Thanks for the replies! I don't understand all the solutions you provided but, I can answer some of your questions.
I did not have any TM back-up.
I remember that I installed El Capitan a couple of weeks ago but I don't remember whether I restarted my computer ever since. But as you suggest, there is no updating OS without restarting, I will elaborate on what happened today.
I was installing a package into R which gave an error that had something to do with Java. My friend told me to de-install java from my Macbook, and so we pasted the following code into terminal:
sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
sudo rm -fr /Library/PreferencesPanes/JavaControlPanel.prefpane
After that, we tried to re-install Java, but after the downloads of Java didn't complete (we tried multiple times), that is: the full package was downloaded, but it didn't open because the download was not definite (or something like that, I don't exactly remember what it said). So my friend suggested I restarted the computer, and I did. After restarting all files were lost. Java was back on the computer, but all further recovery that happened was that of some iCloud back-up that dated back to november 2014, but even that back-up doesn't contain all of the files, so even files from pre-2014 are missing.
I know I did some stupid things, and I hope you can follow through the explanation above, and I just hope somebody knows how I can retrieve the files from yesterday. Right now I am just really scared to do anything that can further harm my computer.