Jeromy Anglim's Notes @jeromyanglim - Tumblr Blog

Not getting message notifications on Apple Watch when using my computer

For a long time, I've been having issues with not getting certain text message notifications on my Apple Watch. It was always very mysterious. I'd often get a text message from an important family member about something time-urgent, yet I would not be notifiied. They'd then ask me whether I got the message, and I'd look at my phone. The message was displayed on my iphone lock screen, but nothing had gone through to my watch.

I'd then try to test the idea that I was not receiving notifications on my apple watch. So I'd send a message from their phone to me, and the text message would go through to my watch perfectly.

I noticed that it would often arise in the late afternoon (but it would occur other times) when I'd be finishing up work for the day and I'd get sent a message. I thought that maybe I just got too absorbed in work and ignored the arm vibration. It was a great mystery.

But I think that I may have finally resolved the problem.

I think that when Apple sends iMessage (i.e., Apple text messages) notifications, it looks for what is the active device. Thus, when I'm using my Mac, it sends the notification to my Mac rather than my watch. This would make sense why I was not getting the watch notifications while working, and why every time I tried to test the issue, I could not reproduce it, because I was away from my computer.

I also hate notifications and interruptions on my computer. So I'd disabled most notifications on my computer. In particular, I'd disabled notifications from "messages" in the notifications center. So, I think when I was on the computer, the notification was directed to the Mac, and then the Mac was applying these notification settings to silence the message, so no notification was received anywhere.

So, it seems that the two solutions are to (a) go to the messages app on the mac and log out of the messages app or (b) enable message notifications on the Mac (and then receive messages on the Mac). For now, I've done both. Hopefullly, it finally solves the issue.

#@osx

How to disable Readcube and Science Direct Viewer?

You can go to the following website: https://www.readcube.com/epdf_settings

Assuming your browser is compatible, this should allow you to set a cookie to disable readcube so that when you click on a pdf it goes straight to the PDF.

To disable elsevier / ScienceDirect PDF viewer, go here: https://www.sciencedirect.com/enhanced-reader/settings

MFC-9970CDW Replace toner warning

The following article described a process for resetting the toner count:

https://www.easyink.co.nz/support/brother-mfc9970cdw-toner-counter-reset/

This also seemed to make the cyan warning I was getting go away.

Endnote makes comments disappear and changes markup settings in Word OSX

I am using Word 2016 on OSX and Endnote X8.

Often, when I'm editing a document and writing text in a Word document with Endnote references, the comment boxes disappear and the review markup options change.

Specifically, Endnote seems to seems to change the "all markup" option to "no markup" in Word. It often seems like it does this all the time.

On closer inspection, it seems that it does this either when you refresh references. It also does this regularly when instant formatting is on. This took me a while to realise, because I think I must disable instant formatting normally. So when I received a document that had instant formatting on that I was trying to provide feedback on, it was driving me crazy.

But anyway, the basic work around is to disable instant formatting on the document.

The issue is described here with regards to Endnote X7 http://community.thomsonreuters.com/t5/EndNote-How-To/Endnot-x7-Turns-Markup-off-in-Word/td-p/130939

Faster navigation to folder on save dialogue on OSX

When I click save in OSX on a file, the first challenge is to navigate to the folder where the file is meant to be saved. Of course, you can click through the links manually, but this is terribly slow if your files are stored several folders deep in a hierarchy.

Traditionally, I have had the folder opened in Finder. I often navigate to the folder using Alfred keyword search.

You can drag and drop the folder name on the top of the Finder window into the save as dialogue box and this will take you to that folder.

However, one problem with this approach is that you have to hold your mouse down for a few seconds to enable this feature. Otherwise, you simply move the Finder window.

A faster approach is to activate the Path bar in finder. https://www.tekrevue.com/tip/show-path-finder-title-bar/

This allows you to drag and drop immediately.

#@osx

How to disable Press and Hold on key repeat in RStudio on OSX?

I use Vim mode in Rstudio. I often hold down letters such as j and k and use key repeat to move the cursor multiple lines, words, and characters.

However, OSX has a feature where when you hold down a letter, instead of repeating the key, it brings up options for character variants.

This is discussed here.

One solution is to run the following at the terminal:

defaults write -g ApplePressAndHoldEnabled -bool false

This changes the global default setting for all applications to disable press and hold.

However, this involves two issues

Stick and hold is actually a nice feature in many apps (e.g., when you need to write european letters).

