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thesis_lore [2011/04/06 00:14]
linda [LaTeXing Your Dissertation]
thesis_lore [2017/08/04 22:31] (current)
dyas [Filing in the Summer]
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 ======Thesis Lore====== ======Thesis Lore======
  
-The [[http://​grad.berkeley.edu/​policies/pdf/dissertation_guide.pdf|Dissertation Guide]] lists the various rules for building and submitting a dissertation,​ so start there. ​ The [[filing timeline]] is also very handy.+The [[http://​grad.berkeley.edu/​academic-progress/dissertation/​|Dissertation Guide]] lists the various rules for building and submitting a dissertation,​ so start there. ​ The [[filing timeline]] is also very handy.
  
 ======Advancing to Candidacy====== ======Advancing to Candidacy======
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 =====What the heck is "​Filing Fee"?​===== =====What the heck is "​Filing Fee"?​=====
  
-"​Filing Fee Status"​ is a special kind of university registration which lets you file your dissertation sometime during a semester ​but leaves you effectively unregistered in all other ways. Notably, you lose many regular student privileges such as Class Pass, use of the gym, and health insurance (but note that your spring SHIP insurance and Class Pass are good through most of the summer, until August ​14 in 2010, even if you are approved for filing fee status before that date, so this is not such a big deal if you file before September).  Then why would someone ever want to do filing fee? It's cheap ($185 as of 2007), far cheaper than registering regularly. ​+"​Filing Fee Status"​ is a special kind of university registration which lets you file your dissertation sometime during a semesterbut leaves you effectively unregistered in all other ways. Notably, you lose many regular student privileges such as Class Pass, use of the gym, and health insurance (but note that your spring SHIP insurance and Class Pass are good through most of the summer, until ~August ​15, even if you are approved for filing fee status before that date). ​ Then why would someone ever want to do filing fee? It's cheap ($243 as of 2012), far cheaper than registering regularly. ​
  
-One case in which Filing Fee might be a good idea is if you already have a sweet postdoc lined up somewhere, but do not quite manage to get your dissertation done in time, so that you need to file in the first week of September, or early January or something like that.  Rather than registering for an entire semester just so you can file your dissertation and then leave, you can pay filing fee, file your dissertation,​ immediately head off to postdoc-land. ​+One case in which Filing Fee might be a good idea is if you already have a sweet postdoc lined up somewhere, but do not quite manage to get your dissertation done in time, so that you need to file in the first week of September, or early January or something like that.  Rather than registering for an entire semester just so you can file your dissertation and then leave, you can pay filing fee, file your dissertation,​ immediately head off to magical ​postdoc-land. ​
  
-When on filing fee status you can't be paid as a GSRyou need to get a special appointment like "​junior specialist".  Once you actually file you will then have to change your appointment (a hassle) to get paid as a postdoc, if you are sticking around for a while. ​ You also have to start paying off any undergrad student loans you've deferred. ​+When on filing fee status you can't be paid as a GSRyou need to get a special appointment like "​junior specialist." ​ Once you actually file you will then have to change your appointment (a hassle) to get paid as a postdoc, if you are sticking around for a while. ​ You also have to start paying off any undergrad student loans you've deferred. ​
  
