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2.prep_empirical_data.R
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2.prep_empirical_data.R
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################################################################################
# Prep raw data for use with DynaRanks #
# #
# #
# By Eli Strauss #
# #
# November 2018 #
################################################################################
rm(list = ls())
library(dplyr)
options(stringsAsFactors = FALSE)
setwd('~/Documents/Research/Longitudinal_Hierarchies/FinalSubmission/0.rawdata/')
####Read in data####
aggressions <- read.csv('tblAggression.csv')
aggressions$date <- as.Date(aggressions$date)
aggressions$Year <- as.numeric(format(aggressions$date, '%Y'))
#demographic information
#hyenas <- read.csv('/Volumes/Holekamp/code_repository/R/1_output_tidy_tbls/tblHyenas.csv')
hyenas <- read.csv('tblHyenas.csv')
#Fix bd
hyenas[hyenas$id == 'bd',]$birthdate <- hyenas[hyenas$id == 'bd',]$first.seen
#remove hyena 44 who disappeared before our data begin
hyenas <- hyenas[-which(hyenas$id == '44'),]
hyenas$birthdate <- as.Date(hyenas$birthdate)
hyenas$death.date <- as.Date(hyenas$death.date)
hyenas$disappeared <- as.Date(hyenas$disappeared)
#sessions and hyenas per session to fix some missing disappeared dates
hps <- read.csv('tblHyenasPerSession.csv', colClasses = 'character')
sessions <- read.csv('tblSessions.csv', colClasses = 'character')
hps$date <- left_join(hps, sessions, by = 'session')$date
hps$date <- as.Date(hps$date)
last.seen <- hps %>% group_by(hyena) %>% summarize(last.seen = max(date, na.rm = T))
hyenas[is.na(hyenas$disappeared),]$disappeared <-
left_join(hyenas[is.na(hyenas$disappeared),],
last.seen, by = c('id' = 'hyena'))$last.seen
#Clan membership after fission
talekMembership <- read.csv('ClanMembership.csv')
excludeResponse <- c("ignores", "ignore", "ct", "counterattack", "counter", "counters", "counterattacks")
aggsWinner <- filter(aggressions, !response1 %in% excludeResponse, !response2 %in% excludeResponse, !response3 %in% excludeResponse)
aggsWinner <- filter(aggsWinner, !context %in% c('ct', 'counter', 'counterattack'))
#aggressions
aggs <- filter(aggsWinner, clan == 'talek')
#################################################################################
############Females
#################################################################################
#contestants
initial.ranks <- read.csv('iranks_talek.csv')
females <- filter(hyenas, clan == 'talek', sex == 'f', !is.na(birthdate) | id %in% initial.ranks$ID)
females$EndYear <- format(do.call(pmin, c(females[,c('death.date', 'disappeared')], na.rm = T)), '%Y')
#Females are added the first *complete* year that they are at least 1.5 years old
females$StartYear <- format(females$birthdate + 365*2.5, '%Y')
females <-females[,c('id', 'StartYear', 'EndYear')]
names(females) <- c('ID', 'StartYear', 'EndYear')
##Remove females that during fisiion in 2000
##Make list of talek east
easties <- filter(talekMembership, Membership == 'e')
for(eh in unique(females$ID)){
ehmom <- filter(hyenas, id == eh)$mom
if(ehmom %in% easties$ID){easties <- rbind(easties, c(eh, 'e', 'kid', 'EDS'))}
}
####remove talek east
females[females$ID %in% easties$ID,]$EndYear <- 1999
first.year <- min(initial.ranks$Year)
last.year <- as.numeric(format(max(aggs$date, na.rm = TRUE), '%Y')) - 1
###Assemble final dataframes
#Initial ranks
initial.ranks <- initial.ranks$ID
female.initial.ranks <- initial.ranks
