I Dragged a PDF into Sente. You Won’t Believe What Happens Next

February 25th, 2014

While Endnote is the most commonly-used bibliographic software, I use Sente, a Mac program by Third Street Software that really got my attention back in my M.A. days. I am not an expert in comparing the latest versions of Sente versus Endnote, but from my use of Sente at home and Endnote for Windows at the School of Nursing, I think that Sente is easier to use and more convenient in many ways.

The feature that really sold Sente to me was the PDF integration. Sente can grab information from a PDF, either automatically or with a little manual coaxing, and fill out the reference information for you. Finally, it links the PDF to the new entry for you, filing it away in its own library. Here is a demonstration:

  1. The first step is to find an article you would like to download and enter into Sente. This editorial on the misinterpretation and limits of the p-value in statistics seems like it would be useful later:

    { The second author is good at coming up with titles, I hear. }

  2.  

  3. After downloading the PDF, fire up Sente and just drag the PDF to the Library section of the sidebar: Sente 2
  4. Sente will open a sheet. The left half shows the PDF, and the right half shows any information it found. As luck would have it, Sente found all of the information necessary to build a typical citation. In case there is not enough embedded information in the PDF, Sente lets you search online sources such as Google Scholar and it will pull the data from the search results itself: Sente 3
  5.  

  6. Click “Add New Reference” in the sheet and Sente does the rest, placing the new entry in the rest of the library: Sente 4

 

Dragging and dropping multiple PDFs will make Sente do them all sequentially. Under the options button/menu in the Citation Lookup sheet, you can set it so a match based on the DOI (Digital Object Identifier) will automatically be accepted as valid without your OK. The color-coding is another nice feature. There is also a tagging system one can use.

The other big feature in Sente is cloud synchronization: you can upload your entire library to Third Street Software’s servers and it will sync across any number of Macs and iPads.

There is a free version of Sente that can handle libraries of under 100 references. Technically, you can get crafty with multiple libraries to work around this limitation, but the full price is a fairly standard $60 for academic use. If you are a researcher and you have a Mac, I absolutely recommend Sente over Endnote.


I Investigated the Mac Dictionary. What I Found Blew My Mind

February 4th, 2014

As I was writing the previous post about multiple language spellchecking in Mac OS X, I wondered what if there was a similar option for the built-in dictionary. In case you didn’t know, you can right-click a selectable word, choose the first menu item (“Look Up”) and it will show a pop-up with the definition.

{ Goldin and Rouse (2000) }

{ Goldin and Rouse (2000). Note that I selected a word from an image of a word, which is pretty impressive. }

Right-clicking on a Spanish word yielded no results, so I went straight to the source: the Dictionary app. Select Preferences from the Dictionary menu in the app and you get a rather impressive list of dictionaries to use:

Dictionaries

Checking the dictionary you want not only enables it in the app, but it instantly makes the right-click pop-up work:

{ Benfer et al. (2007) }

{ Benfer et al. (2007) }

 

Granted, the app has a purely Spanish dictionary, and not a Spanish-English dictionary, but it’s a start. The East Asian dictionaries do give definitions in English.

Next: document management!

 

References

Benfer Jr, R. A., Ojeda, B., Duncan, N. A., Adkins, L. R., Ludeña, H., Vallejos, M., . . . Villarreal, G. (2012). La tradición religioso-astronómica en buena vista. Boletín De Arqueología PUCP, (11), 53-102. Retrieved from Google Scholar.

Goldin, C., & Rouse, C. E. (2000). Orchestrating impartiality : The impact of “blind” auditions on female musicians. The American Economic Review, 90(04), 715-741.


I Poked Around My Mac’s Keyboard Settings. What I Found Changed Everything I Knew About Life

January 29th, 2014

I hate the hyperbolic link bait titles that are all the rage. Don’t you? Anyway, I am starting a new series on neat tech tips that are useful for research. This one is already preinstalled on Macs.

