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05.clean_lh_data_behav_feed.R
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################################################################################
##### 5.0 Cleaning lion-hyena behavior and feeding data #####
################################################################################
########## 5.1 Set working directory & download packages/tables ##########
rm(list = ls())
setwd("~/Documents/R/LionHyena")
options(stringsAsFactors = FALSE)
library(tidyverse)
hyenadata::update_tables("1.2.88")
library(hyenadata)
#Load data
load("02.cleaned_lh_data.Rdata")
load("04.lh_data_mob.Rdata")
#Remove unwanted datasets
rm(lh.indvinfo)
rm(lh.indvsessions)
rm(lh.intx)
rm(lh.intx.all)
rm(lh.intx.checked)
rm(lh.intx.mob)
rm(lh.sessions.all)
rm(lh.sessions.checked)
#tblEats
data("tblEats")
tblEats <- tblEats[,1:5]
########## 5.2 Assign prey_type for all sessions with food_present ##########
#Join with tblEats (prey_type, prey_age, etc)
lh.indvbehav <- left_join(lh.indvbehav, tblEats, by = c("Session" = "session"))
#Check sessions with prey_type that have food_present == F
check.prey <- filter(lh.indvbehav, !is.na(prey_type))
check.prey <- filter(check.prey, Session %in% filter(lh.sessions, food_present == F)$Session)
length(unique(check.prey$Session)) #5 sessions
unique(check.prey[,c(2,6,11,12,15)]) #all scraps, not real food - okay
rm(check.prey)
#Fill in prey_type for sessions missing prey_type
unique(filter(lh.indvbehav, is.na(lh.indvbehav$prey_type))$Food)
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("top", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("top", lh.indvbehav$Food),]$prey_type <- "topi"
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("cow", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("cow", lh.indvbehav$Food),]$prey_type <- "cow"
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("gnu", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("gnu", lh.indvbehav$Food),]$prey_type <- "wildebeest"
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("wildebeast", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("wildebeast", lh.indvbehav$Food),]$prey_type <- "wildebeest"
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("hippo", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("hippo", lh.indvbehav$Food),]$prey_type <- "hippo"
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("zebra", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("zebra", lh.indvbehav$Food),]$prey_type <- "zebra"
unique(filter(lh.indvbehav, is.na(prey_type) &
grepl("tommy", lh.indvbehav$Food))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
grepl("tommy", lh.indvbehav$Food),]$prey_type <- "gazelle"
unique(filter(lh.indvbehav, is.na(prey_type) &
(grepl("small unbgualte", lh.indvbehav$Food) |
grepl("small ungualte", lh.indvbehav$Food)))$Food)
lh.indvbehav[is.na(lh.indvbehav$prey_type) &
(grepl("small unbgualte", lh.indvbehav$Food) |
grepl("small ungualte", lh.indvbehav$Food)),]$prey_type <- "gazelle"
#Check if same prey_type for all lines in a session
check.prey_type <- filter(lh.indvbehav, !is.na(prey_type))
check.prey_type <- check.prey_type %>% group_by(Session) %>%
summarise(num.carc = length(unique(prey_type)))
nrow(filter(check.prey_type, num.carc > 1)) #0
rm(check.prey_type)
#Fill in all lines for the session
for(i in 1:nrow(lh.indvbehav)){
session.i <- lh.indvbehav$Session[i]
feeding.i <- filter(lh.indvbehav, Session == session.i)
if(nrow(filter(feeding.i, is.na(prey_type))) > 0){
lh.indvbehav[lh.indvbehav$Session == session.i &
is.na(lh.indvbehav$prey_type),]$prey_type <-
lh.indvbehav[lh.indvbehav$Session == session.i &
!is.na(lh.indvbehav$prey_type),]$prey_type[1]
}
if(nrow(filter(feeding.i, is.na(prey_age))) > 0){
lh.indvbehav[lh.indvbehav$Session == session.i &
is.na(lh.indvbehav$prey_age),]$prey_age <-
lh.indvbehav[lh.indvbehav$Session == session.i &
!is.na(lh.indvbehav$prey_age),]$prey_age[1]
}
}
rm(session.i)
rm(feeding.i)
#Fill in prey_type for sessions that are still unknown
check.prey <- filter(lh.indvbehav, prey_type == "unknown" | is.na(prey_type))