  
 =====Filing in the Summer===== =====Filing in the Summer=====
  
-As of summer 2007, university regulations have apparently been changed to require ​students to actually ​register for 3 units in the summer if they want to file their degrees in the summer.  ​The web seems to indicate that you can't use Filing Fee to file in the summer, ​but that's actually actually not true ​when ​you go on filing fee it's technically ​for the fall, but it retroactively ​applies to the previous summer+Since summer 2007, university regulations have required ​students to register for 3 units in the summer if they want to file their degrees in the summer.  ​In summer 2012, the cost of 3 units was $1666. 
 + 
 +There has been past confusion about whether the fall filing fee will cover the preceding summer. ​ In other words, even if you intend ​to file during the summer, can you go on filing fee for the fall in order to circumvent ​the summer ​course requirement and save your advisor some cash?  Yesthis IS possible, based on discussions with Dexter in Spring, 2014.  If you receive e-mail or word-of-mouth saying otherwise, your safest option is to walk over to the Graduate Degrees office (318 Sproul) and ask them directly. 
 + 
 +Assuming ​that fall filing fee is a permitted option for filing a summer thesis, here are the tradeoffs: 
 + 
 +Registering for summer units:\\ 
 +- more expensive for your advisor\\ 
 +- keep GSR status\\ 
 +- keep SHIP insurance (see below), Class Pass, student gym rate, etc.\\ 
 +- if you file early in the summer, can get a certificate of completion without waiting for the filing fee to be billed\\ 
 +- file by August deadline to avoid extra registration (or filing fee) expenses ​for the fall\\ 
 +- if you miss the August deadlineyou're still a student 
 + 
 +Fall filing fee:\\ 
 +- save your advisor ~$1400 (as of 2012)\\ 
 +- no GSR status, so your advisor will have to set up a Junior Specialist appointment for you (through RES or one of the Astro HR staff)\\ 
 +- no student privileges over the summer\\ 
 +- SHIP insurance expires in mid August\\ 
 +- regardless of when it is approved, the filing fee will not be billed to you until late July\\ 
 +- you cannot receive a certificate of completion until the filing fee is billed and paid (if you're starting a post-doc, they will likely require this)\\ 
 +- once on filing fee, the August filing deadline no longer ​applies\\ 
 +- file by December deadline or you must re-apply for admission ​to the university 
 + 
 +**For international students:** if you want to use OPT, then you need a new I-20 F1-OPT and employment authorization (EAD) card to work in the US. The starting date of the EAD card depends on your program end date. The rules may be tricky and change over time. Please consult to the Berkeley International Office before making decision of finishing in the Summer or Fall semester. 
  
 ===== Health Insurance Post-Filing ==== ===== Health Insurance Post-Filing ====
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 Health insurance may be the last thing you want to worry about when trying to finish your dissertation. Luckily, you probably do not have to: Spring semester health insurance extends through August 14, regardless of when you file, so you are covered after you graduate. Fall term insurance extends through January 14. See [[http://​uhs.berkeley.edu/​students/​insurance/​aftergraduation.shtml| this page at UHS]]. Health insurance may be the last thing you want to worry about when trying to finish your dissertation. Luckily, you probably do not have to: Spring semester health insurance extends through August 14, regardless of when you file, so you are covered after you graduate. Fall term insurance extends through January 14. See [[http://​uhs.berkeley.edu/​students/​insurance/​aftergraduation.shtml| this page at UHS]].
  
-If you want to buy SHIP insurance while on filing fee after SHIP expires, you can, but it's $1500 (as of 2006). +If you want to buy SHIP insurance while on filing fee after SHIP expires, you can purchase it for one extra semester; ​it'​s ​just under $2,500 (as of 2014). 
  
 ======LaTeXing Your Dissertation====== ======LaTeXing Your Dissertation======
  
-You will need the following ​files in your latex directory (on a Macit's often ~/Library/texmf/tex/latex/misc/ -- if that directory doesn'​t exist, you can make it) or main thesis directory:​ +To get a bomb of all the files you need to start LaTeXing ​your dissertation, 
-  * {{thesis_lore:​ucthesis.cls.txt|ucthesis.cls}} +use [[https://github.com/pkgw/ucastrothesis|the ucastrothesis Git repository]] created 
-  * {{thesis_lore:​tweak_ucthesis.sty.new.txt|tweak_ucthesis.sty}} +by Peter WilliamsYou don't need to know how to use Git to use this[[https://github.com/​pkgw/​ucastrothesis/​zipball/​master|this link]] will give you a Zip of the most recent version, for instance(Although Peter suggests that you both learn [[http://git-scm.com/|Git]] and use it to version-control your thesis!) You can then follow ​the directions in that repository 
-  * {{thesis_lore:bibsetup.sty.txt|bibsetup.sty}} +and start reading the main files to figure out how the pieces fit together.
-  * {{thesis_lore:aasmacros.tex.txt|aasmacros.tex}} +
-  * [[http://nuclear.ucdavis.edu/​~rpicha/​sample/|the uct1x.clo ​and uct1x.sty]] ​files, where x={0,1,2}.+
  
