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Latex invoice template for R&D

so in this video i'm going to show you how to make a completely 100 reproducible r markdown document so when you first open up our studio it should look something like this we're going to start by going ahead and making a new armored down document so we're going to go to file new file and then our markdown it's going to ask us for a title and the author you can call the title whatever you want and we're going to select pdf as the output then i'm going to hit ok and that's going to create a blank our markdown document for me so i'm going to start by erasing everything that's under this first gray chunk here it's going to highlight everything below that and erase that and if you haven't used our markdown before you might not be familiar with why it's so great so i'll just show you really quickly why our markdown is so powerful so our markdown is actually going to allow you to combine our code our code output paragraphs and latex all in the same document so for example here i'm going to put a header and then i'm going to write some paragraph and i can also include some math symbols as well so for example i can say that x squared is equal to 6 and then i can actually add some r code in as well so to insert an r chunk i'm going to use three back ticks which is the button near the escape key on your keyboard and then you're going to use some curly brackets and inside the curly brackets you're going to type r after the curly brackets if you hit enter that will start a a new r chunk for you and then you can put our code directly into this chunk so let's say for example i have some data that i've made in an excel file and i want to load that in and i want to create a quick plot of it so the first thing i'm going to need to do is set my working directory for this document so i'm going to be telling our studio where the file that i want is located so i'm going to use the function set wd for set working directory and then i'm going to pass in quotes the file path where my file is located so if you're on a windows machine that's going to look something like c colon users slash your username and then wherever you've got it saved on your computer next we're going to want to load in our data so for me i'm going to be loading in an excel file so in order to load in that excel file i'm actually going to be requiring a package called the read excel package so first i'm going to load the read excel package by using the library function and then i can go ahead and load the data set so i'm going to give it a variable name so i'm going to call it my data and then i'm going to use the read underscore excel function and i'm going to pass the file name oops so one thing i forgot is you also need to end the chunk with three backticks as well so now that i've ended my code chunk i can hit the play button and that will run all the code in this section and now my data has been loaded in and i can see that up in my environment so let's say i now want to explore what that looks like really quickly so i've got an x variable and a y variable and let's say i want to create a plot of these data so i'm going to use the ggplot2 package to create a plot of these data so i'm also going to need to load the ggplot2 package and again i use the library function for that so now i can use the ggplot function from the ggplot2 package so the first argument is going to be the dataset that you want to create a plot of so that's my underscore data next we're going to pass the aesthetics so the first argument is going to be our x variable so remember my x variable was called x underscore var and my y variable was called y underscore and to create a line plot i'm going to add a geom line layer and if i press play on this code chunk it will run all that and i should have a plot that's created so now let's say i want to turn this entire thing into a pdf so what i'm going to do is press this knit button right here and i'm going to press knit to pdf if it's your first time doing this for this document you're going to be prompted to save the file so i'm just going to call this my our markdown and now it will knit into a pdf and here i've got the pdf that contains my paragraphs the math that i put in using latex i've got my code chunk right here and then i've also got the output from that code so this is a really nice way to put everything all into one document so now let's say you want to make your our markdown document completely reproducible so you want to send somebody your rmd file and you want them to be able to run the entire file on their own computer so that they can also produce that same pdf that you were able to produce on your computer so in order to do that we're going to have a few extra steps so i should note that the strategy that i'm about to do here this is only applicable if you're using our studio so first make sure you've got the package that's called rstudio api so once you've got the rstudio api package installed we can go ahead and use it so in my first code chunk in my document what i'm going to do is i'm going to make a vector that contains all of the packages that i use in my entire our markdown document so i'm going to make a vector called required packages so in here i used the read excel package and the ggplot2 package and then i'm also going to include that rstudio api package that we just installed next we're going to figure out which packages the user that we're trying to send this file to already has installed on their machine so really what we're trying to do here is we're trying to get the user to any packages on their computer that they don't already have installed so that when they try to knit this pdf it will actually go ahead and any of the packages that they don't already have that are going to be used in the document so i'm going to create a vector called need and this vector is going to contain the packages that the person doesn't already have installed on their computer so to do that i'm going to index on the required packages vector that we just created so to index we use square brackets and then we want to know which of the packages in the