check.prey <- filter(check.prey, Session %in% filter(lh.sessions, food_present == T)$Session)
length(unique(check.prey$Session)) #71 - everything not listed below is unknown, checked by TMM
#Serena sessions
# session prey_type prey_age
# "s10894" zebra
# "s11279.2" wildebeest
# "s11340" wildebeest
# "s13695" topi adult
# "s13829" zebra
# "s13944" zebra adult
# "s13964" zebra
# "s16267" elephant juvenile
# "s16358" buffalo adult
# "s3179" wildebeest
# "s3672" hippopotamus juvenile
# "s5434" wildebeest
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s10894",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s11279.2",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s11340",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s13695",]$prey_type <- "topi"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "topi") &
lh.indvbehav$Session == "s13695",]$prey_age <- "adult"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s13829",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s13944",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "zebra") &
lh.indvbehav$Session == "s13944",]$prey_age <- "adult"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s13964",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s16267",]$prey_type <- "elephant"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "elephant") &
lh.indvbehav$Session == "s16267",]$prey_age <- "juvenile"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s16358",]$prey_type <- "buffalo"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "buffalo") &
lh.indvbehav$Session == "s16358",]$prey_age <- "adult"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s3179",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s3672",]$prey_type <- "hippo"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "hippo") &
lh.indvbehav$Session == "s3672",]$prey_age <- "juvenile"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "s5434",]$prey_type <- "wildebeest"
#Talek sessions
# "t1245" wildebeest
# "t1569.3" buffalo
# "t6106" wildebeest adult
# "t6626" gazelle
# "t10764.2" zebra adult
# "t19572" wildebeest
# "t21394" buffalo
# "t24594" wildebeest
# "t29720" zebra
# "t3586" gazelle
# "t56284" warthog
# "t7228" topi adult
# "t77250" topi
# "t8012" wildebeest
# "t80207" topi
# "t82549" buffalo juvenile
# "t9114" gazelle
# "t91670" wildebeest
# "t93710" warthog
# "t94073" zebra
# "t96103" wildebeest juvenile
# "t96608" wildebeest
# "t96685" wildebeest
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t1245",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t1569.3",]$prey_type <- "buffalo"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t6106",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "wildebeest") &
lh.indvbehav$Session == "t6106",]$prey_age <- "adult"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t6626",]$prey_type <- "gazelle"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t10764.2",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "zebra") &
lh.indvbehav$Session == "t10764.2",]$prey_age <- "adult"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t19572",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t21394",]$prey_type <- "buffalo"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t24594",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t29720",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t3586",]$prey_type <- "gazelle"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t56284",]$prey_type <- "warthog"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t7228",]$prey_type <- "topi"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "topi") &
lh.indvbehav$Session == "t7228",]$prey_age <- "adult"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t77250",]$prey_type <- "topi"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t8012",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t80207",]$prey_type <- "topi"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t82549",]$prey_type <- "buffalo"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "buffalo") &
