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Let’s Begin with RStudio

RStudion packages installation
7.1
In this new step let’s see how to start working now with RStudio and how the RStudio interface is easing a lt of the process of working in R-based environment again. As an example, when we see together in the first part of the video, how to open a new project, and then in the second part, how to instal and use packages. So opening a new project before you start work will allow you to do many things. First, it will allow you to keep track of a certain analysis you did, so it will allow you, for example, to retrieve very easily, substeps that you’ve been through and that worked for you.
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And it will also allow you to keep a certain organisation in your files so you can easily work on different projects and each project will have its own script or set of scripts. So how to do that? There are many ways to open a new project. For example, in the top right of your screen, you have a blue icon here that is indicating which project you’re working on. We have no projects right now, so it is indicated as none, so let’s create a new one. If you pull down the project’s options, you will be given the option to create a new one from here, so let’s click on a new project. .
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You will be asked where you want to create it. Let’s select, for example, a new directory, and we want to create it, let’s select New Project. And let’s name it, for example, I will name it Project Test, and where we want to put it is the exercise R folder. So let’s continue using that one. And it is the same that we were using for the R sessions. Then click on Create Project.
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So you will now see a new path appearing here, which says that we are working under this project that we just created. So by default, it will open the console again in its bigger format. You can just simply click on it to reduce it and you can also resize it. That’s absolutely no problem to do that. You can then create, also, new folders and files under this newly created project to contain scripts or data, for example, that will belong to this specific project. This is kind of a good practise that we generally use, because you will have dedicated scripts and dedicated data for each project, and that you can easily retrieve them.
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So you can also load an existing script, as it is the case here with the previous script I created with some very basic commands that we saw in our previous R steps. The script is called “Test R commands,” so I put it in the same exercise R. It is called “Test R commands.” So imagine that this is an existing script where you put interesting commands that you want to retrieve. If I just simply click on it, it will open the different commands I put in the script in here directly, in your source quadrant. A good practise is to leave notes for yourself in your scripts.
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So basically, everything that is written following the hashtag here will be a comment that you leave for yourself or, of course, for someone else that will be using your script. So this allows you to very easily use a script that you generated some time ago, because you will retrieve indications or explanations for each step easily. For example, you can see here that I indicated how to set my working directory for where I want to be here, and how to check that I am in the right place after that using that getwd command. I guess you remember these commands from the previous R steps. So these comments allow me to remember what the command is doing.
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And you can also have comments written at the end of the line. It’s perfectly fine. This will not be read as part of the script as long as it is written after a hashtag. So if you want to run a command from a script, you can then place yourself either at the end of the command or you can just select that command and then click on Run. You just hit that Run button at the top-right of the source quadrant. And you can see that you will be redirected to where you want to be. OK? And you can see that the path changed in here.
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So if I want to go again in Project Test, I can just basically type the same command, and slash, and I will select for Project Test. So if I do it, I can do it from here.
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I will select the Project Test, and then I can again run that command from here, and it will redirect me to that project list. So before we move forward, one very general comment I would like to make about using RStudio is to tell you to please remember that when you end an RStudio session using the Q-command, as we saw it, you will generally be asked to save your workspace, as we saw it together. This can also be changed by accessing the settings and ask RStudio to register automatically your session in a certain directory.
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Now, because we created a new project that we want to work from, when you open again an RStudio session, you can either open the app directly and then use the setwd to access that specific project, or you can simply go to your desktop and to the folder that you’re working on, and then when you select this Project Test and click on it, this will open a new RStudio session with that new project that is called Project Test opened directly. So you can notice that here we have an environment that is empty, whereas in the first one, we had the Iris data set that was pre-loaded. So again, we can resize our console and continue working on that.
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So if I type now getwd here as a command– this is by default kind of a new script, so if I click on Run, it tells me that I am definitely in that Project Test. So I can also open by going into my exercise R. I can open again my commands, and everything is again accessible from that same options. All right. Now, the second example we want to see together, and that, again, will show you how easy it is to use RStudio, is for installing packages. When you are in RStudio, you have different possibilities to instal packages.
