So what is knitr? So knitr is this tool that I'm going to talk about that can help you make these reproducible documents. Knitr is an R package. It's written by Yihui Xie who, while he was a grad student at Iowa State. It's available on CRAN. If you happen to use the package R Studio it's actually built into R Studio, and so it's, it's integrated into the graphical user interface. And so, you don't even have to obtain it separately if you're using R-Studio. So, it supports for the documentation language. It supports, something called RMarkdown. It also supports, LaTeX and HTML. So these are three languages, that are commonly used. And then, it can export to PDF and HTML and and you can also export to other formats if using, using other external tools like Pandoc. It's built right into RStudio for your convenience, as I just mentioned. So, what do you need to use knitr? You need a recent version of R. You need a text editor. You can use the one that comes with RStudio if you happen to be using that, otherwise any old text editor will do. You need some support packages that are available from CRAN. These will be automatically downloaded if you use the install dot packages function. You need some knowledge of one of the three documentation languages. So, you need, need to know Markdown, LaTeX or HTML. And I will talk about Markdown here since it's a fairly simple language to understand. So, what is Markdown? Well, it's a simplified version of common markup languages. So LaTeX and HTML could be thought of as markup languages, where you take regular text and you kind of add things to it, add tags and other types of annotation to kind of tell, to indicate what you want to do with the text. One problem with markup languages is that they can be kind of like with they can be very difficult to read cause all this kind of tags and things that, that, that can, can, that can obscure the actual text. So the purpose of Markdown is just kind of simplify all that, make it easy to read just the text and only have a few kind of formatting elements that you need to enter into the document. There's no special editor required, just a standard text editor, Notepad, you know, whatever you want to use. There are simple, intuitive formatting elements and you can get all of the documentation at this website here. So, what is knitr good for in terms of creating reproducible documents? Well, personally, I think it's good for things like manuals. If you want to instruct someone on how to use a piece of software. Short or medium length technical documents so you're explaining some technical concept. tutorials, if you want to, again, this is like a manual, but maybe more extended, a tutorial on some topic. reports, they're especially useful for reports. If you have to, for example, every week generate a report on some database or some dataset. If you're running a study and you have subjects that are constantly being enrolled in the study and then maybe every week you generate a report on, it, it has summary statistics about about the study that these kinds of live documents are very useful because you can recalculate all the summary statistics as you generate the document. You don't have to do it by hand and then stick it into a report separately. And then also for data preprocessing. So, often it's useful if you're going to preprocess a dataset to create a clean dataset, to create a knitr type document where, that documents all of the things that you do to the dataset to make it clean. Maybe you remove some outliers, maybe you fill in some missing data, maybe you transform a variable here and there. All of that can be documented, in this kind of knitr's file, you know, where you simultaneously say what you did and then you actually do it in the code. What is knitr not good for? Well in, by, in my opinion, it's not very good for very long research articles, so if you're writing, writing a very complex, very involved analysis it, like I said before, because everything is stored in a single document, it can get a little bit confusing to kind of edit this document if there's a lot of code and a lot of text. If you have, if have very complex or time-consuming computations then knitr is often not a good format because you have to recompile this document every time you want to look at it. And so if your computations are very slow this will just kind of make everything slow. And furthermore if you have a document, if you want to create a document that requires very precise formatting. So if you have a special layout and the pictures have to go here and the text has to go here or something like that. Knitr is, again, not a super great tool for that because the formatting tends to be very ad hoc.
