2011-03-23 22:53:41New research papers data visualization ideas
Paul D

chillcast@googlemail...
82.18.130.183

Hi folks.

John asked me to post the new ideas for the research papers data visualization project, which will take data from Johns database and display it in a pleasing manner as well as showing some numbers and other useful stuff.

We didn't get any response when I posted the initial animation. I have mocked up three ideas as still images below. Please take some time to read and view the ideas and PLEASE DO GIVE US SOME FEEDBACK. I will be very unhappy if no one says anything this time round. I and John have personal favourites, although John hasn't seen idea 1 yet!

NOTE: the final project will probably have more text and of course colours and other stuff may change once the chosen idea is developed. Also note that the numbers are made up for the mock-ups, so ignore those.

Idea 1: Clusters
Each circle represents a year of papers of a particular bias. In ths example the mouse has rolled over the 1993 Pro-AGW circle and displays the total number of papers for that bias and year. The circles are clustered according to bias, so a good idea of the totals are shown visually. When a circle is rolled over a list of papers and links that the circlke represents maybe displayed below the diagram (not sure how easy this would be to do).
Moving the slider increases of reduces the number of circles. The slider is effectively a timeline control.

 

Idea 2: Circles
This is the most basic idea. The circles change size as the slider is moved. It's similar to idea 1, but it it doesn't show the seperate years and it won't be possible to display the papers list. It would also be the easiest to implement, although that shouldn't be the deciding factor IMO.

 

 

 

Idea 3: Bubbles
This is similar to Idea 1, but the circles aren't clustered. Each circle with a thick outline represents a year, the the coloured circles inside, represent the different biased papers of that year. So if there was only pro-AGW papers, the whole year circle would be green. Rolling the mouse over the circles will show totals for the year, or the totals for each bias. Note, I haven't drawn many circles/bubbles in the example, to save time. The slider will work in a similar fashion to the other two ideas. This one also has the potential to show the list of papers as in idea 1.

2011-03-23 23:06:20
nealjking

nealjking@gmail...
84.151.43.207

I'm not clear on what kind of information is supposed to be presented. What is the data model?

2011-03-23 23:25:08
Paul D

chillcast@googlemail...
82.18.130.183

Hi Neal, here is the link to the previous post on the subject:

http://www.skepticalscience.com/thread.php?t=1138&r=2

This is the database data rendered as a page:

http://www.skepticalscience.com/peerreview.php

Another point I should have made, is that the displays will be 'dynamic' in that they will display whatever is in the database. So as it changes so will the display.

2011-03-23 23:26:16Data model
John Cook

john@skepticalscience...
121.222.20.55

The raw data is here:

http://www.skepticalscience.com/peerreview.php

Basically, we want to show the weight of peer reviewed papers endorsing AGW.

2011-03-24 00:08:45
Daniel Bailey
Daniel Bailey
yooper49855@hotmail...
97.83.150.37

#3 is not visually clean enough for quick reader internalization.

#2 is very clean, but lacks the visual punch of #1

#1 Despite presenting more info than #2, but is still very impactful and understandable.  Better conveys the extent and beadth of the science underlying climate change and the paucity of the same behind the denialist positions.  If implentable, would be the one I would approve, if in charge.

2011-03-24 00:08:47
nealjking

nealjking@gmail...
84.151.43.207

So it seems like the data model for the display is:

 

Year  ----  Bias (AGW, ?, Skeptic)  --- Cumulative Number of Papers

 

where the CNoP is derived from the database

or:

Year  ----  Bias (AGW, ?, Skeptic)  ---  Number of Papers/Year

2011-03-24 00:12:50
Paul D

chillcast@googlemail...
82.18.130.183

Yes that is correct Neal.

The final project would have some text describing what the graphics represented.
Which one do you prefer?

2011-03-24 00:15:23
Paul D

chillcast@googlemail...
82.18.130.183

Actually anyone spot the mistake in the Idea 1 image??
(the dates I used)

2011-03-24 00:34:19Not I, says the frog
Daniel Bailey
Daniel Bailey
yooper49855@hotmail...
97.83.150.37

Slider says 1987 while popup box shows 1993?