-Chop off the "​.txt"​ (and "​.new"​) at the ends of these filenames. ​ Then, use this {{thesis_lore:​thesis.tex.txt|thesis.tex}} file as a template ​for the overall thesis document, which uses the UC Thesis environment and imports individual chapter tex documents from appropriate subfolders. ​ Modify this {{thesis_lore:​frontmatter.tex.txt|frontmatter.tex}} file to make your appropriate preliminary pages. ​ Use this {{thesis_lore:​topic.tex.txt|topic.tex}} file as a template for individual chapter files (and put it in a folder called "​topic"​). ​ Also, use this {{thesis_lore:​approvalpage.tex.txt|approvalpage.tex}} file as a template for your dissertation approval page, which your committee signs. ​ These files should have enough stuff to make typesetting your thesis possible without having to learn too much of the guts of LaTeX+Old instructions ​for getting ​the LaTeX files are farther below.
- +
-If you have two co-chairs, then some of the files need to be altered to note this.  In this case, use these modified versions of {{thesis_lore:​ucthesis.cls.cochairs.txt|ucthesis.cls}},​ {{thesis_lore:​tweak_ucthesis.sty.cochairs.txt|tweak_ucthesis.sty}},​ and {{thesis_lore:​frontmatter.tex.cochairs.txt|frontmatter.tex}}. Just cut the "​.cochairs.txt"​ off the filenames.+
  
 ====Margins==== ====Margins====
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 They will reject your dissertation if it does not have the right margins. ​ The limits are 1 inch all around, and the page number must be no closer than 3/4 inch from the edge (and consistently placed and on every single page, even chapter pages). ​ These are minimums, so you cannot go wrong if you give yourself some buffer room. They will reject your dissertation if it does not have the right margins. ​ The limits are 1 inch all around, and the page number must be no closer than 3/4 inch from the edge (and consistently placed and on every single page, even chapter pages). ​ These are minimums, so you cannot go wrong if you give yourself some buffer room.
  
-The margins set up in the above files should be correct (they have been accepted ​for at least two dissertations as of May 2010) If for some reason you want/need to tweak your marginsthere is a command in ucthesis.clsfor instancewhich reads "\topmargin xxxxin" ​where xxxx is some number of inches for the top column ​-- change that until you have at least 1 inch If you are using a Mac with Preview, you can measure the PDF margins by using the "​select"​ tool in conjunction with "show inspector"​.+Don't use the "​twoside"​ option ​in the ucthesis style for your submitted versionThe Dissertation Guidelines state that page numbers should be in a "​consistent"​ location in your dissertation,​ but since the move to electronically submitted thesesthis location ​is what you see scanning through the PDF, **not** what you'd get printing out the thesis with duplexing printerThe "​twoside"​ option makes things look nicer if you're going to be printing the PDF out yourself on a capable printerthough. 
 + 
 +If you run into problems with your marginstweak the options given to the "geometry" ​package. The "​showframe"​ option prints out the margins it's using making it relatively easy to spot overflows ​-- though this option only works on all pages for geometry version >= 5.0. If you are using a Mac with Preview, you can measure the PDF margins by using the "​select"​ tool in conjunction with "show inspector"​.
  
