I am new in the PhD field (hydroinformatics). I have a question: How can I understand a research paper thoroughly? I am perplexed about how the authors got the results. How can they calculate it? How did they get their graphs, tables, etc.? In general, I can understand the abstract and conclusion, but the methodology and discussion part of a research paper are quite a pain.
Understanding comes with practice, experience, and discussion. Good abstracts and conclusions are written to be easily digestible, and in my experience a good number of academics primarily skim those two sections to see if a paper is "worth it" before diving into the methodology and discussion. That's because understanding those sections can take some serious effort, even for people who are well versed in the field! So don't lose heart if those are the scary sections.
To get there, you have to do a lot of work, read a lot of papers, and talk about those papers with lots of people. A PhD is very much not a solo effort. Do you have an advisor, labmates, or other professors in your department/field/organization? Ask them (particularly your advisor) about what their favorite papers are in the field, or if there are any good review articles recently. Then read those papers, take notes, and follow up by having discussions with other academics. "I read that paper you suggested, but I didn't quite follow their method of doing X. Do you have some time to talk about it?" They probably have insight that you're still developing and are often able to guide you in the direction of the right answer.
One of the best ways to learn about papers is to join a journal club which senior academics attend. They will know about all the little hidden things in papers 'They wrote that they did X, but we all know that really means they did Y'. They will be able to parse the complicated methodology that confuses you. Take notes, annotate the papers and keep them for later reference.
If there isn't a journal club, start one! Try and invite some senior academics to join - even post docs can be very helpful in learning about how to read and evaluate papers. The senior academics might be busy, but you'd be surprised at how much they enjoy talking and giving their opinion about papers once they get the chance...
I can't stress how much joining them has helped me critially analayse the literature and learn how to better design experiments and analyses. There's a whole trove of useful information hidden away in the minds of senior academics and one of the best things you can do as a student is to try and tap into it.