lh.indvbehav$Session == "t82549",]$prey_age <- "juvenile"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t9114",]$prey_type <- "gazelle"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t91670",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t93710",]$prey_type <- "warthog"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t94073",]$prey_type <- "zebra"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t96103",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "wildebeest") &
lh.indvbehav$Session == "t96103",]$prey_age <- "juvenile"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t96608",]$prey_type <- "wildebeest"
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "unknown") &
lh.indvbehav$Session == "t96685",]$prey_type <- "wildebeest"
#Recheck unknown sessions
check.prey <- filter(lh.indvbehav, prey_type == "unknown" | is.na(prey_type))
check.prey <- filter(check.prey, Session %in% filter(lh.sessions, food_present == T)$Session)
length(unique(check.prey$Session)) #37 left - all unknown, checked by TMM
#Fill in prey_type as unknown for these sessions
for(i in 1:nrow(lh.indvbehav)){
session.i <- lh.indvbehav$Session[i]
if(session.i %in% check.prey$Session){
lh.indvbehav$prey_type[i] <- "unknown"
}
}
rm(session.i)
#Double-check for remaining NAs
check.prey <- filter(lh.indvbehav, is.na(prey_type))
check.prey <- filter(check.prey, Session %in% filter(lh.sessions, food_present == T)$Session)
length(unique(check.prey$Session)) #0
rm(check.prey)
########## 5.3 Assign prey_age for all sessions with food_present ##########
#Fill in prey_age
unique(filter(lh.indvbehav, is.na(prey_age) &
grepl("subadult", lh.indvbehav$Food))$Food)
unique(filter(lh.indvbehav, is.na(prey_age) &
grepl("adult", lh.indvbehav$Food))$Food)
unique(filter(lh.indvbehav, is.na(prey_age) &
grepl("juvenile", lh.indvbehav$Food))$Food)
unique(filter(lh.indvbehav, is.na(prey_age) &
grepl("baby", lh.indvbehav$Food))$Food)
lh.indvbehav[(is.na(lh.indvbehav$prey_type) | lh.indvbehav$prey_type == "gazelle") &
lh.indvbehav$Session == "t91208",]$prey_age <- "juvenile"
########## 5.4 Assign carc_cat for all sessions with food_present ##########
#Categorize carcasses by species into the categories used for tblFeedingScans
lh.indvbehav$carc_cat <- NA
summary(as.factor(lh.indvbehav$prey_type))
summary(as.factor(lh.indvbehav$prey_age))
#Assume adult when prey_age is NA
#Adults
lh.indvbehav[(lh.indvbehav$prey_type == "buffalo" | lh.indvbehav$prey_type == "elephant" |
lh.indvbehav$prey_type == "giraffe" | lh.indvbehav$prey_type == "hippo") &
!is.na(lh.indvbehav$prey_type) &
(lh.indvbehav$prey_age != "juvenile" | is.na(lh.indvbehav$prey_age)),]$carc_cat <- "xl"
lh.indvbehav[(lh.indvbehav$prey_type == "cow" | lh.indvbehav$prey_type == "hartebeest" |
lh.indvbehav$prey_type == "topi" | lh.indvbehav$prey_type == "wildebeest" |
lh.indvbehav$prey_type == "zebra") & !is.na(lh.indvbehav$prey_type) &
(lh.indvbehav$prey_age != "juvenile" | is.na(lh.indvbehav$prey_age)),]$carc_cat <- "l"
lh.indvbehav[(lh.indvbehav$prey_type == "gazelle" | lh.indvbehav$prey_type == "impala" |
lh.indvbehav$prey_type == "shoat"| lh.indvbehav$prey_type == "warthog") &
!is.na(lh.indvbehav$prey_type) &
(lh.indvbehav$prey_age != "juvenile" | is.na(lh.indvbehav$prey_age)),]$carc_cat <- "m"
#Juveniles
lh.indvbehav[(lh.indvbehav$prey_type == "buffalo" | lh.indvbehav$prey_type == "elephant" |
lh.indvbehav$prey_type == "giraffe" | lh.indvbehav$prey_type == "hippo") &
!is.na(lh.indvbehav$prey_type) &
(lh.indvbehav$prey_age == "juvenile" & !is.na(lh.indvbehav$prey_age)),]$carc_cat <- "xl"
lh.indvbehav[(lh.indvbehav$prey_type == "cow" | lh.indvbehav$prey_type == "hartebeest" |
lh.indvbehav$prey_type == "topi" | lh.indvbehav$prey_type == "wildebeest" |
lh.indvbehav$prey_type == "zebra") & !is.na(lh.indvbehav$prey_type) &
(lh.indvbehav$prey_age == "juvenile" & !is.na(lh.indvbehav$prey_age)),]$carc_cat <- "m"
lh.indvbehav[(lh.indvbehav$prey_type == "gazelle" | lh.indvbehav$prey_type == "impala" |
lh.indvbehav$prey_type == "shoat"| lh.indvbehav$prey_type == "warthog") &
!is.na(lh.indvbehav$prey_type) &
(lh.indvbehav$prey_age == "juvenile" & !is.na(lh.indvbehav$prey_age)),]$carc_cat <- "s"
summary(as.factor(lh.indvbehav$carc_cat))
#Any remaining to be assigned?