In my desired line of work, I have to write in both Spanish and English. For example, research papers to Latin American Antiquity and other journals require both English and Spanish abstracts. I found out during my dissertation writing process that my computer can spellcheck multiple languages at once. The setting is hidden in different places depending on the OS version. In the current Mavericks:

  1. Open System Preferences
  2. Click on Keyboard (yeah, not Language & Region)
  3. Click the Text tab: Languages Step 1
  4. Click the menu labeled “Spelling:”
  5. Choose the last option: “Set Up…”: Languages Step 2
  6. A sheet appears! Read the instructions on this sheet. Basically, check the languages you want checked automatically: Languages Step 3
  7. Click Done
  8. Make sure that the Spelling: menu says “Automatic by Language”

From now on, any typed text in an application that uses Apple’s text functions (e.g., TextEdit, Pages) will spell check the languages you selected. Sorry, this does not work in Microsoft Word, which is why most drafts of my dissertation were written Pages.

{Correct and incorrect words are accurately processed in two languages. }

{Correct and incorrect words are accurately processed in two languages. }

I hope you find this useful, even if it did not change everything you knew about life.


Short Term Fluctuations in Style

January 10th, 2014

When I released the first version of mobile Anthropomotron, I had to design an icon for it. The process was described in these posts. Little did I know, that a major change in design aesthetics would occur, which would demand a change in both the design of the icon, and the app’s general interface as well. As mentioned innumerable times by the media in the fall of 2013, the visual style of iOS changed with the arrival of iOS 7. Gone was the “stylized reality” of the previous incarnations of the software, replaced by abstract simplicity.

As a side note, this is very much a pendulum shift, since back in the day (2000), there was a move spurred by Apple to go from stylized icons of Mac OS 9 to the large, colorful, and more realistic icons of OS X. This article has a great overview of icon style evolution.

Anyway, while I personally did not feel like changing the style of Anthropomotron, going with the flow and reworking the appearance has a few advantages. Even if the content is the same, staying in touch with what a modern app looks like gives a feeling of quality and professionalism. Also, not all change is bad, and being moved to make an overhaul in the user interface allowed me to fix and improve elements from the previous version. Following Apple’s official design guidelines to “interpret reality in an artistic way,” I went back to an idea I had when making the original icon to have the three objects (the femur, caliper, and ruler) be flat shapes.

{ The mock-up I made while coming up with ideas. }

{ The mock-up I made while coming up with ideas. }

Working with the Photoshop file for the first icon, where I had kept all of the layers of the different elements, I quickly hid the textures from the old icon and made filled shapes for the three objects. Each object has little accent marks to more clearly show what they are supposed to represent. For some reason, the official iOS 7 designers love tick marks or other types of repeating lines (for example, pick up your nearest iOS device or see this webpage and look at the icons for Safari, Compass, Stocks, Voice Memos, and Settings), so I added such lines to the ruler and caliper. For the femur, I added lines to demarcate the femoral head and the intertrochanteric crest (I think the posterior femur has prettier lines than the anterior!). The official icons also have gradients for backgrounds so I got rid of the gridlines from before, noting the irony, and went for a blue-to-blue gradient that goes from the dark blue in the app’s UI to the light blue. For balance, the gradient is darker behind the white bone and lighter behind the black caliper.

Anthropomotron iOS 7 Icon

Overall, I think the new icon has its own charm. I’m keeping the Photoshop layers of the old icon, though, for when the stylistic pendulum shifts back again.


Anthropomotron 2.0 is Here!

November 11th, 2013

My ‘summer’ project has finally been finished, and I am proud to present Anthropomotron 2.0 to the world. I have been adding features since the end of April, both immediately visible and internal enhancements as my Javascript and XHTML/CSS have improved. The whole list of improvements is here, but in summary you will find:

  • Consolidation of calculation code means more trustworthy internal mechanism and easier addition of more formulae in the future
  • New color palette makes text easier to see
  • Juvenile and adult anatomical (full body) stature estimation
  • More recent adult stature estimation equations
  • Info sheets are now organized in collapsible menus.

