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For workshop lecturers: editing lecture and exercise pages and posting files

The lecturers and assistants in the workshop have been given the secret password enabling them to add pages to the blog, or to edit pages on the blog, or to post files and make links to them.

Editing an existing web page on the blog

  1. Make sure you have logged in to the blog’s WordPress site (for example, using the Login page of the blog).  In the upper-right corner of the page, you should see “Howdy, fhleqg”
  2. Find the blog page by  (a) using the Schedule and clicking on the lecture or exercise link for that page, or (b) going to the Dashboard and looking at Pages and choosing All Pages, then going through the list till you find the one you want.
  3. Click on the Edit link, which is either visible on the page, or becomes visible on moving your cursor over the page name in a list of pages, or which may appear in the stripe at the top of the Dashboard.
  4. Once the page opens for editing, you may want to choose the Visual tab (upper right area).  Then you can type in text, and then mark it and boldface or italicize it with the usual B and buttons, right/left/center justify using the usual buttons for that, or choose a new font or change the font size for the marked text.
  5. … or you can choose Text mode — then you’re typing raw HTML, so you’d better know what you are doing.
  6. Save your changes using the  Update  button in the right column of the browser page — you may need to scroll some to see it.  Unless you  Update  all recent changes will get lost when you are done.

Adding a new lecture or exercise web page

This can be done using the  +New  tab in the top area of the Dashboard, or the  Add New menu item in the left column of the Dashboard.   Some things to do:

  1. In the box at the top, type in the name of the web page.  It must start with the year, followed by a blank space.  Thus if it is a page for Exercise 3.4, it will look like this:  “2018 Exercise 3.4”.  This is important — the year must be there to allow us to retain pages from previous years, and not overwrite them.
  2. You want to have a link to the next page in sequence (the next one in the Schedule).  This is a small link in the upper-right part of the page.  You can make this by figuring out the name of the next page, and then going into Text mode and inserting as the first line in the page a line like the following:
    <p style=”text-align: right”><a href=”http://blogs.uw.edu/fhleqg/2018-lecture-2-1/”>Lecture 2.1</a> →</p>
    (you could just copy this one, paste it in, and then change it to the correct year, to be “lecture” or “exercise”, whichever the next page is, and to have the right numbers).
  3. It is best to be in Visual mode when typing in most page content. When you finish doing that, it is essential to push the Publish button in the right-hand column of your browser page. You may need to scroll there to find it.  If you do further editing while still editing the page, be sure to push the Update button (which will have replaced the Publish button once the page is published).  Forgetting these will cause your carefully crafted content to be lost.
  4. You will also want to go to the Schedule page and create a new line for the new page, with a link to it. Before you go there, copy the URL for the new page. It can be copied from the “permalink” that appears at the top of the editing page when you were finished editing the page content, after you had Published or Updated the page.

Posting files to be linked to from the web page

Files such as lecture projections (PPT or PDF), or supplementary documents, or R exercises, or audio recordings, are not to be posted on the workshop blog.  Instead, open the Google Drive for the  fhleqg  account, which is not a gmail account but a  uw.edu  account.  It has the secret password we mentioned above.

Find the “Shared folder” and open it, then find the folder for this year (such as “2018”) and open that.  Find the folder for the lecture or exercise, and open that.  If it does not exist, right-click or Ctrl-click and choose New Folder, and give it the appropriate name such as  Lecture 4.3.

Then you should be able to tow the file from your system onto the page and drop it there.  You can change its name once it is there, if you want.

Getting the link for one of those files

But there is still the matter of getting the address of the file, and posting a link to it on the lecture or exercise web page.

  1.  Open a window with the Google Drive page, with you logged in appropriately.
  2. Find the folder with the file, and open that folder.
  3. (You may need to do this only once)  The files you put in the Google Drive folders should be accessible by anyone who has the link.  This ensures that clicking on the link in the blog reaches the file.  To make that select the file and click on the icon above and to the right that looks a person with a + sign on their shoulder.  Choose the setting that states that “anyone with the link can view” the file (not just anyone at UW with a link).
  4. Right-click or Crtl-click on the file name.
  5. A menu will open.  Choose “Get Sharable Link”.
  6. A box will open with the URL address for the link.  Select it and copy it.
  7. Now go to the Edit screen for the blog page, in Visual mode.  Have the text that will indicate the link selected.
  8. Choose the symbol for Insert/Edit Link, which looks like a little chain with three links.
  9. Insert the URL in the box provided.
  10. Press the return-arrow button which immediately follows the URL field.
  11. Don’t forget to Publish or Update the web page after that.

