library(pokedex)
library(tidyverse)
library(tidymodels)
library(showtext)
showtext_auto()

theme_set(theme_pokedex())

knitr::opts_chunk$set(fig.showtext=TRUE)  ## The Heros Journey Pokemon games have a very familiar cycle. You start with one of 3 Pokemon. You adventure out with your new buddy, facing tougher and tougher Pokemon, in greater variety. Many of your Pokemon evolve over time, and eventually you find the end-game legendaries in a climactic battle of titans! You can even see this story in the data. Here is the base_experience of all the Pokemon, identified by game generation. The base_experience is the basic amount of experience that is gained by the winner of a battle from a specific species. e.g. If you beat a Bulbasaur, your Pokemon gains experience based on a formula which uses Bulbasaurs base_experience . Because of that we can see it as a proxy value for how powerful a Pokemon is. If it’s more powerful, it will be harder to beat, and so reward you with more experience when you win. pokemon %>% ggplot(aes(x = id, y = base_experience, colour = generation_id)) + geom_point() + labs(title = "Base Experience for each Pokemon")  In each generation you can see a few attributes: • power level - 3(ish) tiers, grouped in different vertical lanes • progression - a (generally) increasing trend in the base power value • the up-ticks at the start and the end of each gen are the starters top-tier evolution (Woo Blastoise!) and the Legendaries at the end-game Lets see if we can group each Pokemon into a power_level . A categorical grouping which relates it to other Pokemon with similar base_experience ## Grouping and counting Maybe we can explicitly describe the power levels of each tier of Pokemon with a simple process? Can we group each Pokemon by evolutionary chain, and then count each Pokemons order within the group? pokemon %>% group_by(evolution_chain_id) %>% mutate(power_level = row_number()) -> pokemon_group_count ggplot(pokemon_group_count, aes( x = id, y = base_experience, colour = as_factor(power_level) )) + geom_point() + labs(title = "Power level by group count", colour = "power_level")  Sort of? Generally we capture the pattern, but we don’t actually get it very right. First off, there are more than 3 evolutionary tiers in our engineered feature. We can also see there are some Pokemon are classified as a power_level higher than 1, but still in the lowest group on this list. Why might have caused this? pokemon_group_count %>% filter(power_level > 3) %>% pull(evolution_chain_id) -> pokemon_group_count_mistakes pokemon_group_count %>% filter(evolution_chain_id %in% pokemon_group_count_mistakes) %>% select(id, name, base_experience, generation_id, evolution_chain_id, power_level) %>% arrange(evolution_chain_id) %>% select(id, name, base_experience, evolution_chain_id, power_level) %>% knitr::kable()  id name base_experience evolution_chain_id power_level 43 Oddish 64 18 1 44 Gloom 138 18 2 45 Vileplume 221 18 3 182 Bellossom 221 18 4 60 Poliwag 60 26 1 61 Poliwhirl 135 26 2 62 Poliwrath 230 26 3 186 Politoed 225 26 4 106 Hitmonlee 159 47 1 107 Hitmonchan 159 47 2 236 Tyrogue 42 47 3 237 Hitmontop 159 47 4 133 Eevee 65 67 1 134 Vaporeon 184 67 2 135 Jolteon 184 67 3 136 Flareon 184 67 4 196 Espeon 184 67 5 197 Umbreon 184 67 6 470 Leafeon 184 67 7 471 Glaceon 184 67 8 700 Sylveon 184 67 9 265 Wurmple 56 135 1 266 Silcoon 72 135 2 267 Beautifly 178 135 3 268 Cascoon 72 135 4 269 Dustox 173 135 5 280 Ralts 40 140 1 281 Kirlia 97 140 2 282 Gardevoir 233 140 3 475 Gallade 233 140 4 789 Cosmog 40 413 1 790 Cosmoem 140 413 2 791 Solgaleo 306 413 3 792 Lunala 306 413 4 So there are some clear problems with this approach. In Gen 1 we had some branching evolution with the Eevee family. Not only was this family expanded in multiple generations to eventually 8 variations, but we also saw more branching evolution trees as well. We also got ‘baby’ Pokemon. Pokemon that are actually pre-cursors to other Pokemon, but are listed later in the Pokedex. Luckily there is another variable we can use, that should be a whole lot better. evolves_from_species Each Pokemon that evolves from another Pokemon has the Pokemon they evolve froms id as the value in the evolves_from_species_id variable. Maybe we can use that to break up the Pokemon into their ‘power levels’. The following code is not my best work, however I spent some time on a more recursive strategy, but it was honestly miles more confusing. For the purposes of a silly example for a blog, I think this is prefferable. pokemon %>% mutate(power_level = case_when(is.na(evolves_from_species_id) ~ 1)) %>% filter(power_level == 1) -> pokemon_1 pokemon %>% mutate(power_level = case_when(evolves_from_species_id %in% pokemon_1$id ~ 2)) %>%
filter(power_level == 2) -> pokemon_2

pokemon %>%
mutate(power_level = case_when(evolves_from_species_id %in% pokemon_2\$id ~ 3)) %>%
filter(power_level == 3) -> pokemon_3

bind_rows(pokemon_1, pokemon_2, pokemon_3) %>%
arrange(id) %>%
mutate(power_level = as_factor(power_level)) -> pokemon_evolves_from

pokemon_evolves_from %>%
ggplot(aes(x = id, y = base_experience, colour = power_level)) +
geom_point() +
labs(title = "Power level by evolves_from")