The setting seems to get reset over time. I'm not sure what program restores the global setting to enable press and hold, but I do find that after a few days, the setting has been reset.

Thus, I thought a solution would be to try to disable press and hold just for Rstudio. Perhaps whatever resets it globally would not reset it on Rstudio.

I saw in another forum discussing a different application that the following would disable press and hold for com.github.atom

defaults write com.github.atom ApplePressAndHoldEnabled -bool false

I then tried

defaults write Rstudio ApplePressAndHoldEnabled -bool false

I think this may have worked. But we will see.

Workaround for Word 2016 OSX and MathType

At the time of writing MathType is ostensibly not compatible with Word 2016 on OSX (see here).

In addition, I've long had others issues with MathType:

Equations objects are converted into non-editable images. This is caused by auto-save in Word. I don't use this, but collaborators do, so equations become non-editable.

I also somtimes get issues with others being able to correctly view equations.

Thus, I've been thinking about workarounds. This is one that I am experimenting with.

Write equation in MathType.

Copy and paste the equation into Word 2016

If the equation then needs to be edited, copy and paste back into MathType, edit, and copy back.

It seems to work and the images seem to continue to be editable. This contrasts with the bug whereby MathType field codes are converted to images. These images are no longer editable.

Pipeline publications

2002 to 2004 member of the publication team for COP Victorian Section.

The Pipeline. (2002, Summer-Autumn) APS College of Organisational Psychologists (Victorian Section). Online PDF

The Pipeline (2002, Winter-Spring) APS College of Organisational Psychologists (Victorian Section). Online PDF

The Pipeline (2003, Summer-Autumn) APS College of Organisational Psychologists (Victorian Section). Online PDF

The Pipeline. (2003, Winter) APS College of Organisational Psychologists (Victorian Section). Online PDF

The Organisational Psychologist (2004, 1, 1) APS College of Organisational Psychologists. Online PDF

Little differences between Excel 2011 and 2016 on OSX

The shortcut key for insert cells is command + shift + = (perhaps this was always the case, but I just had just had a different shortcut)

The shortcut keys in the paste special dialog (e.g., command plus v for paste as value) no longer work with command; instead you have press fn + v (i.e., use the fn key as the modifier). UPDATE: This seems to work now (not sure if it was after an update) without any modifies. So just press v in that dialog box and it selects the past as value option.

Setting up terminal on OSX to be more like iTerm2

I like iTerm2, but quite a few Apps (e.g., RStudio, ) and others open Terminal by default. So I wanted to get Terminal working reasonably well.

A few things I did:

Set up the fonts in the profile; in particular I changed the font colours, I also quite like Monaco 12pt as a font.

I quite like 100 columns as a witdh.

I had to copy .bashrc into .bashprofile to get my bash customisations to load http://apple.stackexchange.com/a/13019/11747

I had to use this trick to remove the text that it displays by default http://stackoverflow.com/a/16181082/180892

Can not edit image in Word 2016 on Mac OSX

I recently installed Word 2016 on OSX. I noticed that when I selected an image, the image editing ribbon did not appear, and the option to edit the image was greyed out.

My file was in the older ".doc" format. When I saved the file as "docx" the image ribbon reappeared when the image was selected.

#@osx

How to post about code on blogger

I have often been frustrated by the blogspot post editor. In particular, if you write about code, then it often feels like it does all sort of weird things if you accidentally move between compose and HTML mode. Anyway, here as some notes on working better with it.

Switch post settings to compose mode = "show HTML literally"

Switch post settings - options to "Press Enter for line breaks"

The above settings seem to persist across posts.

There is a courier font for code

I'm still working on making line breaks attractive.

How to export references that cite a particular article using Google Scholar?

It seems like you can do this with Publish or Perish (Free software that uses Google Scholar as its underlying database).

Procedure:

Search for the article in Publish or Perish and find the article

Right click on the article in Publish or Perish and select "Lookup Citations" (this will bring up the citing references)

Save the references in your preferred format (e.g., BibTeX, Endnote, csv, etc.)

Example

Search for the journal (e.g., search for title, author or some combination):

Selecting the article and choosing lookup citations:

Here are the citing articles:

Select save as

Debugging knitting from rmarkdown using ProjectTemplate

This post summarises some general and specific points about debugging an rmarkdown file.

