”. You learn to recognize a Latex-ed document and to like it, and soon you will respect it. Anyway, is something a scientist should know how to use and is becoming more and more popular among biologists and more “user friendly”; it used to be more a physics thing.

So, here’s what you need:

Congratulations! You are now all set to start writing beautiful latex homeworks.

How to Git

Good news! You will need to connect to the course Bitbucket repository to download the data.

The repository is version controlled in Git, and I think is a good idea that you learn how Git works, at least at the very basic level (which is how I use it anyway).

But what is Git?

Is a version control system that allows you to keep track of changes you do to whatever you store in a git repository. Think of it as a superpowerful dropbox. Git is used to control source code changes in collaborative software projects, and is the way the linux kernel is mantained. So it works, because keeping an eye on the linux kernel is not a minor thing and the world still exists. So it works.

Anyway, you’ll need to do the following:

  1. Install Git on your system. I recommend you install the command-line version, is easier to use than the more complex GUI systems I’ve seen so far.

  2. Read the tutorials on how to use it. Most likely you are only going to need to read about the basics.

  3. Create an account on Bitbucket. Is free, don’t worry, and if you use your academic email to register you get as many private repositories as you want for free! You should have an invitation to join the Geostatistics repository in your mailbox, before you read this ;-).

  4. Connect to the repository and synchronize the contents of it to a folder located on your computer, anywher on your computer, it doesn’t matter where. But try not to move this folder around. My recommendation is to create a folder called repositories and there you can create folders for the repositories you are connected to.

You are all set, so, please connect to the repository Geostatistics and start working on your first homework.

Happy homeworking!

Delivering your homework

You are required to deliver your homework using the Git repository. To do this please create a folder with your lastname and store your homeworks in this folder using subfolders named 01_Homework, 02_Homework, etc.

For each homework, you are required to write one paragraph of Materials and Methods and one paragraph of Results. Whatever graphs and tables you need to prepare to comunicate your Results must be included at the end of the document and must have adequate legends.

This text must be written in Latex and must compile.

Homework 1

Delivery: 29.04.2015

  1. Read the following paper:

    Yasuhara, M and Stepanova, A and Okahashi, H and Cronin, TM and Brouwers, EM. 2014. Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean. Micropaleontology, 60: 399-444. doi:10.5061/dryad.r2170

    You can find the pdf and associated data for this study in the Geostatistics repository under Data/10.5061.dryad.r2170.

  2. Using PAST and R (yes R) and the data from this paper produce the following summary statistics for each genus in Table 2:

    • Number of observations

    • Mean

    • Median

    • Variance

    • Standard deviation

    • Standard error of the mean

    • Range (Min and Max)

    • First and third quartile, which is the same to say 25th and 75th percentile

What would be a problem if you try to do the same at the species level?