Hmm, that’s actually worse? Lets focus on the Pokemon labelled

power_level 1, but are up where we would expect level 3 Pokemon to be.

pokemon_evolves_from %>%
filter(base_experience > 200 & power_level == 1) %>%
select(id, name, base_experience) %>%
knitr::kable()

id name base_experience
144 Articuno 261
145 Zapdos 261
146 Moltres 261
150 Mewtwo 306
151 Mew 270
243 Raikou 261
244 Entei 261
245 Suicune 261
249 Lugia 306
250 Ho-Oh 306
251 Celebi 270
377 Regirock 261
378 Regice 261
379 Registeel 261
380 Latias 270
381 Latios 270
382 Kyogre 302
383 Groudon 302
384 Rayquaza 306
385 Jirachi 270
386 Deoxys 270
480 Uxie 261
481 Mesprit 261
482 Azelf 261
483 Dialga 306
484 Palkia 306
485 Heatran 270
486 Regigigas 302
487 Giratina 306
488 Cresselia 270
489 Phione 216
490 Manaphy 270
491 Darkrai 270
492 Shaymin 270
493 Arceus 324
494 Victini 270
531 Audino 390
638 Cobalion 261
639 Terrakion 261
640 Virizion 261
642 Thundurus 261
643 Reshiram 306
644 Zekrom 306
645 Landorus 270
646 Kyurem 297
647 Keldeo 261
648 Meloetta 270
649 Genesect 270
716 Xerneas 306
717 Yveltal 306
718 Zygarde 270
719 Diancie 270
720 Hoopa 270
721 Volcanion 270
785 Tapu Koko 257
786 Tapu Lele 257
787 Tapu Bulu 257
788 Tapu Fini 257
793 Nihilego 257
794 Buzzwole 257
795 Pheromosa 257
796 Xurkitree 257
797 Celesteela 257
798 Kartana 257
799 Guzzlord 257
800 Necrozma 270
801 Magearna 270
805 Stakataka 257
806 Blacephalon 257
807 Zeraora 270

So these Pokemon are nearly all ‘Legendary’. They are big end-game Pokemon, with real rarity in game. They also don’t evolve from, or to, anything, so our rule doesn’t classify them effectively.

pokemon_evolves_from %>%
filter(base_experience < 200 & base_experience > 100 & power_level == 1) %>%
select(id, name, base_experience) %>%
knitr::kable()

id name base_experience
83 Farfetch’d 132
127 Pinsir 175
128 Tauros 172
131 Lapras 187
132 Ditto 101
142 Aerodactyl 180
201 Unown 118
203 Girafarig 159
206 Dunsparce 145
213 Shuckle 177
214 Heracross 175
222 Corsola 144
225 Delibird 116
227 Skarmory 163
234 Stantler 163
241 Miltank 172
302 Sableye 133
303 Mawile 133
311 Plusle 142
312 Minun 142
313 Volbeat 151
314 Illumise 151
324 Torkoal 165
327 Spinda 126
335 Zangoose 160
336 Seviper 160
337 Lunatone 161
338 Solrock 161
351 Castform 147
352 Kecleon 154
357 Tropius 161
359 Absol 163
369 Relicanth 170
370 Luvdisc 116
417 Pachirisu 142
440 Happiny 110
441 Chatot 144
442 Spiritomb 170
455 Carnivine 159
479 Rotom 154
538 Throh 163
539 Sawk 163
550 Basculin 161
556 Maractus 161
561 Sigilyph 172
587 Emolga 150
594 Alomomola 165
615 Cryogonal 180
618 Stunfisk 165
621 Druddigon 170
626 Bouffalant 172
631 Heatmor 169
632 Durant 169
676 Furfrou 165
701 Hawlucha 175
702 Dedenne 151
707 Klefki 165
741 Oricorio 167
764 Comfey 170
765 Oranguru 172
766 Passimian 172
771 Pyukumuku 144
772 Type: Null 107
774 Minior 154
775 Komala 168
776 Turtonator 170
777 Togedemaru 152
778 Mimikyu 167
779 Bruxish 166
780 Drampa 170
781 Dhelmise 181
803 Poipole 189

These Pokemon are not end game, but they either have very short evolution trees (2 Pokemon long), or no evolution tree at all.