The 1.5 release received more attention than I expected, considering my minimal attempt to publicize my app. I will be more proactive with this release, reaching out to different online and offline media that may be interested in all things Anthropomotron. Try out Anthropomotron 2.0 on iPhone/iPad, Android, or web browser!

Update: For the curious, this is day 313, going by the count I started in my early development posts!


I Have the Best Friend-Fan

November 6th, 2013

 

My friend calynn sent me this absolutely fantastic rendition of the cover to Keeley: Comic Hero Extraordinaire #2! Each difference in shade is its own piece of felt and it has all been cut and assembled with incredible precision. Even the fist’s speedlines are accurate to the original drawing! The piece is the size of a vinyl record sleeve and calynn even sent it to me framed (in the most well protected package ever).

Here is the original image for reference:

 

Thank you so much for the crafty gift!

 

{ See how happy I am! }

{ See how happy I am! }


Read Keeley: Comic Hero Extraordinaire #4!

August 29th, 2013

With all of the things going on, I forgot for a time that issue 4 of my comic was incomplete on this very site! I have begun work on issue 5, mostly at the weekly Geek Night at Eastside Tavern with a side of San Diego trip, so I think now is a good time to unleash a freely accessible issue 4. Enjoy!


If I Could Make One Suggestion…?

August 8th, 2013

I’m new to this teaching thing, but I seem to be a hit with my students, so I have a tip for someone even newer than I. The anthropology course I am teaching online is writing intensive, as online courses tend to be. There are multiple weekly discussions and writing assignments that culminate in a final paper. All of this takes place in just a five week span, a “crash course” as I see it. Given so little time to help a student learn both human culture and academic culture, I devised a strategy to make the most of my comments on their writing.

My idea is based on the “80/20 rule,” or the Pareto principle. While the actual numbers are not relevant in my case, I take from this concept that a few strategic corrections can make a disproportionately large improvement in one’s essays. The challenge is for me to read a student’s paper, and find the one thing to recommend in my comment section that would benefit future papers the most. (To be clear, I note a variety of things such as misspellings and content problems in the text that could be fixed, but I choose just the biggest bad habit to address in my comments section).

For example, one student either ended a sentence with a question mark or ellipses… In every case, a simple period would have been the best choice? I remarked on this pattern by saying that he should make his statements with confidence and in the following assignment, there were no gratuitous ?’s or …’s, and as a result there was a great jump in how professional his paper looked. Success! Of course the recommendation varies among students, and also within one student’s body of work. Now that the punctuation problem was solved, I could find the next biggest issue (for example, too much quoted text relative to his own words) and work on that. It is a continuous process or tuning one’s writing habits until only minor issues remain. Over the span of each course, I get three or four shots to correct each student’s gaffes, which does not sound like much, but following the 80/20 rule, I find that in week five most student’s writing is noticeably improved. It is my hope that they then take their new skill to their next course, where it will be further polished.

I think this technique has several advantages. Students may feel discouraged when confronted with a litany of their writing mistakes. Giving them one issue to work on breaks up the overall task into manageable pieces. Introducing one suggestion at a time also probably helps the student remember the comment for longer since it’s not commingled with several other comments. Lastly, it helps me-as-grader track improvement more clearly as well when I see that he or she has or hasn’t taken my advice.

As I teach each session, I feel that I am also learning my chosen craft at a tremendous pace. I hope this little bit of personal insight is helpful for others faced with thirty papers to grade and no conceptual model for handling them all!


Hood Ornaments

July 15th, 2013

Besides the inner workings of Anthropomotron, I am also adding new features readily visible to anthropologists. Adult stature estimation gets some new neighbors as I add juvenile stature estimation and full body stature estimation. Juvenile stature estimation also turns long bone lengths to an estimated stature using findings from two teams of researchers. Full body estimation takes the height of 29 bones that form an individual’s standing height. It is the best estimate since it involves direct measurements of what constitutes stature. At first I thought adding this feature would be an easy undertaking since the procedure simply adds everything together plus a little extra to account for the lost fleshy bits. Implementing the calculation has provided several unexpected challenges!

