Introduction to org-ref

or Graff is out on Melba now so I want to show people a little bit of how to use it we're going to open a vanilla Emacs that uses this configuration file I'll describe it later and we're going to use this now to create a new manuscript file and from that export to a PDF so let's create manuscript org it's an empty file and we're going to write a little short paper first let's define a bibliography this is a link and or graph is already telling me that it doesn't exist because we haven't made it yet but we can click on our link and it opens the bib file and now we want to add some entries the first thing I'll show you is that we can drag a PDF onto it and our graph will find the DOI and download the PDF and allow you to read it and enter automatically the tech entry if you have a free freeform citation let's look at at reference ten here we would like to add this one as well would copy that and we run a command crossref at Tech entry paste in our citation select our bibliography and this will reach out to cross ref and show me some menu of options that we can choose the first one is the one that I want so there it is it downloads a PDF as well you can see this should be type typed as a chemical formula so let's go ahead and fix it this will mean we have to add a package later for export to PDF okay so you can add all kinds of references like that we can also look at website so here is a website with a URL I can grab the URL and drag it on to my bib tech file and it also will add a PDF and download it for me like that and the final way I want to show you is that we can if we have a DOI let's say reference 7 here we have a DOI right here that we might want to copy and we could come over here and say do I add and paste in the do I press enter and enter and this will also automatically download a bib tech country ok it didn't get a PDF because ApS makes it difficult for people to automatically download them ok so there is our bibliography file that has 4 references in it that we can start to use in our paper ok so let's add an introduction and we can cite a paper will use the or breath menu first and cite the first one that's there and there it is a or graph off automatically tells you down here what you put in so you can see it we can select more than one and we can also do alternate sites so if you know you want this author or the year or something like that we can do this and we can say just do the reference number okay that's pretty helpful and looks pretty easy but we can mouse over any of these to remind ourselves what we cited and that's pretty helpful as you start getting very very large numbers of references okay let's look at a couple of other features let's say we're doing some work and we have an equation and let's put in put in that equation right here and that equation is y equals Cinch of X you can see a label here we might want to see in the text we might want to refer to an equation so let's look again at our menu we have insert reference and we'll get a menu of options now it's conventional to use an equation reference not a regular reference so we can get to a menu where we select that and there we have what we're interested in okay if you put your cursor again on this you get a message at the bottom that says what it refers to okay moving on to results one of the features of org-mode is that you can integrate source code into your documents okay so here is a little python script that will plot the Cinch of x and save it as a figure we'd configure it here to export nothing and let's also make the results silent and run this and what we'll get is there's nothing because we just ran it and we didn't have it output anything but we can see that something happened because there is now a cinch PNG and you can click on this to see what it looks like you can also display it in the buffer but it's a little bit inconvenient to to look at here let's add a caption and we want to label this so we can refer to it also or graph makes it easy to generate unique labels so you can see here that we're on the create new label and that means that this one is unique and we can then refer to the figure and we can choose with what label to reference we'll use the default one and there it is okay you can do this from tables sections all kinds of other other references alright we want to now consider what happens if we use a more comprehensive bibliography right in or graph we can just add a comma separated list and this file has a lot of different references in it so let's get to conclusions and now let's do a search there are about a thousand different bibtex entries in here let's simplify this down to papers by me that are tagged or work mode okay and we'll select them all and insert them that's the end of conclusions again we can click on any one of these and maybe you want to see what this one is let's say open it in a browser there it is let's say we want to find how about related articles in web of science of course you have to have a subscription to web of science to do that but here we have a whole bunch of these and if you clicked on any one of these we could just copy this DOI and add it very easily to our bibliography okay that's about ready to wrap it up let's add a bibliography style so we can generate PDF we'll just use a simple on sort unsorted file and let's go to the top and add a title and some options and tell it to use the extra packages that we want let's see let's add an attribute here so that this figure gets put exactly here and for that we'll need the float package and here we'll just give it a title turn off the table of contents we'll use this image can package for the citations that contain chemical formulas and we'll use the float package for for this they all we have to do now is run the export command will select l4 la Tech and O for the PDF file and open what's happening now is org-mode is exporting this simple text file to la Tech and then compiling it through PDF low tech okay here's our results title my name here's our introduction our citations this is the site now here's the equation reference here's our figure where we want it and the reference here's all of the papers that have used org-mode and here is the formatted bibliography the way we asked for ok that's basically it it shows I hope house how straightforward it is to go from a nearly empty document to a PDF that is almost formatted in a way that could be used for a report including some source code some cross references and all of the useful things like tool tips that or graph makes possible that's it I hope you find or graph to be as useful as we do and I hope everybody has a happy new year and a great year Nestor

Channel: John Kitchin

Views: 40,208

Rating: 4.9665737 out of 5

Keywords: emacs, orgmode, org-ref

Id: 2t925KRBbFc

Length: 9min 59sec (599 seconds)

Published: Tue Dec 22 2015