General Strategy

In general, users realise they have a problem when something that is working when in manual mode, does not work when they press the knit button in RStudio.

A common cause of this problem is that objects in current workspace are not in the knitr workspace.

it is common to get errors like:

Line ... Error in eval (expr, envir, enclos) : object 'foo' not found

where foo is an object like a data frame or something else you are working with.

In some cases, there will be an obvious error in your code that you can quickly fix up.

After that, a first general step in debugging the problem is to clear the workspace (e.g., by pressing the broom button in rstudio, or typing rm(list=ls()) into the console). Then run each code chunk consecutively starting from the first one in the knitr file. There are shortcut keys in RStudio for running both the current and next code chunk. This can speed up the process. If you get an error, then fix that code.

Sometimes you can get issues, if you issue some commands that are not meant to appear in the knitr documents. In partiuclar, requesting help for a function can cause knitr to hang. So remove any instances of that.

If everything is working after you have cleared the workspace and run all the code manually, its possible that the relationship between the rmarkdown file other files is broken. So, you need to check that the working directory in manual mode is the same as when you run knitr. You can get the current manual-mode working directory by typing getwd(). By default, knitr will use the folder that it is in as the working directory. However, if you are using my modified ProjectTemplate structure, I find it tider to keep the rmarkdown files in a subdirectory called reports. If you do this, then you need to include a command in the first code chunk to tell knitr to treat the working directory as one level up.

Thus, the first code chunk should have the following code inside:

library(knitr) opts_knit$set(root.dir = normalizePath('../')) # required when rmd is in subdirectory

Alternatively, you can just move the rmd file up one level manually and not include the above chunk.

Other assorted errors

Need a later version of rmarkdown: Sometimes RStudio will indicate that it needs a later version of rmarkdown. I've seen in some cases that RStudio's script for this can fail. if so, just install the rmarkdown package with install.packages("rmarkdown")

Can't knit to PDF: In general, you need to install a tex distribution. This is free and fairly large download: https://www.latex-project.org/get/

#@rstats

A few notes on Michael Levy’s talk on teaching R

Michael Andrew Levy presented a talk at User2016 on how to teach R to new users. I thought had a few good tips that I imagine I'll incorporate into my teaching. Here's the video, and I have a few notes below:

https://channel9.msdn.com/Events/useR-international-R-User-conference/useR2016/Teaching-R-to-200-people-in-a-week

A few ideas which I liked:

Motivate students first; then get into details

Code live when teaching; it slows down the pace; it shows the process of coding including recovering from errors, looking up help and so on.

Include frequent exercises; it increases in engagement and it is crucial for learning

Initial exercises are very structured and gradually make them less structured.

Use real time multiple choice questions using Google Forms to assess understanding.

It's useful to have basic and advanced exercises given that skills will vary a lot across students.

White boxes instead of image files displaying in Word OSX 2011

I recently had this strange problem where all my images in Word files using Word OSX 2011 were displaying as white boxes.

The problem originally arose when I received a file from a Windows user. So I assumed it was some compatability issue. But then when I looked around, I saw that the issue applied to other documents as well.

It turned out an option in the preferences at been inappropriate activated.

I just had to deativate preferences - view - image placeholders.

I'm not sure how it was activated in the firs place. I sometimes toggle field shading, so it might have been accidentally selected. Alternatively, I wonder whether a document sent to me could have overrided the setting, although that seems a little strange. Or perhaps there's some keyboard shortcut I'm not aware of.

#@osx

Thoughts on Publons: Verified peer review website

I recently received an invitation to join publons a site that verifies journal review activity.

Overall, it was a fairly pleasant experience. The website is clear and clean. It was relatively straightforward to set up a profile.

Then I just needed to search my emails and forward emails thanking me for reviewing an article to publons. They then use these email receipts to verify a particular review activity. I imagine it would just be a matter of remembering to automatically forward these emails in the future.

There's some nice export options that allow you to compile your review statistics for CV related purposes.

The statistics on your profile also allow you see various features of your reviewing activity. For example, you can see:

How many reviews you are doing over time

the impact factor of the journals you are reviewing for and how that compares to your field.

The days of the week that you submit your reviews

You can have a look at my profile here or here's what a more established professor's review profile might look like.

Overall, I like the premise of the site. Academia needs more systems to recognise and celebrate those who do lots of peer review.

That said, I always have my concerns when a presumably commercial company takes on the curation of scholarly data.

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