For example, there is the issue of paired limbs. The published procedure is that if both femora, tibiae, or feet are available, the average is taken (Raxter et al. 2006, 2007), so that is an additional calculation for each pair. Anthropomotron has to know if both bones in a pair are present and average them for the final calculation, or if only one is present, to use that value.

I also have to account for the work of two separate sets of researchers. The oldest commonly used method is by Fully (1956), but Raxter and colleagues (2006, 2007) made improvements. I think both have value (and it is interesting to compare their results) so I am implementing both methods. Raxter and colleagues’ actually has an option to account for age in the estimate, so there has to be a separate set of calculations for that area.

The sheer number of measurements also needed some changes to the interface. In other sections of Anthropomotron, the placeholder describes what should go in a given text box. For example:

Placeholder

When the user enters the measurements, the placeholder is overwritten. The negative of this display is that the user loses information on the purpose of the text box. On the positive side, some clutter is removed (this push and pull seems to be the crux of a lot of device design issues, such as the iOS7 redesign). In Anthropomotron, usually there is text nearby to reinforce what the text boxes are for:

{ Oh yeah. }

{ Oh yeah. }

With full body estimation, there is no such reinforcement:

{ Um, where was I? }

{ Um, where was I? }

To fix this issue, I removed the placeholder and placed a label to the left of each text box. Now CSS tweaking made the text wrap properly for longer labels and it all should fit on a vertical iPhone screen.

{ Ah, yes. }

{ Ah, yes. }

This looks so good that I considered going back to redesign all of the other text boxes, but I quickly talked myself out of it. While the full body measurement labels are static, in many of the other estimation modes, the labels will have to change with what options are selected. Since there is no actual issue to be fixed, I will leave them be.

While adding full body estimation (a much requested feature) is getting more involved than I had planned, it will add greatly to Anthropomotron’s usefulness. I plan to get the section running and release version 1.6. Then, I feel it is time to get drawing again!


Under the Hood

July 8th, 2013

Working two jobs eased out a lot of my prior free time in the evenings. I stopped playing WoW (at least until the next expansion), and I’ve had less time to work on my major hobby, which is currently Anthropomotron. It is not surprising then that I have made additions at a slow but consistent pace. I did kick into a higher gear when I noticed during some copying and pasting of code that in certain cases, the kilogram to pound conversion made no sense. I fixed it and rushed out the 1.5.1 update before anyone else noticed and/or told me about it.

In the week between my online courses, I had the previous breadth of free time. I got into a new game (Marvel Heroes, which is basically free Diablo with comic characters). More importantly I cranked out several major changes to Anthropomotron for a future update. Stature estimation received a new category: estimation of juvenile stature from limb bone length via two different team’s research (Ruff [2007] and Robbins Schug et al. [2013]).

The new section runs on a new set of code. In the older formulae, there are multiple copies ofthe same mathematical functions. For example, adult stature estimation with one long bone has code to perform a calculation with a linear regression formula with the right values plugged in. Body mass estimation using the femoral head diameter has its own section of code to perform a calculation with a linear regression formula with its own values. The same duplication appears for other processes, such as converting centimeters to feet and inches, and displaying the result on screen. The code works, but it is not elegant.

Juvenile stature estimation is written differently. I wrote a single linear regression formula function that will now handle all requests for this calcuaiton. Whether one uses the Ruff or Robbins Schug and colleagues method, the specific values are passed to this one function, which hands back the calculated result for further processing. I also wrote single functions for unit conversion and the display of the result, like an assembly line of steps. The benefits of coding this way are that the code is shorter and there are fewer chances for error with duplicated code (for example, miscalculating kilograms to pounds in some occasions).

Over time, I plan to transition the old code to use the new functions, making the whole thing even more efficient. Elegant, even, as programmers say. Stay tuned for the 1.6 release with the juvenile stature estimation and a little something extra, possibly detailed in an upcoming blog post!