 The most common problems with margins come from formulae, tables, and figures. ​ Tables and Figures are discussed below. ​ Check all of your formulae (especially in-line formulae!) and make sure they conform! ​ You may need to re-format some of them, or shrink the font. The most common problems with margins come from formulae, tables, and figures. ​ Tables and Figures are discussed below. ​ Check all of your formulae (especially in-line formulae!) and make sure they conform! ​ You may need to re-format some of them, or shrink the font.
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 ====Tables==== ====Tables====
  
-If you use deluxetable ​because you have a huge table than runs over many pagesit won't play nice with the ucthesis class file.  The biggest problem is that it creates a new table on each page, so the list of tables ​after the table of contents will list the table multiple times It also has a habit of putting ​the last page of the table a page late, leaving text interrupting the table. ​ To fix this, use [[http://​www.astro.psu.edu/​gradinfo/​psuthesis/​longtable.html|longtable]], a package ​included with latex. ​ The linked website has all of the details.+The deluxetable ​package sometimes works in theses but breaks down other timesespecially for very long tables. ​Try using the [[http://​www.astro.psu.edu/​gradinfo/​psuthesis/​longtable.html|longtable]] package ​instead.
  
 If your tables run wide (which happens a lot with these fat margins) there are a few tricks you can try to get them to fit.  The first is to make your columns closer together with this command: If your tables run wide (which happens a lot with these fat margins) there are a few tricks you can try to get them to fit.  The first is to make your columns closer together with this command:
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   \setlength{\tabcolsep}{0.05in}   \setlength{\tabcolsep}{0.05in}
  
-Adjust to taste. ​ If that's not enough, you can use the lscape ​package and invoke the landscape environment to make your tables landscaped (don't use the \rotate command;  it's flaky).  ​Here's how a table might begin:+Adjust to taste.  ​If you're really desperate, you can make the columns separation negative 
 + 
 +   % change 
 +   ​\begin{deluxetable}{l*{14}{r}ccc} 
 +   % to 
 +   ​\begin{deluxetable}{@{\extracolsep{-6pt}}l*{14}{r}ccc} 
 +    
 +If that's not enough, you can use the pdflscape ​package and invoke the landscape environment to make your tables landscaped(Don't use \rotate command.) Here's how a table might begin:
  
   \begin{landscape}   \begin{landscape}
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   \begin{longtable}{l@{ }rccccccccccr}   \begin{longtable}{l@{ }rccccccccccr}
  
-It's all on the longtable website. ​ A nice PDF with a description of the longtable package is at [[http://​www.cs.brown.edu/​system/​software/​latex/​doc/​longtable.pdf|this link]].+It's all on the longtable website. ​ A nice PDF with a description of the longtable package is [[http://​www.cs.brown.edu/​system/​software/​latex/​doc/​longtable.pdf|here]]
 + 
 +The downside to using the landscape environment is that you have to put it outside of the floating table environment. ​ This results in LaTeX putting the table in that exact place relative to the text, meaning you could end up with half the page before the table being empty. ​ Another alternative,​ at least for tables that are wide, but short, is to use the "​sidewaystable"​ environment in the "​rotating"​ package. Whether or not this would suffer the same problems as deluxetable when also dealing with very long tables is unknown.
  
-The downside to using the landscape environment is that you have to put it outside of the floating table environment. ​ This results in LaTeX putting the table in that exact place relative to the text, meaning you could end up with half the page before the table being empty. ​ Another alternative,​ at least for tables that are wide, but short, is to use the sidewaystable environment in the "​rotating"​ package. ​ Whether or not this would suffer the same problems as deluxetable when also dealing with very long tables is unknown. 
  
 ====Figures==== ====Figures====
  
-For figures, make sure your figures are not too big.  If you have played with axes and such you might find the figures are pushing your captions out beyond the margins. ​ If this happens, open up the actual eps file in a text editor and play with the line that reads "​BoundingBox:"​ and play with the numbers there. ​ These numbers tell LaTeX where the edges of the figure are, so by tweaking them you can trick LaTeX into making the figure take up less room.+For figures, make sure your figures are not too big.  If you have played with axes and such you might find the figures are pushing your captions out beyond the margins. ​ If this happens, ​the "​pdfcrop"​ tool is great for removing extraneous whitespace. (If you're generating figures from EPS files, you can open up the file in a text editor and play with the line that reads "​BoundingBox:"​ and play with the numbers there.)
  