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The first one is to write the command as we saw it in our steps again– so basically writing instal packages in the console, and then simply typing the name of the package in quotes, as you can see it here. For dplyr or ggplot2 packages that I put you here as examples, because these are two packages that we will be needing. So you remember the dplyr from the previous step that we used. And for the next steps, we will be using ggplot2 a lot. I could hit the Run button from here directly, but I want to show you what happens if you type a command in the console directly. In fact, it opens a pop-up window.
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So if I start typing instal packages, it opens that first pop-up window to give me all the possible commands. And once I click on the one I want, it will open another pop-up window to show me the usage of the command. And this can be very helpful sometimes if you forgot some usage of this command. And this is also possible with other commands you type in RStudio, of course. It is not something that is particular to instal packages. So let me just imagine that I’m trying to instal dplyr. You need to remember that, by default, you have some packages that are pre-installed.
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And specifically, if you installed a newer version of RStudio, there are many that should be pre-installed, including here the dplyr package. They are organised in an alphabetical order. So in fact, you can easily retrieve any package that you’re looking for. So this shows me that I don’t need to instal the package again. This is already done from RStudio. However, if I look for ggplot2, I’m not finding it here at all. And this is totally fine if you don’t find it by default from the beginning, simply because it is not pre-installed as a pre-installed package in RStudio. So let’s launch the installation for ggplot2.
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So you will see a stop sign in here saying that you will not be able to use your console while it is installing. So you have to wait a few moments for it to be installed. So here, the connection was quite rapid. And I did try it before, so it is quite rapid. And then I removed it to show you this example. But it might take a couple of minutes, in fact, to instal it, with a lot of different codes that is written, as long as you go for installing the package. Don’t worry. Don’t touch anything. Leave it until it will give you the prompt again, that creator sign that is particular to R sessions.
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There is another option to instal a package from RStudio. You can just go to the package, hit the Instal button, and then it will allow you to search on CRAN for your package of interest. If you remember, CRAN is a repository from which the packages can be accessed, and that we used previously in this course. Then you will simply have to type or select the package you want and wait for the installation to proceed. So if I start typing ggplot2, it will show me different options. I will only have to select ggplot2 and then click on the Instal button. It will do exactly the same as it was done here.
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So I will click on Cancel, but you can Instal it in here. All right. Now that we’ve installed the packages we want, before being able to use them, we will need to load them into our session, as we saw it in our steps. So you have, again, two ways of doing that in RStudio. One would be to do it directly from the console using the library function, as we saw it previously in this course. The second option you have is to open the available packages and simply click on the package name to select it.
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Now, because I showed you how to use the console to Instal the package, let me show you how to easily load the package from the packages tab directly. So you basically just have to select your package of interest. You can see now ggplot2. That is installed. And then simply click on it, and you can see that automatically it recognises that click as being your willingness to load that package. And it will write library for you to call that package. And it is as simple as that. So one important thing to remember, however, is that you will have to Instal the package you want to use only once. You need to do it only once.
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When you will open new R sessions, ggplot2 will be pre-installed now. However, you will need to load the packages you want each time you open a new RStudio session. So if we take again the example of dplyr, dplyr was pre-installed, but it was not loaded. So if I want to use dplyr, I just simply click on it, and it will load that package. So make sure to keep that in mind. Otherwise, you will not be able to use the functions that comes with a package.
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However, you might have noticed that some packages that are previously pre-installed are also pre-loaded– such as, for example, the data sets package– you remember that was the one we used to select the Iris data set– and also the graphics package that are pre-loaded, and that we use in this R session So we can take some time now to get familiarised with this display in RStudio before moving forward in the upcoming steps. But you should have noticed that it is very easy and simple to use. And you have many things that you can do with either script-based options, as in R, or interactive options, by just clicking and selecting things as you would do it classically in your machine.
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Now you’re ready to go with RStudio.

Watch this screencast by Fatma on beginning to use the RStudio, and try to follow along!

Do leave any comments that you might have in the comments section below.

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