Correction to MCMCglmm code

The correct syntax for calling the inverse of the numerator relationship matrix is (last line of the MCMCglmm statement):

ginverse=list(animal=invA$Ainv))

Please use this syntax for all the MCMCglmm model statements I gave you this morning.

Thanks!

Pat

 

Unfamiliar with matrix algebra?

If you aren’t familiar with matrix algebra (or with matrix algebra in R), you might want to practice with a couple of tutorials before the course starts on June 4th.  Go to the Schedule and click on Exercise 1.2.  The first part of this exercise is two matrix algebra tutorials.  You could work through those tutorials before you arrive.  That will make doing this exercise a little easier on the first day of the course.  Have fun!

How to get ready for the course!

Our five day course at Friday Harbor will be fast-paced, so here are some points to keep in mind in getting ready for Monday, June 4th.  As you can see from the Schedule, we generally have a lecture on a topic, followed by some discussion, then (but not always) a computer exercise on that topic and then finally some more discussion.  Before the start of the week, you may want to look over the Schedule and do a little background reading for the lectures that interest you the most.  The problem that you will now confront is that all the material for the lectures of interest may not be posted and will not be posted until the day of the lecture.  No worries!  Go to the Schedule for last year’s version of the course (click Previous years in the top ribbon) and find the most relevant lecture.   There which will often be very similar to the one in this year’s schedule.  On the 2017 Schedule you will find powerpoints/pdfs for lectures, videos of lectures and audio recordings, as well as suggested readings.  You can use all of those to prepare for the lectures of special interest to you.

To prepare for the computer exercises, it is important to realize that the exercises are of two types.  Some of exercises use special websites and software (e.g., see the exercise on estimating G-matrices or the one on G-matrix evolution).  Using the instruction documents from 2017, you could try doing those exercises beforehand if you want.  Other exercises are tutorials in R, in which you will follow along as the instructor guides you through the tutorial.  You will not need much knowledge to follow along, but you will need to execute commands in R and look at and possibly save graphical output.   Often the instructor will use R Studio and so it will be useful for you to have R Studio installed on your laptop so you can more easily follow along.  R Studio is a user-friendly front end for R.  Free downloads are available at https://www.rstudio.com/products/rstudio/download2/  After you have successfully downloaded R Studio you might practice with it by loading R script and running it.  You can find instructional videos on YouTube that may help you get acquainted with R Studiio. -SJA

Mac and Linux users, please install wine

Some of the programs we will be using have been compiled for Windows. To get them to work on Unix machines (e.g., Macs and Linux distributions) you need to use wine, an open source application. Information about wine can be found here. It can take about 30-45 minutes for wine to install, depending on your internet connection, so be sure to have it installed and ready to go before the first day.

In Exercise 1.2 we provide tips for downloading wine for both Mac OS X and Ubuntu.

Write a comment below if you are having trouble downloading and installing wine on your machine.

Need help using R?

R Tutorial

I have attached some files below which may help if you are new to R.  The first two files are from a past workshop run by Marguerite Butler; you should start with these.  Other files show you how to install packages into R on your laptop (read them before the course) and provide general reference information.  A general way to get help in R when you are stuck is to enter a query in Google.  For example, if you can’t figure out how to do labels on plots, type something like ‘Adding labels in R’.  You can also get help within R by typing a ? followed by a noun that is the name of an object in R.  In general, if you are writing a program, the simplest way forward is to find a program that does something close to what you want.  Modify that program in small steps, testing after each change, until you get to where you need to be.-SJA

Day2_workflow

Day2_dataobjects

Installation_of_Packages

R-intro

R-manual

Install/update R

R is a free statistical computing program that will be used throughout the course. If you haven’t done so already, please download R and install it on your computer from this site before June 5th.  If you already use R you might want to install the most up-to-date version so that new package installations are easier. -SJA