 The default LaTeX effect on figures will be to put large-ish figures on their own page (even when text could easily fit around them on the page) and smaller figures on the top of pages, with text underneath. ​ Feel free to have all figures take up their own page by making them fill the page: The default LaTeX effect on figures will be to put large-ish figures on their own page (even when text could easily fit around them on the page) and smaller figures on the top of pages, with text underneath. ​ Feel free to have all figures take up their own page by making them fill the page:
  
-   ​\includegraphics[width=13cm]{figure.eps}+   ​\includegraphics[width=13cm]{intro/​figure1}
  
 though this is by no means a requirement. ​ You can also force your figures to be on a "page of floats"​ (= no text) in the figure command: ​ though this is by no means a requirement. ​ You can also force your figures to be on a "page of floats"​ (= no text) in the figure command: ​
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 though again, there is no formal rule requiring a figure to be on its own page. though again, there is no formal rule requiring a figure to be on its own page.
  
-If you have wide figures that you want to have rotated sideways, you could use the landscape environment,​ but it may not be ideal. The problem is that you have to put it outside of the floating figure environment. ​ This results in LaTeX putting the figure in that exact place relative to the text, meaning you could end up with half the page before the figure being empty. ​ Another alternative is to use the sidewaysfigure environment in the "​rotating"​ package.+If you have wide figures that you want to have rotated sideways, you could use the landscape environment,​ but it may not be ideal. The problem is that you have to put it outside of the floating figure environment. This results in LaTeX putting the figure in that exact place relative to the text, meaning you could end up with half the page before the figure being empty. ​ Another alternative is to use the sidewaysfigure environment in the "​rotating"​ package.
  
 ====Captions==== ====Captions====
 +
 The captions of your tables and figures will appear in the lists of figures and tables after the table of contents. ​ If you'd like shorter table and figure (or even chapter!) names, use the optional argument in the caption (or chapter!) command: The captions of your tables and figures will appear in the lists of figures and tables after the table of contents. ​ If you'd like shorter table and figure (or even chapter!) names, use the optional argument in the caption (or chapter!) command:
  
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 ====== Filing Your Dissertation ====== ====== Filing Your Dissertation ======
  
-**Dissertations must now be filed electronically**,​ thus "​saving of approximately half a million pages of paper per year, make Berkeley doctoral dissertations more widely accessible, and spare doctoral candidates the cost of purchasing archival-quality paper."​+**Dissertations must now be filed electronically**,​ thus "​saving of approximately half a million pages of paper per year, making ​Berkeley doctoral dissertations more widely accessible, and sparing ​doctoral candidates the cost of purchasing archival-quality paper."​
  
 The filing must be done online four business days before the end of the semester. ​ Once you receive a confirmation email from the Degrees Office, you will need to bring them hard copies of the required documentation:​ two surveys, a release form, and the approval page signed by your committee. ​ None of these documents needs to be on archival paper. The filing must be done online four business days before the end of the semester. ​ Once you receive a confirmation email from the Degrees Office, you will need to bring them hard copies of the required documentation:​ two surveys, a release form, and the approval page signed by your committee. ​ None of these documents needs to be on archival paper.
  