females[females$ID %in% initial.ranks,'StartYear'] <- first.year
#Contestants
females <- filter(females, StartYear <= last.year,
StartYear <= EndYear)
contestants <- data.frame()
for(id in females$ID){
contestants <- rbind(contestants, data.frame(id, period = seq(from =filter(females, ID == id)$StartYear, to = filter(females, ID == id)$EndYear, by = 1)))
}
contestants <- filter(contestants, period >= first.year, period <= last.year)
contestants$convention1 <- left_join(contestants, hyenas, by = 'id')$mom
contestants$convention2 <- left_join(contestants, hyenas, by = 'id')$litrank
contestants <- filter(contestants, convention1 != '' | id %in% initial.ranks)
contestants <- arrange(contestants, period)
female.contestants <- contestants
#Interactions
interactions <- filter(aggs,
aggressor %in% c(initial.ranks, contestants$id),
recip %in% c(initial.ranks, contestants$id),
Year <= last.year,
Year >= first.year) %>%
semi_join(contestants, by = c('aggressor' = 'id', 'Year' = 'period')) %>%
semi_join(contestants, by = c('recip' = 'id', 'Year' = 'period')) %>%
rename(winner = aggressor, loser = recip, period = Year) %>%
dplyr::select(winner, loser, period) %>%
arrange(period)
female.interactions <- interactions
#################################################################################
#####Males
#################################################################################
hyenas$first.seen <- as.Date(hyenas$first.seen)
hyenas[hyenas$id == 'gaza','first.seen'] <- hyenas[hyenas$id == 'gaza','birthdate']
males <- filter(hyenas, clan == 'talek', status %in% c('i', 'immigrant'), sex == 'm')
##add males that never disperse - include them after they turn 5
males <- rbind(males, filter(hyenas, id %in% c('foz', 'ldv', 'pene', 'ziti')))
hyenas[hyenas$id %in% c('foz', 'ldv', 'pene','ziti'),]$first.seen <-
hyenas[hyenas$id %in% c('foz', 'ldv', 'pene','ziti'),]$birthdate + 365*5
males <- males[order(males$first.seen),]
males$end.year <- as.numeric(format(do.call(pmin, c(males[,c('death.date', 'disappeared')], na.rm = T)), '%Y'))
males <- males[,c('id', 'first.seen', 'end.year')]
males$start.year <- as.numeric(format(males$first.seen, '%Y'))
###Crocuta crocuta male contestants
ids <- filter(males, end.year >= 1988)
ids <- na.omit(ids)
ids <- filter(ids, start.year <= end.year)
contestants <- data.frame()
for(ID in ids$id){
contestants <- rbind(contestants, data.frame(id = ID,
first.seen = filter(ids, id == ID)$first.seen,
period = seq(from =filter(ids, id == ID)$start.year, to = filter(ids, id == ID)$end.year, by = 1)))
}
contestants <- filter(contestants, period >= 1988, period <= 2015)
contestants <- arrange(contestants, period, first.seen)
contestants$convention1 <- contestants$first.seen
contestants <- contestants %>% dplyr::select(period, id, convention1)
male.contestants <- contestants
#####Crocuta crocuta male initial.ranks
male.initial.ranks <- filter(male.contestants, period == 1988)$id
###Crocuta crocuta male interactions
male.interactions<- filter(aggsWinner, clan == 'talek',
aggressor %in% c(initial.ranks, contestants$id),
recip %in% c(initial.ranks, contestants$id),
Year >= 1988) %>%
semi_join(contestants, by = c('aggressor' = 'id', 'Year' = 'period')) %>%
semi_join(contestants, by = c('recip' = 'id', 'Year' = 'period')) %>%
rename(winner = aggressor, loser = recip, period = Year) %>%
dplyr::select(winner, loser, period)
save(file = '../3.hyena_data.RData',
list = c('female.contestants', 'female.initial.ranks', 'female.interactions',
'male.contestants', 'male.initial.ranks', 'male.interactions'))
setwd('../')