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Pokemon GO nest migration table - oddish removed, with gen 5 and no Eevee - 10-03-19
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| # Pokemon GO nest migration table - oddish removed, with gen 5 and no Eevee - 10-03-19 | |
| # taxa in full nesting list not in NEW nesting list | |
| removeTaxaNew <- c("Oddish", "Eevee") | |
| # taxa in full nesting list not in OLD nesting list | |
| # this is often an empty set because | |
| # the nesting list was fully utilized before an event | |
| # if full list before migration, just do `""` | |
| removeTaxaOld <- c("Eevee") | |
| # REVERSE MIGRATION | |
| reverseMigration <- FALSE | |
| # where do you want the files / what do you want them named | |
| filename <- "remove_oddish_plus_some_gen_5" | |
| path<-"~/Documents/" | |
| #################################### | |
| ################################### | |
| fullNestingList<-c( | |
| # pre-halloween-2018 nesting list, as estimated by u/Clyphox and u/SnipeThemAll | |
| # with hippopotas added, and gen 5 added as following u/MGDuck | |
| ############### | |
| # Gen 1 | |
| ############## | |
| "Bulbasaur", "Charmander", "Squirtle", | |
| # "Caterpie", "Weedle", "Pidgey", "Rattata", "Spearow", "Ekans", #REMOVED - u/Clyphox | |
| "Pikachu", | |
| # "Sandshrew", "Nidoran-F", "Nidoran-M", #REMOVED - u/Clyphox | |
| "Clefairy", "Vulpix", | |
| # "Jigglypuff", "Zubat", #REMOVED - u/Clyphox | |
| "Oddish", | |
| # "Paras", "Venonat", "Diglett", "Meowth", #REMOVED - u/Clyphox | |
| "Psyduck", | |
| # "Mankey", #REMOVED - u/Clyphox | |
| "Growlithe", "Poliwag", "Abra", "Machop", | |
| # "Bellsprout", #REMOVED - u/Clyphox | |
| "Tentacool", | |
| # "Geodude", #REMOVED - u/Clyphox | |
| "Ponyta", | |
| # "Slowpoke", #REMOVED - u/Clyphox | |
| "Magnemite", "Doduo", "Seel", "Shellder", "Gastly", "Onix", | |
| # "Drowzee", "Krabby", #REMOVED - u/Clyphox | |
| "Voltorb", "Exeggcute", "Cubone", "Rhyhorn", "Horsea", | |
| # "Goldeen", "Staryu", #REMOVED - u/Clyphox | |
| "Scyther", "Jynx", "Electabuzz", "Magmar", "Pinsir", | |
| "Magikarp", "Eevee", | |
| "Omanyte", "Kabuto", | |
| #"Dratini", #CD Pokemon | |
| ################# | |
| ############### | |
| # Gen 2 | |
| ############## | |
| "Chikorita", "Cyndaquil", "Totodile", | |
| # "Sentret", "Hoothoot", "Ledyba", "Spinarak", #REMOVED - u/Clyphox | |
| "Chinchou", | |
| # "Natu", #REMOVED - u/Clyphox | |
| #"Mareep", # CD Pokemon | |
| # "Marill", #REMOVED - u/Clyphox | |
| "Sudowoodo", #### ADDED - u/Clyphox ##### | |
| # "Hoppip", #REMOVED - u/Clyphox | |
| "Aipom", | |
| # "Sunkern", #REMOVED - u/Clyphox | |
| "Yanma", | |
| # "Wooper", #REMOVED - u/Clyphox | |
| "Misdreavus", "Wobbuffet", "Girafarig", "Dunsparce", "Snubbull", | |
| "Qwilfish", "Shuckle", "Sneasel", "Teddiursa", | |
| # "Slugma", #REMOVED - u/Clyphox | |
| "Swinub", | |
| # "Remoraid", #REMOVED - u/Clyphox | |
| "Mantine", "Skarmory", #### ADDED - u/Clyphox ##### | |
| # "Houndour", #REMOVED - u/Clyphox | |
| "Phanpy", "Stantler", #### ADDED - u/Clyphox ##### | |
| #"Larvitar", #CD Pokemon | |
| ################### | |
| ############### | |
| # Gen 3 | |
| ############## | |
| "Treecko", "Torchic", "Mudkip", "Poochyena", | |
| # "Zigzagoon", "Wurmple", #REMOVED - u/Clyphox | |
| "Seedot", | |
| # "Tailow", #REMOVED - u/Clyphox | |
| "Wingull", "Surskit", "Shroomish", | |
| # "Whismur", #REMOVED - u/Clyphox | |
| "Makuhita", "Nosepass", "Skitty", | |
| "Sableye", #### ADDED - u/Clyphox ##### | |
| # "Aron", #REMOVED - u/Clyphox | |
| "Meditite", "Electrike", | |
| "Plusle", "Minun", #### ADDED - u/Clyphox ##### | |
| # "Gulpin", #REMOVED - u/Clyphox | |
| "Carvanha", "Wailmer", "Numel", "Spoink", "Swablu", | |
| # "Barboach", #REMOVED - u/Clyphox | |
| "Corphish", "Baltoy", | |
| "Lileep", "Anorith", #### ADDED - u/Clyphox ##### | |
| "Shuppet", "Duskull", | |
| # "Spheal", #REMOVED - u/Clyphox | |
| "Luvdisc", | |
| #"Beldum", #CD Pokemon | |
| ################## | |
| ############### | |
| # Gen 4 | |
| ############## | |
| "Turtwig", "Chimchar", "Piplup", | |
| "Bidoof", | |
| "Hippopotas", | |
| ############### | |
| # Gen 5 | |
| ################# | |
| "Snivy", "Tepig", "Oshawott", | |
| "Patrat", "Lillipup", "Purrloin", | |
| "Blitzle", "Foongus" | |
| ) | |