So our ‘group count’ process doesn’t work well, and neither does our ‘ evolves_from_species ’ process. We’re going to have to to learn some new moves.

## TM01 (e.g. Tidy Models 01)

Clustering is the process of using machine learning to derive a categorical variable from data. The simplest form of clustering that seems relevant to our problem is k-means. Seeing as we have a pretty good intuition that 3 groups implicitly exist in this data, and a clear visualisation supporting us, lets cut straight to asking R for 3 groups. k-means clustering aims to divide the data into a known number of groups which is set in the centers argument, and doesn’t require any data to be fed to it as examples of what makes up a ‘group’. That sentence might be a little confusing, as we do obviously give it some data. What we don’t give it is a training data set which has examples of what Pokemon are supposed to be in a given group, labelled with the group they are supposed to be in, e.g. Squirtle is in group 1, Wartortle is in group 2, Blastoise is in group 3, and then give it unlabelled data to classify, e.g. “What group is Charmeleon in?”. k-means will figure out how to split the continuous variable base_experience into 3 groups.

set.seed(68)

pokemon %>%
select(base_experience)  %>%
kmeans(centers = 3) %>%
augment(pokemon) -> pokemon_cluster


### How kmeans works

First, we set centroids to be at random positions in the data. To make sure this doesn’t effect consistency in my article I’ve used set.seed

so k-means starts looking for the centres of our clusters from the same position each time. A ‘centroid’ can be seen as a ‘centre point’ for each cluster. We have the same number of centroids set as the value set in the centers argument. Each data point is then assigned to it’s closest centroid.

The Sum of Squared Errors (SSE) from the centroids is then used as an objective function towards a local minimum.

This is the core concept of how k-means calculates a solution. The Sum of Squared Errors are calculated like this:

\sum^n_{i-1}(x_i-\bar{x})^2

What this means is for each group, the distance from the centroid to each observation is measured, and then squared. Then each of those squared distances, one per observation in the group, is totalled.

The centroid is then moved to the average value of it’s group. Because the centroids are now no longer in the same position as when the SSE was calculated, the SSE is now recalculated for all observations, to each of the new centroid positions. This means that some observations are now closer to a different centroid, and so get assigned to a different cluster.

Then the centroids are moved again to the new average of the new cluster. Each cluster then gets new distances calculated. This will go on until termination when, each centroid is in the average position of the cluster, and each observation in the cluster is closest to the centroid it is currently assigned to.

That’s a slightly wordy description of a complicated process. I recommend that you have a look at the k-means explanation in tidy models to really cement the concept. It also contains the most adorable animation of a statistical concept in existance.

### How to use it

Here, I’ve simply selected the one column of data, base_experience , and piped it into kmeans , which is part of base R. This returns a super un-tidy list like object of class "kmeans" , however, with

tidymodels we can easily make it usable.

augment helps us to match the output of the kmeans function back to our data for easier processing. The output of kmeans doesn’t actually contain any of the other information about our data, it only got given one column remember? augment goes through the return of kmeans , finds the relevant bit, and matches it neatly back to our original data ready for plotting in one step!

pokemon_cluster %>%
ggplot(aes(x = id, y = base_experience, colour = .cluster)) +
geom_point() +
labs(title = "Power level by kmeans clustering")


This is a lot better. It gives us really clear groups, in exactly where we expected them. It’s also tonnes simpler code!

Lets check some of our boundary positions, just to make sure it makes sense.

pokemon_cluster %>%
filter(.cluster == 1 & base_experience > 100) %>%
select(id, name, base_experience) %>%
knitr::kable()

id name base_experience
132 Ditto 101
440 Happiny 110
699 Aurorus 104
762 Steenee 102
772 Type: Null 107
pokemon_cluster %>%
filter(.cluster == 2 & base_experience > 200) %>%
select(id, name, base_experience) %>%
knitr::kable()

id name base_experience
189 Jumpluff 207

Ditto and Type: Null are just a plain weird Pokemon due to their abilities messing with their type. Happiny is a baby type, but from a family with an insane base_experience. Jumpluff is an awkward edge case. Technically the 3rd evolution, it’s still got an extremely low base_experience. Potentially this is for game balancing as they are relatively regularly encountered? Aurorus and Steenee I do not have a good hypothesis for.

Generally I think that this is a pretty good solution. There are maybe a few edge cases that are open to interpretation, but that’s just what we get sometimes with machine learning. Lacking a labelled training data set, we can’t compute a confusion matrix or ROC-curve.

## Conclusion

We’ve found a situation in the ‘real’ world where we know from context there is a categorical relationship, but from the data available it’s not possible to classify that precisely. However we can create this categorisation using machine learning! Even better, we can use the

tidymodels package to help us do it quickly and cleanly.

This post is also available on DEV.