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Softwares to learn and use in PhD


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People have been telling me softwares that are especially useful/essential in grad school and that they wish they had known/used them earlier. They are:

Writing: LaTex

article/citation management: Mendeley

version control: git

Are there other suggestions as to what softwares people should be familiarized with before going into PhD programs? 

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Zotero is an alternative article and citation management software that works well with LaTex. BibDesk is also useful for Mac users. 

Stats wise, R is where most of the discipline is focusing its training since it's free and open source. That said, a lot of people still use Stata. Knowing both is helpful so that you can move from one to the other. I haven't done a replication yet that had code published in R. Stata handles massive datasets well (100,000+ observation panel datasets in particular). If you're into web-scraping data and text as data work, Python is another coding language that is worth putting time into picking up, though there are ways to get R to do the same work. 



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10 hours ago, deutsch1997bw said:

I've heard that understanding R might be helpful. 

Second this. Also helpful are Sweave/ Knitr if you already know R. These are for making reproducible PDF documents using LaTex.

Edited by dr.strange
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Some things you should learn:

LaTeX -- it's industry standard for typesetting
--- learn any additional subsets or add-ons to LaTeX that might be useful, such as BibTeX, etc. 

A statistical programming software. Ask someone in your department what is standard. Many departments use R due to its free and open-source character, but some will still use STATA or even SPSS. Once you know one stat programming language, it is fairly easy to pick up the syntax for another, but you're best off focusing on whichever one your department uses. 
--also learn add-ons to these programs. For R, you should probably learn RStudio, sweave, Knitr, and RMarkdown at the very least. 

A reference management software. In this case, conformity with your department is less important. Just pick one, learn it, and use it. Mendeley, Zotero, etc. 

Other useful apps. You might find Instapaper or Pocket to be helpful, particularly in terms of saving and later referencing non-academic articles. In my own research, I read a lot of magazine/popular articles that I am unlikely to reference, but I might want to find later for some reason. 


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R or STATA for stats (or, if you are really averse to learning programming languages, Minitab is a 'point and click' based statistical software)

Netlogo as intro to agent-based modeling 

Zotero for reference management 

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The citation manager software is definitely something I wish I learned more a bout and forced myself to use from the beginning of grad school. I was printing out journal articles and taking notes in classes with pen and paper and after a couple of semesters my "separate stacks of paper against the wall" method of organizing was proving not to be effective. I had played around with Zotero at one point after reading about it on a blog, but I really didn't give it much of a chance and just dismissed it, partly because I didn't want to learn a new software package. I saw a blog post about Mendeley about 2 years ago and decided I was going to force myself to learn the software, which entailed reading through the website and watching videos. Once I started to fully integrate it into my reading, note-taking, and writing, I was floored at how much easier organizing the work was. Additionally, being able to do a software-wide search of both my notes and journal text is incredibly helpful when trying to find that quote you remember reading. Also, if you use your laptop in class and have the articles loaded in Mendeley, you can use the search function to find passages much quicker than other students who are flipping pages of printed articles.

The common feedback I hear from others when I mention Mendeley (which is just my preferred citation manager) is that it would take too long to upload and convert everything they already have either in paper form or spread in different folders. This is why using a software package like this from the beginning is especially important. I didn't like taking notes on a digital copy of an article, which is part of why I stuck with the old pen and paper; this was a mistake. After forcing myself to use the software for a couple of weeks I got over my pen and paper bias. I also started using pdf copies of ebooks instead of physical books as they can be read and annotated in Mendeley with the same benefits of the search function.

In short, I strongly recommend picking a citation manager from the beginning and taking the time to learn its features. 

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