Naw, coffee isn't doing its magic yet...

2011-03-24 00:34:46
nealjking

nealjking@gmail...
84.151.43.207

The slider is set to 1987, but the circle for 1993 shows up. Whoops!

I hate concept 3: Too complicated

Concept 2: Simple, but kind of basic; in fact, the visualization hardly adds anything.

Concept 1: How do the topics 1 - 3 at the bottom of the page tie into the visualization? Is the "3" in the box a topic # or a number of papers?

2011-03-24 00:41:14
Paul D

chillcast@googlemail...
82.18.130.183

Neal:

The papers listed at the bottom are linked to the circle rolled over.
haven't really thought about the interactionin detail, but probably if the circle is clicked on, the list for that year/bias would be displayed, then you could click on one of the links to go to view the paper/journal.

2011-03-24 00:49:59
Paul D

chillcast@googlemail...
82.18.130.183

Just fixed the mistake in idea 1 image.

2011-03-24 01:14:39
nealjking

nealjking@gmail...
84.151.43.207

If the list of papers pops out when you roll over a circle, what happens when you hit a big circle (lots of papers)? Does the list boot the image off the screen?

Is this just for display, or did you also intend this to be a gateway to the database?

2011-03-24 02:22:59
Paul D

chillcast@googlemail...
82.18.130.183

Neal:

It's a combination of display and gateway. The primary function is display/visualization. The list is an add on feature which I thought might be useful. The list could help deflect skeptism. eg. where's your data?
eg. without the list, some dick could ask for proof. However with the list, they can see for themselves what the source is.

Having said that, I don't have to implement the list if peeps don't like it. I'm not even sure how easy or hard the list would be to do. The first priority would in any case be the graphic display, the list would be added later.

I don't think the list would appear with just a rollover, otherwise it would be impossible to click on a link in the list. I think it would appear if you clicked on a circle. So each click on a different cirlcle would display a different list. The image wouldn't be booted off the screen, that would only happen if you scrolled down the list (although if the list was in a frame, that wouldn't happen either).

2011-03-25 02:58:02
Paul D

chillcast@googlemail...
82.18.130.183

If there are no more comments, I'll start having a stab at the code.
All votes seem to be for idea 1 (including John).

2011-03-25 03:28:23
Rob Honeycutt

robhon@mac...
98.207.62.223

This is going to be really nice, The Ville.  I think the real impact is going to come from the visual effects when moving the slider as you, essentially, watch the consensus on AGW grow.

2011-03-25 05:43:47
Rob Painting
Rob
paintingskeri@vodafone.co...
118.93.202.17

Another vote for concept 1. 

2011-03-25 06:51:10
BaerbelW

baerbel-for-350@email...
93.231.172.217

My vote is for concept 1 as well.

2011-03-25 08:39:14Idea 1 is very cool
John Cook

john@skepticalscience...
121.222.20.55
My main concern was that there is a strong visual message, that there is a sea of green compared to red. That's why I initially favoured Idea 2 but #1 achieves the same effect while cramming in a whole bunch of other very cool info. Cannot wait to see this take form, Ville.

And to all other SkSers, the larger our database of peer review papers, the more powerful the impact of the visuals. So please get into the habit of sending in any papers into the database as you encounter them, or even better, go looking for papers. The offer of a free signed copy of 'Climate Change Denial' still holds.

2011-03-25 12:48:52
Rob Painting
Rob
paintingskeri@vodafone.co...
118.92.90.117

Apart from the Firefox add-on is there another way of adding papers?. I use Google Chrome and don't want to go back to Firefox.

2011-03-25 13:07:00Adding papers without the Firefox Addon
John Cook

john@skepticalscience...
121.222.20.55

Yes, there is a web form at:

http://www.skepticalscience.com/resources.php?a=addlinkform

This is how I added articles before the Add-on. Unhappy days!