nrow(filter(lh.indvbehav, prey_type != "unknown" & !is.na(prey_type) & is.na(carc_cat))) #0
#Final check - be sure prey_type, prey_age, and carc_cat are the same for all lines in a session
check.prey_type <- lh.indvbehav %>% group_by(Session) %>%
summarise(num.carc = length(unique(prey_type)))
nrow(filter(check.prey_type, num.carc > 1)) #0
rm(check.prey_type)
check.prey_age <- lh.indvbehav %>% group_by(Session) %>%
summarise(num.carc = length(unique(prey_age)))
nrow(filter(check.prey_age, num.carc > 1)) #0
rm(check.prey_age)
check.carc_cat <- lh.indvbehav %>% group_by(Session) %>%
summarise(num.carc = length(unique(carc_cat)))
nrow(filter(check.carc_cat, num.carc > 1)) #0
rm(check.carc_cat)
########## 5.5 Create final dataset lh.sessions.food ##########
lh.indvbehav.food <- lh.indvbehav[,c(2,12,13,16)]
lh.indvbehav.food <- unique(lh.indvbehav.food)
lh.sessions.food <- left_join(lh.sessions, lh.indvbehav.food, by = "Session")
#Check that food_present matches prey_type and carc_cat columns
nrow(filter(lh.sessions.food, food_present == T & is.na(prey_type))) #0
nrow(filter(lh.sessions.food, food_present == T & is.na(carc_cat))) #37 unknown prey_type
nrow(filter(lh.sessions.food, food_present == F & !is.na(prey_type))) #5 - checked earlier, okay
lh.sessions.food[lh.sessions.food$food_present == F & !is.na(lh.sessions.food$prey_type),]$prey_type <- NA
lh.sessions.food[lh.sessions.food$food_present == F & !is.na(lh.sessions.food$prey_age),]$prey_age <- NA
lh.sessions.food[lh.sessions.food$food_present == F & !is.na(lh.sessions.food$carc_cat),]$carc_cat <- NA
#Clean columns
lh.sessions.food$prey_type <- as.factor(lh.sessions.food$prey_type)
lh.sessions.food$prey_age <- as.factor(lh.sessions.food$prey_age)
lh.sessions.food$carc_cat <- as.factor(lh.sessions.food$carc_cat)
lh.sessions.food$carc_cat <- ordered(lh.sessions.food$carc_cat, levels = c("s", "m", "l", "xl"))
#Remove lh.indvbehav.food - used to determine food at session level
rm(lh.indvbehav.food)
########## 5.6 Categorize behaviors in mobbing sessions ##########
#Filter lh.indvbehav to only sessions with mobbing
lh.indvbehav.behav <- filter(lh.indvbehav, Session %in% lh.indvbehav.mob$session)
lh.indvbehav.behav <- left_join(lh.indvbehav.behav, lh.indvbehav.mob[c(1,12)], by = c("ID" = "event"))
#Create behav_cat and assign mobs
lh.indvbehav.behav$behav_cat <- NA
lh.indvbehav.behav[!is.na(lh.indvbehav.behav$mobID) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "mob"
##### Assign behaviors to feeding category #####
unique(filter(lh.indvbehav.behav, grepl("fd", lh.indvbehav.behav$Behavior) &
!grepl("drop", lh.indvbehav.behav$Behavior) &
!grepl("abandon", lh.indvbehav.behav$Behavior) &
!grepl("lv fd", lh.indvbehav.behav$Behavior) &
!grepl("attempt", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("fd", lh.indvbehav.behav$Behavior) &
!grepl("drop", lh.indvbehav.behav$Behavior) &
!grepl("abandon", lh.indvbehav.behav$Behavior) &
!grepl("lv fd", lh.indvbehav.behav$Behavior) &
!grepl("attempt", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("feed", lh.indvbehav.behav$Behavior) &
!grepl("other", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("feed", lh.indvbehav.behav$Behavior) &
!grepl("other", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("food", lh.indvbehav.behav$Behavior) &
!grepl("find", lh.indvbehav.behav$Behavior) &
!grepl("tussel", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("food", lh.indvbehav.behav$Behavior) &
!grepl("find", lh.indvbehav.behav$Behavior) &
!grepl("tussel", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("chew", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("chew", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("scrap", lh.indvbehav.behav$Behavior) &
!grepl("lose", lh.indvbehav.behav$Behavior) &
!grepl("abandon", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("scrap", lh.indvbehav.behav$Behavior) &
!grepl("lose", lh.indvbehav.behav$Behavior) &
!grepl("abandon", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("carr", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("carr", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("steal", lh.indvbehav.behav$Behavior) &