 If your dissertation contains previously published material, you will need to obtain a signed letter from your committee chair (adviser) stating that this constitutes dissertation-level work.  You will also need a letter from every co-author stating that it is okay for you to reproduce this material in your dissertation. ​ Alternatively,​ a printed email from each co-author stating the same thing can be included with the application,​ sent to Graduate Services along with copies of the published material. ​ If you have a very large number of co-authors, a letter from your adviser to the dean stating that this requirement is a hardship for you since all of the many co-authors can not be reached and that your adviser speaks for all of them in approving the use of this material may be sufficient. ​ This has worked in at least one case (Dexter has a copy of the letter that worked in her records), but it has also been known to fail, so if you want to try this, start several months in advance. If your dissertation contains previously published material, you will need to obtain a signed letter from your committee chair (adviser) stating that this constitutes dissertation-level work.  You will also need a letter from every co-author stating that it is okay for you to reproduce this material in your dissertation. ​ Alternatively,​ a printed email from each co-author stating the same thing can be included with the application,​ sent to Graduate Services along with copies of the published material. ​ If you have a very large number of co-authors, a letter from your adviser to the dean stating that this requirement is a hardship for you since all of the many co-authors can not be reached and that your adviser speaks for all of them in approving the use of this material may be sufficient. ​ This has worked in at least one case (Dexter has a copy of the letter that worked in her records), but it has also been known to fail, so if you want to try this, start several months in advance.
 +
 +====== Old LaTeX File Links ======
 +
 +(Peter Williams suggests you check out the ucastrothesis files mentioned above rather than these, but here's the info for posterity.) You will need the following files in your latex directory (on a Mac, it's often ~/​Library/​texmf/​tex/​latex/​misc/​ -- if that directory doesn'​t exist, you can make it) or main thesis directory:
 +  * {{thesis_lore:​ucthesis.cls.txt|ucthesis.cls}}
 +  * {{thesis_lore:​tweak_ucthesis.sty.new.txt|tweak_ucthesis.sty}}
 +  * {{thesis_lore:​bibsetup.sty.txt|bibsetup.sty}}
 +  * {{thesis_lore:​aasmacros.tex.txt|aasmacros.tex}}
 +  * [[http://​nuclear.ucdavis.edu/​~rpicha/​sample/​|the uct1x.clo and uct1x.sty]] files, where x={0,1,2} -- if this has moved, google the file names.
 +
 +Chop off the "​.txt"​ (and "​.new"​) at the ends of these filenames. ​ Then, use this {{thesis_lore:​thesis.tex.txt|thesis.tex}} file as a template for the overall thesis document, which uses the UC Thesis environment and imports individual chapter tex documents from appropriate subfolders. ​ Modify this {{thesis_lore:​frontmatter.tex.txt|frontmatter.tex}} file to make your appropriate preliminary pages. ​ Use this {{thesis_lore:​topic.tex.txt|topic.tex}} file as a template for individual chapter files (and put it in a folder called "​topic"​). ​ Also, use this {{thesis_lore:​approvalpage.tex.txt|approvalpage.tex}} file as a template for your dissertation approval page, which your committee signs. ​ These files should have enough stuff to make typesetting your thesis possible without having to learn too much of the guts of LaTeX.
 +
 +If you have two co-chairs, then some of the files need to be altered to note this.  In this case, use these modified versions of {{thesis_lore:​ucthesis.cls.cochairs.txt|ucthesis.cls}},​ {{thesis_lore:​tweak_ucthesis.sty.cochairs.txt|tweak_ucthesis.sty}},​ and {{thesis_lore:​frontmatter.tex.cochairs.txt|frontmatter.tex}}. Just cut the "​.cochairs.txt"​ off the filenames.
 +
 +tweak_ucthesis.sty is the one that sets the margins. ​ Warning: the newest version of TeXShop for Macs is currently off on the left hand margin by 1mm.  You'll need to change the textwidth, etc... in this file if you find you are having this problem.
 +
 +The margins set up in the above files should be correct (they have been accepted for at least two dissertations as of May 2010). ​ If for some reason you want/need to tweak your margins, there is a command in ucthesis.cls,​ for instance, which reads "​\topmargin xxxxin"​ where xxxx is some number of inches for the top column -- change that until you have at least 1 inch.  If you are using a Mac with Preview, you can measure the PDF margins by using the "​select"​ tool in conjunction with "show inspector"​.
 +