| oldNesting <- fullNestingList | |
| whichRemoveOld <- sapply(oldNesting, | |
| function(x) all(x != removeTaxaOld)) | |
| oldNesting <- oldNesting[whichRemoveOld] | |
| newNesting <- fullNestingList | |
| whichRemoveNew <- sapply(newNesting, | |
| function(x) all(x != removeTaxaNew)) | |
| newNesting <- newNesting[whichRemoveNew] | |
| if(reverseMigration){ | |
| newNesting1 <- newNesting | |
| newNesting <- oldNesting | |
| oldNesting <- newNesting1 | |
| } | |
| ######################################### | |
| # for nest migrations - source functions, modify vectors of lists of nesting species, then run | |
| # use kable to produce markdown table for pasting to Silph Road | |
| #approximate ranges for each species in the nesting lists | |
| getRangesForNestingSpecies<-function(nestingSpecies, arbMax=256){ | |
| nNesting<-length(nestingSpecies) | |
| intLength<-arbMax/nNesting | |
| lowBound<-((1:nNesting)-1)*intLength | |
| upperBound<-lowBound+intLength | |
| res<-cbind(lowBound,upperBound) | |
| rownames(res)<-nestingSpecies | |
| return(res) | |
| } | |
| # find new species for each old nesting seed range | |
| findNew<-function(oldRange,newRanges){ | |
| newRanges<-round(newRanges,5) | |
| oldLow<-round(oldRange[1],5) | |
| oldHigh<-round(oldRange[2],5) | |
| # | |
| newLowRow<-which(newRanges[,1]<=oldLow & newRanges[,2]>oldLow) | |
| newHighRow<-which(newRanges[,1]<oldHigh & newRanges[,2]>=oldHigh) | |
| # | |
| #print(c(newLowRow,newHighRow)) | |
| newRows<-newLowRow:newHighRow | |
| newNestNames<-rownames(newRanges)[newRows] | |
| # calculate proportion of overlap (prob of shift) | |
| propOverlap<-sapply(newRows,function(x) | |
| getPropOverlap(X=newRanges[x,],Y=oldRange)) | |
| # paste them together | |
| res<-paste0(newNestNames," (",round(propOverlap*100,1),"%)") | |
| return(res) | |
| } | |
| getPropOverlap<-function(X,Y){ | |
| # calculate how much range X overlaps with range Y | |
| overlapRange<-c(max(X[1],Y[1]),min(X[2],Y[2])) | |
| overlap<-overlapRange[2]-overlapRange[1] | |
| # divide by length of Y | |
| propOverlap<-overlap/(Y[2]-Y[1]) | |
| return(propOverlap) | |
| } | |
| # master function | |
| predictNestingShifts<-function(oldNestingList,newNestingList){ | |
| oldRanges<-getRangesForNestingSpecies(oldNestingList) | |
| newRanges<-getRangesForNestingSpecies(newNestingList) | |
| # | |
| nestShifts<-apply(oldRanges,1,findNew,newRanges=newRanges) | |
| if(length(dim(nestShifts))!=2){ | |
| # need to add NAs when there are uneven number of possible species | |
| # for different nests to potentially migrate to | |
| maxNSlength<-max(sapply(nestShifts,length)) | |
| nestShifts<-sapply(nestShifts,function(x){ | |
| if(length(x)<maxNSlength){ | |
| res<-c(x,rep(NA,maxNSlength-length(x))) | |
| }else{ | |
| res<-x | |
| } | |
| return(res) | |
| }) | |
| } | |
| nestShifts<-t(nestShifts) | |
| #print(nestShifts) | |
| nestShifts<-cbind(oldNestingSpecies=rownames(nestShifts),nestShifts) | |
| colnames(nestShifts)[2:ncol(nestShifts)]<-paste0("NewNestingSpecies", | |
| 1:(ncol(nestShifts)-1)) | |
| rownames(nestShifts)<-NULL | |
| return(nestShifts) | |
| } | |
| ################################################### | |
| nestShifts<-predictNestingShifts( | |
| oldNestingList=oldNesting, | |
| newNestingList=newNesting) | |
| # get path | |
| filename <- paste0(path, "nesting_species_predictions_", | |
| filename, "_", | |
| format(Sys.time(), "%m-%d-%y")) | |
| # use knitr to convert the table of nest shifts to markdown | |
| x<-knitr::kable(nestShifts) | |
| cat(x,file=paste0(filename, ".txt"), sep = "\n") | |
| rmarkdown::render(paste0(filename, ".txt")) | |
| system(paste0("xdg-open ", filename, ".txt")) | |
| system(paste0("xdg-open ", filename, ".html")) | |
| ############################################# | |
| #nestShifts | |
| # 05/17/2019: typical nesting list length is 88 | |
| # previous nesting list length | |
| print(paste0("Old Nesting List Length: ", length(oldNesting))) | |
| # new nesting list length | |
| print(paste0("New Nesting List Length: ", length(newNesting))) | |
| # full nesting list of all potentially nesting species | |
| print(paste0("Full Nesting List Length: ", length(fullNestingList))) |
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Here's the forced migration table