!grepl("attempt", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("steal", lh.indvbehav.behav$Behavior) &
!grepl("attempt", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("carc", lh.indvbehav.behav$Behavior) &
(grepl("get", lh.indvbehav.behav$Behavior) |
grepl("take", lh.indvbehav.behav$Behavior) |
grepl("grab", lh.indvbehav.behav$Behavior) |
grepl("w/", lh.indvbehav.behav$Behavior) |
grepl("has", lh.indvbehav.behav$Behavior) |
grepl("tow", lh.indvbehav.behav$Behavior) |
grepl("move", lh.indvbehav.behav$Behavior) |
grepl("tug", lh.indvbehav.behav$Behavior) |
grepl("return", lh.indvbehav.behav$Behavior) |
grepl("reclaim", lh.indvbehav.behav$Behavior) |
grepl("drag", lh.indvbehav.behav$Behavior)) &
!grepl("rushes to grab carc", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("carc", lh.indvbehav.behav$Behavior) &
(grepl("get", lh.indvbehav.behav$Behavior) |
grepl("take", lh.indvbehav.behav$Behavior) |
grepl("grab", lh.indvbehav.behav$Behavior) |
grepl("w/", lh.indvbehav.behav$Behavior) |
grepl("has", lh.indvbehav.behav$Behavior) |
grepl("tow", lh.indvbehav.behav$Behavior) |
grepl("move", lh.indvbehav.behav$Behavior) |
grepl("tug", lh.indvbehav.behav$Behavior) |
grepl("return", lh.indvbehav.behav$Behavior) |
grepl("reclaim", lh.indvbehav.behav$Behavior) |
grepl("drag", lh.indvbehav.behav$Behavior)) &
!grepl("rushes to grab carc", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, (grepl("spine", lh.indvbehav.behav$Behavior) |
grepl("pelvis", lh.indvbehav.behav$Behavior) |
grepl("leg", lh.indvbehav.behav$Behavior) |
grepl("bone", lh.indvbehav.behav$Behavior) |
grepl("steal", lh.indvbehav.behav$Behavior) |
grepl("scapula", lh.indvbehav.behav$Behavior) |
grepl("skin", lh.indvbehav.behav$Behavior)) &
!grepl("foreleg", lh.indvbehav.behav$Behavior) &
!grepl("drop", lh.indvbehav.behav$Behavior) &
!grepl("attempt", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[(grepl("spine", lh.indvbehav.behav$Behavior) |
grepl("pelvis", lh.indvbehav.behav$Behavior) |
grepl("leg", lh.indvbehav.behav$Behavior) |
grepl("bone", lh.indvbehav.behav$Behavior) |
grepl("steal", lh.indvbehav.behav$Behavior) |
grepl("scapula", lh.indvbehav.behav$Behavior) |
grepl("skin", lh.indvbehav.behav$Behavior)) &
!grepl("foreleg", lh.indvbehav.behav$Behavior) &
!grepl("drop", lh.indvbehav.behav$Behavior) &
!grepl("attempt", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("picks up kill", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("picks up kill", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "fd"
unique(filter(lh.indvbehav.behav, grepl("tug of war", lh.indvbehav.behav$Behavior))$Behavior)
lh.indvbehav.behav[grepl("tug of war", lh.indvbehav.behav$Behavior),]$behav_cat <- "fd"
#Remove feeding on introduced foods (dog biscuit)
unique(filter(lh.indvbehav.behav, grepl("dog", lh.indvbehav.behav$Food))$Food)
lh.indvbehav.behav[grepl("dog", lh.indvbehav.behav$Food),]$behav_cat <- NA
#Check for mismatch between behav_cat and Food columns
unique(filter(lh.indvbehav.behav, behav_cat == "fd" & is.na(Food))$Behavior) #ok - all feeding
unique(filter(lh.indvbehav.behav, (is.na(behav_cat) | behav_cat != "fd") & !is.na(Food))$Behavior) #ok - all NOT feeding
##### Assign affiliative behaviors to categories #####
unique(filter(lh.indvbehav.behav, (grepl("soc", lh.indvbehav.behav$Behavior) |
grepl("son snf", lh.indvbehav.behav$Behavior) |
grepl("so snif", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[(grepl("soc", lh.indvbehav.behav$Behavior) |
grepl("son snf", lh.indvbehav.behav$Behavior) |
grepl("so snif", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "soc snf"
lh.indvbehav.behav[lh.indvbehav.behav$Session == "t61001" &
grepl("brt snf spot", lh.indvbehav.behav$Behavior),]$behav_cat <- "soc snf"
lh.indvbehav.behav[lh.indvbehav.behav$Session == "t31592" &
grepl("brt snf", lh.indvbehav.behav$Behavior),]$behav_cat <- "soc snf"
unique(filter(lh.indvbehav.behav, grepl("parallel", lh.indvbehav.behav$Behavior) &
!grepl("t2", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("parallel", lh.indvbehav.behav$Behavior) &
