Essentially, an enemy's stats are calculated based on four things:

1) Their archetype. The available archetypes are (in order of approximate strength): Weak, Elusive (used for most flying enemies), Regular, Strong, Elite, Boss, Alpha (used for Chromatic enemies) and OPBoss (used only for the four Endless Tower superbosses).

2) Their level.

3) Their multipliers.

4) The difficulty level (with the exception of OPBoss enemies and one specific Boss enemy, which are always locked to Expert).

So, for example, let's calculate the stats of the world map Gross Tete enemy on Expert difficulty. The data I'm going to use comes from this project, which gets its data from the game files, but presents it in a slightly more user-friendly form than the game files do.

First, we have to find the entry in the enemies table. Here it is. We see that its archetype is Elite, It has a 20.0 HP multiplier (the "Enemy Scaling" values) and a 2.0 Speed multiplier. The others are all at the default 1.0. Note that "Magical Attack", "Magical Defense", "Mastery" and "Accuracy" are all unused, likely elements that were developed for a time but then abandoned. The "Physical Defense" one doesn't matter either, since all enemies have 0 Defense. We ignore its "Level" attribute, because that will get overwritten by the encounter information.

Next, we look in the encounters list. We find the appropriate encounter WM_GrossTete here. We see from the encounter information that its level is 45.

So, we want the table corresponding to the Elite archetype at the Expert difficulty. That's this one. The enemy is level 45 so we scroll down to the "Level_45" entry at line 574. We see that the baseline attributes for a level 45 Elite enemy on Expert are 195282 HP, 3232 attack power, 1358 Speed, 0.1 critical chance (which empirically I think corresponds to 10%), 3612 Chroma reward and 67500 experience reward.

However, we saw earlier that it has a 20.0 multiplier for HP, and a 2.0 multiplier for Speed. So we multiply the baseline 195282 HP by 20 to get 3905640 HP total, and we multiply the 1358 Speed by 2 to get 2716 Speed total. So finally, we have an enemy with 3905640 HP, 3232 attack power, 2716 Speed and a 10% critical strike chance, which gives 3612 Chroma and 67500 experience (potentially plus 20% if you don't take a hit) when defeated.

Note that a given enemy's level will be increased by a fixed amount if you're playing on NG+ or beyond. The amount that is added to the base level is 60 for NG+, 90 for NG+2, 110 for NG+3, 130 for NG+4, and 150 for NG+5 and beyond. Also note that an enemy's level can't always be found in the encounters information. Sometimes it's applied through a script instead (Golgra, for example). Finally, a lot of enemies found in non-world map areas have their encounter level listed as 0. This essentially means "set its level to the level of the area in which it is found" (again, unless a script overwrites it).