required packages vector is not so the explanation mark means not in their list of installed packages and you can find out what your installed packages are by using the installed stop packages function so if we just take a look at what this part looks like without the exclamation mark first so right now without the exclamation mark this is going to be the list of packages out of the ones that you put here that the user has installed on their computer so if we add an exclamation mark it's going to be the packages that the user doesn't have installed on their computer so for me since i've already installed these three packages on my computer when i run this i should see nothing in return so let's just verify that and that's the case but when you send your file to someone else it might be possible that they don't have all of these packages installed okay so now we've defined a vector that contains the required packages that the person will need and we've created a vector that contains the list of packages that they need to before they can run your our markdown file okay so now we're going to all of the packages that are in the need underscore vector so if the length of that vector is greater than zero so in other words if there's a package that they need to before they can run your markdown document then what we're going to do is that package and we can actually multiple packages at the same time so if we pass in that vector it's going to all of the packages from this list that the person doesn't already have installed on their computer okay so next we're going to load all the packages so just like when we were using library earlier to load a single package now we're going to load all of the packages all at once so to do that we're going to use the l apply function and we're going to pass in the list of required packages um and then we're going to use the function require rather than library and we're going to pass an argument to the required function that is called character.only and we're going to set that to true so if i run this bit of code it's going to load every single package that's in this list that we created up here in this vector sorry okay so next we're going to need to set the working directory but if we're sending our file to someone else they're not going to have the exact same file path that we have on our computer so what we want to do instead is we want to figure out the location on the other person's computer where this our markdown file is located so in order to do that we're going to use a function from the r studio api package that we just installed earlier so i'm going to create a variable called directory of the script that i'm currently working in and i'm going to use the dura name function directory name inside of that function i'm going to pass the file path where the our markdown document is located for the person who is running your code so the rstudio api package actually has a function that will grab the file path location of the file that you're currently working on so that's get source editor context and then if you use the dollar sign operator you can get the file path using that so if you want to see what that looks like on my own computer if i run just this highlighted part of the code you can see that this is the file path that i had defined earlier so when you send this to someone else this will update with whatever folder they're currently working from on their computer so now once we've defined what the directory is we want to actually set the working directory as that path so we're going to use the set wd function just like we did earlier but this time we're going to pass the directory of the file that we're currently working on which is what we just defined on the previous line so once we've done that we can actually get rid of the previous lines of code that we had where we were loading in packages and now this should be a fully reproducible script so as a quick recap what this is going to do is it's going to define the packages that you're going to need in your entire markdown document it's going to check which of those packages need to be installed on the computer that is going to run the arm markdown document it's going to any of the packages that aren't already installed it's going to load all of the packages and then it's going to set the working directory to wherever this our markdown document is saved on the person's computer okay so now i'm going to knit to pdf again just to show you that it does still work the exact same okay so now to make this fully reproducible we have one final step we're going to create a zip folder that contains this our markdown document as well as any of the dependencies that we use within our markdown document and then once we send that zip folder to someone else they should be able to unzip that folder and run everything without needing to change literally anything at all which is magic okay so i'm going to navigate to the folder on my computer where this our markdown document and the associated dependencies are located and i'm going to put all of them into a new folder and then i'm going to zip that folder okay so now i'm going to close our studio okay so now i'm going to move this zip folder to a different location on my computer and then i'm going to unzip it and show you that the whole thing runs without me needing to change anything i'm going to unzip these files here now i'm going to open that our markdown document and see that i'm in a different file location than i was before okay so now i'm in a completely different folder path so let me just show you where we're working from this time so you can see that the folder path that i have now is different than the one that i had before so ideally i should be able to run this file and even though i'm in a different file location it should still find the correct working directory and load in my data properly so just to show you that i'm going to knit once again to pdf and just like that my our markdown document has found the correct location for the excel file so now i can send that zip folder to anyone i want and i've completed a 100 percent completely fully reproducible our markdown document