Hoping to see some names creeping up the list:

http://www.skepticalscience.com/stats.php?Action=peerreviewlinks

I notice Poptech has submitted some papers - I'm surprised he hasn't submitted 850! Although when we publish this animation and make our database of peer-reviewed papers public, I'm sure he will. We might need to pre-empt that before we launch the animation but that's a discussion for another time.

2011-03-25 15:40:36
Glenn Tamblyn

glenn@thefoodgallery.com...
124.180.74.163

Sorry to come in a bit late on this. Of the 3 options shown, 1 is definitely better. However have you considered any other general styles - why circles. Would a 3d graphic be possible. 3D bar chart, X/Y axes are Year and Bias. Or a 3D pie chart with height as count - the sight of Pro-AGW slice climbing away might work well.

Showing the time history clearly would be powerful. When did the first anti-AGW papers appear?

Just thinking outside the square a bit. The basic concept is good.

 

2011-03-26 02:31:20
Paul D

chillcast@googlemail...
82.18.130.183

I have found some software which does the circle clustering. It looks quite promising and potentially customisable (open source) with some work. So am going ahead with idea 1 (at some point you have to make an executive decision!).
This is likely to take some time, although depending on how things go, I might show some previews/beta versions.

Things could change though so don't get to excited.

2011-03-26 03:20:40
nealjking

nealjking@gmail...
91.33.106.251

John,

How will duplication of entries be prevented?

2011-03-26 07:00:21
citizenschallenge
Peter Miesler
citizenschallenge7@gmail...
96.14.48.163

your resident dummy reviewer definitely votes for #1, looks like it'll be fun to play with.

2011-03-26 07:06:19Duplication
John Cook

john@skepticalscience...
121.222.20.55
The worst possible answer - manual moderation :-(

however it is something all authors can check on, perhaps a thread for pointing out flaws in the db?

2011-03-26 07:24:50
nealjking

nealjking@gmail...
91.33.106.251

Maybe someone can develop some tools to look for likely duplication?

It would be embarrassing if some denialist checks our database and finds that we claim 846 pro-AGW papers but 23 of them are duplicates.

2011-03-26 11:00:22
Rob Painting
Rob
paintingskeri@vodafone.co...
118.92.75.3

Boy, sure is a pain in the arse adding papers. It's a convoluted process trying access the peer-reviewed papers on a topic, to prevent duplication. I do have Firefox still installed on my computer, but it doesn't see the Firefox add-on. I prefer to surf with Chrome anyway.

Watch out Ari Jokimaki, you're soon to be overtaken!. 

2011-03-26 12:20:46How many names?
James Wight

jameswight@southernphone.com...
112.213.158.190

How many author names do we list when submitting papers?

2011-03-26 13:11:45Well, you don't have to list any
John Cook

john@skepticalscience...
121.222.20.55

Originally, I entered papers with the title taking the form:

Paper Title (Author Year)

But I've stopped doing that of late, I just enter the paper title. So you don't need to enter any author.

Yes, it requires a bit of clearing up, a fair degree of weeding. The important thing is to register whether it's proAGW, neutral or skeptic. If in doubt, make it neutral. It's not important to pad out the proAGW, just to build a big database. But I'm fairly confident there are many proAGW papers not yet listed.

2011-03-26 13:14:19Tools looking for duplication
John Cook

john@skepticalscience...
121.222.20.55

This is a good point. I write 100% of the code on SkS. But I have no experience with open source - how does that work? Is there a way I can open it up so others can contribute code without compromising security and quality? If there's a way to remove the programming bottleneck and open up possibilities in this area, I think we could make big steps forward as creative people try different things at the programming level. So much community and creativity here, with a very powerful, growing and unique database and enthusiastic crowd sourcing potential - there's a potent combination!

2011-03-26 13:21:49
Daniel Bailey
Daniel Bailey
yooper49855@hotmail...
97.83.150.37

Check with Oslo/Preben

2011-03-26 14:44:50Problem with long URL
James Wight

jameswight@southernphone.com...
112.213.158.190

I’ve tried to add this paper but the URL is very long and the end of it keeps getting cut off so the link doesn’t work:

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WPN...