!grepl("t2", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "parallel wlk"
unique(filter(lh.indvbehav.behav, grepl("pres", lh.indvbehav.behav$Behavior) &
!grepl("hyenas", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("pres", lh.indvbehav.behav$Behavior) &
!grepl("hyenas", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "pres"
##### Assign vocal behaviors to categories #####
unique(filter(lh.indvbehav.behav, grepl("low", lh.indvbehav.behav$Behavior) &
!grepl("follow", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("low", lh.indvbehav.behav$Behavior) &
!grepl("follow", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "low"
unique(filter(lh.indvbehav.behav, (grepl("whoop", lh.indvbehav.behav$Behavior) |
grepl("Whoop", lh.indvbehav.behav$Behavior) |
grepl("whp", lh.indvbehav.behav$Behavior) |
grepl("woop", lh.indvbehav.behav$Behavior) |
grepl("wp", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[(grepl("whoop", lh.indvbehav.behav$Behavior) |
grepl("Whoop", lh.indvbehav.behav$Behavior) |
grepl("whp", lh.indvbehav.behav$Behavior) |
grepl("woop", lh.indvbehav.behav$Behavior) |
grepl("wp", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "whoop"
unique(filter(lh.indvbehav.behav, grepl("alarm", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("alarm", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "alarm rumble"
unique(filter(lh.indvbehav.behav, (grepl("gig", lh.indvbehav.behav$Behavior) |
grepl("yikker", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[(grepl("gig", lh.indvbehav.behav$Behavior) |
grepl("yikker", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "giggle"
unique(filter(lh.indvbehav.behav, grepl("groan", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("groan", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "groan"
unique(filter(lh.indvbehav.behav, grepl("growl", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("growl", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "growl"
unique(filter(lh.indvbehav.behav, (grepl("squeal", lh.indvbehav.behav$Behavior) |
grepl("squel", lh.indvbehav.behav$Behavior) |
grepl("sqeal", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[(grepl("squeal", lh.indvbehav.behav$Behavior) |
grepl("squel", lh.indvbehav.behav$Behavior) |
grepl("sqeal", lh.indvbehav.behav$Behavior)) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "squeal"
##### Assign remaining behaviors to categories #####
unique(filter(lh.indvbehav.behav, grepl("paste", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("paste", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "paste"
#Distances recorded during scans (often scanned behavior is "here")
unique(filter(lh.indvbehav.behav, grepl("scan", lh.indvbehav.behav$Behavior) &
!grepl("fd", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("scan", lh.indvbehav.behav$Behavior) &
!grepl("fd", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "scan"
unique(filter(lh.indvbehav.behav, grepl("dis", lh.indvbehav.behav$Behavior) &
!grepl("displace", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat))$Behavior)
lh.indvbehav.behav[grepl("dis", lh.indvbehav.behav$Behavior) &
!grepl("displace", lh.indvbehav.behav$Behavior) &
is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- "dist"
#Add any distances from lions that were missing a behavior
unique(filter(lh.indvbehav.behav, is.na(behav_cat) & !is.na(Distance) &
grepl("lion", lh.indvbehav.behav$Target) &
!grepl("lion", lh.indvbehav.behav$Hyena))$Behavior)
lh.indvbehav.behav[is.na(lh.indvbehav.behav$behav_cat) & !is.na(lh.indvbehav.behav$Distance) &
grepl("lion", lh.indvbehav.behav$Target) &
!grepl("lion", lh.indvbehav.behav$Hyena),]$behav_cat <- "dist"
##### Uncategorized behaviors #####
sort(table(filter(lh.indvbehav.behav, is.na(behav_cat))$Behavior), decreasing = T)
unique(filter(lh.indvbehav.behav, is.na(behav_cat))$Behavior)
#Checked by TMM
#Check categorized behaviors
sort(table(lh.indvbehav.behav$behav_cat), decreasing = T)
########## 5.7 Categorize feeding by size of piece in mobbing sessions ##########
