The purpose of this guide is to make money off of the stuff you produce. If you don't care about money, then ignore this.
For everyone else, though, here is the Golden Rule of MMO Economics:
If you craft with the materials you farm, then you are giving up the EC you could have made by selling them.
For example, you might want 10 Radiogenic Particles to make 10 Superior Beams Upgrades. You could do 10 advanced PVE queues to get them or buy them for 440,000 EC on the exchange (the current price as I'm writing this). If you do the queues, you could either use them to craft those Superior Beam Upgrades or you could sell them for 440,000 EC on the exchange. Whether you grind them or not, you're still faced with a choice between 440,000 EC or 10 Radiogenic Particles.
The only thing that is different if you grind them is that you have 440,000 EC in more in assets. If that's the best way you have of getting 440,000 EC, then go for it! But if you can get 440,000 EC in a faster/more fun way, then why not do that instead and then buy the Radiogenic Particles?
This guide is about making stuff to sell it, specifically superior upgrades. I like to make those for money because they're easy, they sell quickly, and they don't require dilithium.
If you want to put in more effort and learn how to make gear for profit, then you would (I'm just guessing) make more money than with this but you'd have to deal with the random outcomes, pay dilithium, and actually learn the markets and the chances of getting something profitable and generally putting in more work than a lazy player like me is willing to do.
This might not be the most profitable way to make EC from R&D, but it's the lowest EC-to-effort ratio that I know of.
The step-by-step guide1. Pick an R&D school. I specialize in engineering upgrades, and my 4 favorite characters are all level 20 in that school because they've spent the last year and a half operating sweatshops on their ships. My newest well-loved character is getting there; she is already profiting from her sweatshop.
A higher level means a higher crit rate. Critting on crafting Superior Upgrades means you get 2 Superior Upgrades for the same time and materials. So focusing on 1 school means more profit. It also means less effort since selling a lot of 1 thing is easier than selling a little bit of 7 things.
2. Get the characters you like to play to level 15 in that school with the 20-hour daily projects and the daily bonus mission at the Fleet Research Lab.
3. Unlock the last 2 R&D project slots by getting 2 other schools to level 5 and by buying an extra slot at the Fleet Research Lab for 100,000 FC.
4. Buy 6 purple Research Lab Scientist doffs for each character you play regularly. Traits don't matter.
Yes, this might be a little pricey for you, but they're worth the investment and you can start with greens or blues at first if you don't have the 30 to 40 million EC these doffs cost (per toon). Your crit rate increases with doff rarity, and you can always sell them later if you change your mind.
Since they're not bound to character, you could even get 1 set of 6 for each faction and mail them between characters. I'm way too lazy for that, but it might be a way to get started.
5. Buy 6 purple Fabrication Engineers on one of your toons to make components.
6. OK, now it's time to figure out your market. This step requires a little arithmetic, so open a spreadsheet or get a pen and some paper. Or skip this step and just assume you'll make EC. You probably will, but I'm not responsible for you losing EC because you managed to be lazier than me.
A math example is in the next comment on this thread.
In your spreadsheet, calculate the cost to make each component with
Cost = (total cost of components)/(1+2*crit rate)
* means multiplication. / means division. + means addition.
You can find the crit rate for a component by clicking to make it and selecting the appropriate doff. If you crit, you get 3 times the number of components you slotted, which is the same as having 2 times your normal crit rate.
So, for example, the cost of making a Rerouting Lattice is
Cost of 1 Rerouting Lattice = (price of z-particle + 2 * price of tetrazine)/(1 + 2 * 0.30)
Figure that out for both components.
Now figure out the cost for upgrades with the formula:
Cost = (cost of first component + cost of second component + cost of purple material + 15000) / (1 + crit rate)
Critting gets you 1 extra Upgrade, so you don't multiply it by 2 this time.
Should you use the cost of components that you calculated above or the price that component is listed for on the exchange? Whichever is lower. If you can produce a component cheaper than you can buy it on the exchange, then you should produce it. If you can buy it cheaper, then you will buy it.*
If the cost of producing 1 Superior Tech Upgrade is lower than the price you can sell it for on the exchange, then you're good to move on to the next step.**
7. Buy materials that you need to make components. I like to just get a bunch of these done at once so I don't have to worry about this for a while, but you might not have the capital to buy 1000 or 2000 of each blue material in your first go. It's up to you. If you're buying components instead of making them, then buy a bunch of those.
Do this on the toon that has the 6 purple Fabrication Engineers, who should also be the toon with the highest level in your R&D school.***
8. Mail or use the account bank to give a stack of the purple material and the 2 blue components to the toons you like to play.
9. Every 15 minutes, go through and set up 6 projects to make these kits. Have fun playing the game normally outside of the 10 seconds it takes to set these up.
10. Check the market regularly and find a good time to sell. I wouldn't hold on to too many of these at first because you'll need the EC to buy more materials, but eventually you'll be able to figure out for yourself when a good time to sell is (spoiler: during an upgrade weekend).
11. Post the upgrades in groups of at least 10 because buyers often skip single Upgrades so they don't have to click so much. I do that with materials too. If I want 1000 Rubidium, I'm not going to spend 2 hours buying each one individually. I'll pay a little more per unit to get them all at once.
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When DR hit in October 2014 and upgrading became a part of STO, I made insane (for me) amounts of EC but assumed that in a few weeks, maybe a few months, the profit margin on upgrades would be razor-thin. Well, it's been a year and a half and while the prices of materials and upgrades have all dropped a lot and EC/hour is lower than it was before, but there's still nothing better in the game for getting EC than R&D.
The only reason it stayed that way is that most STO players haven't figured it out, either because it looks complicated and scary or because they can't understand the Golden Rule of MMO Economics.
It also helps that there are always nice players who post propaganda on the official forums like "Don't get into R&D for profit because you can't make any money unless you're level 20 with purple doffs and even then you might lose so don't even try!" Less competition for me!
*I recently adjusted my spreadsheet formula to say that if I can't save more than 10,000 EC per component by crafting it myself then I'll just buy it. I'm that lazy.
**You can also calculate EC/hour with
EC/hour = (price of upgrade on exchange - cost to make an upgrade from above) * (1 + crit rate for tech upgrades) * 24
Why calculate EC/hour instead of Price/Cost of making an Upgrade? Because you are limited by the number of R&D project slots and you're looking for the best way to use those. If you have a choice between making two things that each would double your EC in the same amount of time, the one that costs more initially is the more profitable choice because it would have the bigger profit margin.
For example, if you could make Widget A for 10 EC and sell it for 20 EC and Widget B for 20 EC and sell it for 40 EC, and it takes 1 hour to make each, which is the better choice? Both double your EC, but Widget B gets you 20 EC/hour instead of 10 EC/hour.
***You can make component production less work by putting all your purple materials in your account bank (or mailing them to yourself) and turning the filter in your school to "Show with met reqs." This puts the blue components at the bottom of the UI, and since it scrolls down when you go back to your school after setting one project, you won't have to scroll back up.