2011-03-26 14:56:42Abstracts
James Wight

jameswight@southernphone.com...
112.213.158.190

Also, the above is only an abstract; I can’t access the full version. Is it okay to just link to abstracts?

2011-03-26 15:55:26Abstracts
John Cook

john@skepticalscience...
121.222.20.55

Yes, fine to link to abstracts. In fact, I try to link to the 'official' link wherever possible which is usually the abstract. But linking to the full paper is fine also.

Re that long URL, I replaced it with http://linkinghub.elsevier.com/retrieve/pii/0033589472900695

2011-03-26 15:57:22I notice the # of peer reviewed papers is building, very cool!
John Cook

john@skepticalscience...
121.222.20.55

Rob Painting has already gone past Ari and James is steadily leapfrogging a bunch of others. Reminds me of Mr Burns in the stonecutters episode - "keep climing the ladder, Monty" :-)

2011-03-27 00:40:46Dates
James Wight

jameswight@southernphone.com...
112.213.158.190

There are many papers in the database that are incorrectly dated. But if the visualisation is going to have a timeline slider then the dates had better be correct.

I've already corrected a few of the more obvious ones, but someone will have to go through them systematically. And John, could you make it possible to add dates in the Firefox addon, to prevent papers submitted in future from being inaccurately dated?

There are also broken links which need fixing.

2011-03-27 08:21:07
Paul D

chillcast@googlemail...
82.18.130.183

Yep, the visualisation will only be as good as the data.

I have started writing some code now. Going down the object oriented route now I am getting used to it.

2011-03-27 17:22:43What do we do with papers that are difficult to assign to specific arguments?
James Wight

jameswight@southernphone.com...
112.213.158.190

For example this one:

Greenhouse effect of trace gases, 1970-1980

I can't think of an argument that it rebuts but it is clearly pro-AGW.

2011-03-27 19:29:57What about this argument?
John Cook

john@skepticalscience...
124.185.238.238
"co2 is just a trace gas"

I must point out that this effort to build a database of papers is not just useful for Ville's animation - this will have a score of flow on benefits, not the least being a rich resource of papers related to many skeptic arguments so whenever we research a topic, we will have a pile of peer review at our fingertips.

2011-03-27 20:25:16
Rob Painting
Rob
paintingskeri@vodafone.co...
118.93.250.188

John, are you able to program the system so that it recognizes "article title" duplication?. It spits it out if the same URL is used, but there are many ways of linking to the same study. Would speed things up considerably. 

If ya can, I'll put thousands in there myself. Take a few weeks though!.

2011-03-27 21:11:10Nice graphics
oslo

borchinfolab@gmail...
90.149.33.182

Found this site which have quite a few interesting graphs:

I'm also looking into this tool for producing live interaction graphs (may require a updated browser).

The new capabillities in modern browsers is very exciting, and may certainly be useful for communicating science.

2011-03-27 21:35:03Thousands of papers, Rob?
John Cook

john@skepticalscience...
124.185.238.238
That'd be fantastic, how will you do it? You'll be breaking James' heart though, I think he's trying to catch up to you.

I'll write some code to check for duplication this week. Very easy to check for titles that exactly match. Not sure about how to check for titles that closely match but not exactly. If any MySQL gurus can help with that, would be cool.

BTW, Shine Tech are now back to working on the firefox add-on so I'll ask if they can add a date field.

2011-03-27 21:56:40
Rob Painting
Rob
paintingskeri@vodafone.co...
118.93.250.188

I reckon there must be thousands, I put in over a hundred and forty odd on ocean acidification alone, one's I know of, and most OA research is pretty much less than a decade old. And those were just the pro AGW ones too.

We'll soon find out, and just like Dana's cyclon brethren, I have a plan! (secret of course, don't want James to catch up).  

2011-03-27 22:11:30Dates again
James Wight

jameswight@southernphone.com...
112.213.158.190

I think we should go back to John's original style of adding (Author Year) to the end of the paper titles. That way it is easy to check whether the paper is correctly dated or not. I've been doing the same for this reason.

2011-03-27 22:57:25
nealjking

nealjking@gmail...
84.151.56.15

John,

Yes, we have to expect typing errors from time to time.