lh.indvbehav.behav$size_cat <- NA
##### Look in lh.indvbehav$Food #####
#Pieces
unique(filter(lh.indvbehav.behav, lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
!(grepl("scrap", lh.indvbehav.behav$Food) | grepl("skin", lh.indvbehav.behav$Food)) &
(grepl("leg", lh.indvbehav.behav$Food) | grepl("rib", lh.indvbehav.behav$Food) |
grepl("scapula", lh.indvbehav.behav$Food) | grepl("spin", lh.indvbehav.behav$Food) |
grepl("pelvis", lh.indvbehav.behav$Food) | grepl("vertibrae", lh.indvbehav.behav$Food) |
grepl("head", lh.indvbehav.behav$Food) | grepl("riib", lh.indvbehav.behav$Food) |
grepl("meat", lh.indvbehav.behav$Food)))$Food)
lh.indvbehav.behav[lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
!(grepl("scrap", lh.indvbehav.behav$Food) | grepl("skin", lh.indvbehav.behav$Food)) &
(grepl("leg", lh.indvbehav.behav$Food) | grepl("rib", lh.indvbehav.behav$Food) |
grepl("scapula", lh.indvbehav.behav$Food) | grepl("spin", lh.indvbehav.behav$Food) |
grepl("pelvis", lh.indvbehav.behav$Food) | grepl("vertibrae", lh.indvbehav.behav$Food) |
grepl("head", lh.indvbehav.behav$Food) | grepl("riib", lh.indvbehav.behav$Food) |
grepl("meat", lh.indvbehav.behav$Food)),]$size_cat <- "piece"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "spine and skull scrap" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "piece"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "subadult topi carcass piece" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "piece"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "gnu \"something\"" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "piece"
#Scraps
unique(filter(lh.indvbehav.behav, is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("scrap", lh.indvbehav.behav$Food) | grepl("bone", lh.indvbehav.behav$Food) |
grepl("skin", lh.indvbehav.behav$Food) | grepl("old", lh.indvbehav.behav$Food) |
grepl("jaw", lh.indvbehav.behav$Food) | grepl("offal", lh.indvbehav.behav$Food) |
grepl("rumen", lh.indvbehav.behav$Food) | grepl("horn", lh.indvbehav.behav$Food) |
grepl("skull", lh.indvbehav.behav$Food) | grepl("scap", lh.indvbehav.behav$Food) |
grepl("srap", lh.indvbehav.behav$Food)))$Food)
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("scrap", lh.indvbehav.behav$Food) | grepl("bone", lh.indvbehav.behav$Food) |
grepl("skin", lh.indvbehav.behav$Food) | grepl("old", lh.indvbehav.behav$Food) |
grepl("jaw", lh.indvbehav.behav$Food) | grepl("offal", lh.indvbehav.behav$Food) |
grepl("rumen", lh.indvbehav.behav$Food) | grepl("horn", lh.indvbehav.behav$Food) |
grepl("skull", lh.indvbehav.behav$Food) | grepl("scap", lh.indvbehav.behav$Food) |
grepl("srap", lh.indvbehav.behav$Food)),]$size_cat <- "scrap"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "few mouthfulls" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "scrap"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "something with feathers" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "scrap"
#Carcasses
unique(filter(lh.indvbehav.behav, is.na(lh.indvbehav.behav$size_cat) & !grepl("site", lh.indvbehav.behav$Food) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("carcass", lh.indvbehav.behav$Food) | grepl("carc", lh.indvbehav.behav$Food) |
grepl("kill", lh.indvbehav.behav$Food)))$Food)
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) & !grepl("site", lh.indvbehav.behav$Food) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("carcass", lh.indvbehav.behav$Food) | grepl("carc", lh.indvbehav.behav$Food) |
grepl("kill", lh.indvbehav.behav$Food)),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "buffalo" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "cow" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "zebra" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "giraffe" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "impala" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "wildebeast" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Food == "topi cascass" &
!is.na(lh.indvbehav.behav$Food),]$size_cat <- "carcass"