2011-03-28 21:30:54
Paul D

chillcast@googlemail...
82.18.130.183

Just a bit of an update.

The code is coming along now and although I say it myself, is looking good (much better OO structure than before).
Even got some circles being drawn, using the xml files john has provided.

The next stage is to get some animation going. It would be nice to have that going this week, but along with other activities (DIY, chores, job hunting, organising green events, worrying about the roof etc) and the inevitible unplanned features (code for bugs), I'll do my best though.

I'm hoping this will give me a better chance of employment, which has been a problem for some months now. Certainly boosting my confidence.

Keep filling that database!

2011-03-30 06:48:51Harvesting peer-reviewed papers
John Cook

john@skepticalscience...
124.185.238.238

I'm just going to put this out there, Rob, and it's entirely up to you, but if it helps others add papers to the database and hence strengthen the message when we launch Ville's animation, I'd suggest sharing your "secret plan" on the best way to get harvest papers to put into the database. I've had a slightly unpleasant experience with another climate blogger recently who sees SkS as competition and I tried to explain to them that there is no such thing as competition among us - we're all brothers-in-arms in the battle for our future. If in battle, I wouldn't begrudge the soldier next to me being more successful - it would mean less enemy to shoot at me! But getting off my soapbox, it's no big deal, whatever you prefer :-)

On another note, James suggests adding the (Author Date) at the end of the title - to make it easier to check the database date. I dunno, James, I think that ship has sailed, we have over 1000 papers now and most without the (Author Date).

2011-03-30 18:30:35
Rob Painting
Rob
paintingskeri@vodafone.co...
118.93.204.120

John, some thoughts:

- You're perhaps assuming that, if you open it up, there'll a big uptake. I'm not so sure, my experience in life is if something involves a lot of work, volunteers are scarce. The children's story The Little Red Hen always springs to mind. I'll be happy to be proven wrong though.

- The library could end up a real shambles, kinda defeating the purpose. Just look at all those naughty people who haven't dated their studies.

- "Skeptics" might fill it with a whole lotta garbage. That Poptech douchebag for starters.

- Your "competitor", what a silly attitude to adopt.

If you can hold fire, I'll keep adding to the peer-review library, and try to maintain some sort of quality control at least. Your call.

2011-03-30 19:04:37
nealjking

nealjking@gmail...
84.151.31.5

Are you going to have some scheme to protect against random people adding crap to the database? Otherwise, one troll could spoil weeks of work by many people.

Perhaps some kind of change control; also, I would suggest a password scheme to iidentify users that add items.

2011-03-30 20:37:52I wasn't talking about opening it to the public
John Cook

john@skepticalscience...
124.185.238.238
Rob, I meant sharing here on the forum. Even just a few people beavering away would be huge. With you and James going great guns, I don't see any need to make this a public effort. If either (or both!) of you go past my # of papers, the database will be looking quite healthy.

For the record, the way moderation works for incoming links is this - as people submit comments, if their bias is clear (skeptic or proAGW), I classify their user account as skeptic or proAGW. Then whenever someone submits a link, if their user account is proAGW, the link is automatically approved. If the link is skeptic or unclassified, the link needs to be approved by a moderator before it's accepted.

2011-03-30 21:34:02So skeptics are subjected to quality control but warmists arenâ??t?
James Wight

jameswight@southernphone.com...
112.213.158.190

No wonder there are so many more warmist links in the database! Conclusive proof that not only has peer review been corrupted by we warmists, but now even blog review! This could be the beginning of SkSGate…

*sarcasm alert*

2011-03-30 21:57:49
Rob Painting
Rob
paintingskeri@vodafone.co...
118.93.204.120

Rob, I meant sharing here on the forum.

Errrrr, okay. My bad.

2011-03-31 07:50:50Moderation system
John Cook

john@skepticalscience...
124.185.238.238
I know, it's not a perfect system but with limited resources, it was the most optimal arrangement I could come up with. For the record, very few skeptics submit links. But if Poptech knew we were going to publish our list of papers, I bet he would've submitted all 800 on his list.