##### For ones still blank, get info from lh.indvbehav$Behavior/Notes #####
View(filter(lh.indvbehav.behav, (is.na(lh.indvbehav.behav$size_cat) | lh.indvbehav.behav$size_cat == "carcass") &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("scrap", lh.indvbehav.behav$Behavior) | grepl("scrap", lh.indvbehav.behav$Notes)) &
!grepl("MIKE", lh.indvbehav.behav$Notes)))
lh.indvbehav.behav[(is.na(lh.indvbehav.behav$size_cat) | lh.indvbehav.behav$size_cat == "carcass") &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("scrap", lh.indvbehav.behav$Behavior) | grepl("scrap", lh.indvbehav.behav$Notes)) &
!grepl("MIKE", lh.indvbehav.behav$Notes),]$size_cat <- "scrap"
View(filter(lh.indvbehav.behav, (is.na(lh.indvbehav.behav$size_cat) | lh.indvbehav.behav$size_cat == "carcass") &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("leg", lh.indvbehav.behav$Behavior) | grepl("piece", lh.indvbehav.behav$Behavior))))
lh.indvbehav.behav[(is.na(lh.indvbehav.behav$size_cat) | lh.indvbehav.behav$size_cat == "carcass") &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("leg", lh.indvbehav.behav$Behavior) | grepl("piece", lh.indvbehav.behav$Behavior)),]$size_cat <- "piece"
View(filter(lh.indvbehav.behav, is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("carc", lh.indvbehav.behav$Behavior) | grepl("kill", lh.indvbehav.behav$Behavior))))
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("carc", lh.indvbehav.behav$Behavior) | grepl("kill", lh.indvbehav.behav$Behavior)),]$size_cat <- "carcass"
View(filter(lh.indvbehav.behav, (is.na(lh.indvbehav.behav$size_cat) | lh.indvbehav.behav$size_cat == "carcass") &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
!grepl("carc", lh.indvbehav.behav$Behavior) & !grepl("carry", lh.indvbehav.behav$Notes) &
!grepl("pick", lh.indvbehav.behav$Notes) &
(grepl("w/", lh.indvbehav.behav$Behavior) | grepl("with", lh.indvbehav.behav$Behavior)) &
(grepl("av", lh.indvbehav.behav$Behavior) | grepl("bo", lh.indvbehav.behav$Behavior))))
lh.indvbehav.behav[(is.na(lh.indvbehav.behav$size_cat) | lh.indvbehav.behav$size_cat == "carcass") &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
!grepl("carc", lh.indvbehav.behav$Behavior) & !grepl("carry", lh.indvbehav.behav$Notes) &
!grepl("pick", lh.indvbehav.behav$Notes) &
(grepl("w/", lh.indvbehav.behav$Behavior) | grepl("with", lh.indvbehav.behav$Behavior)) &
(grepl("av", lh.indvbehav.behav$Behavior) | grepl("bo", lh.indvbehav.behav$Behavior)),]$size_cat <- "piece"
View(filter(lh.indvbehav.behav, is.na(lh.indvbehav.behav$size_cat) & !grepl("dog", lh.indvbehav.behav$Food) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("steal", lh.indvbehav.behav$Behavior) | grepl("stl", lh.indvbehav.behav$Behavior) |
grepl("steal", lh.indvbehav.behav$Behavior) | grepl("stl", lh.indvbehav.behav$Behavior) |
grepl("app", lh.indvbehav.behav$Behavior))))
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) & !grepl("dog", lh.indvbehav.behav$Food) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
(grepl("steal", lh.indvbehav.behav$Behavior) | grepl("stl", lh.indvbehav.behav$Behavior) |
grepl("steal", lh.indvbehav.behav$Behavior) | grepl("stl", lh.indvbehav.behav$Behavior) |
grepl("app", lh.indvbehav.behav$Behavior)),]$size_cat <- "piece"
View(filter(lh.indvbehav.behav, is.na(lh.indvbehav.behav$size_cat) & !grepl("dog", lh.indvbehav.behav$Food) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
!grepl("little", lh.indvbehav.behav$Notes) &
(grepl("fd", lh.indvbehav.behav$Behavior) | grepl("feed", lh.indvbehav.behav$Behavior))))
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) & !grepl("dog", lh.indvbehav.behav$Food) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
!grepl("little", lh.indvbehav.behav$Notes) &
(grepl("fd", lh.indvbehav.behav$Behavior) | grepl("feed", lh.indvbehav.behav$Behavior)),]$size_cat <- "carcass"
lh.indvbehav.behav[is.na(lh.indvbehav.behav$size_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$Notes == "lion abandon carc hyenas rush in, very little left" &
!is.na(lh.indvbehav.behav$Notes),]$size_cat <- "scrap"
lh.indvbehav.behav[lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat) &
lh.indvbehav.behav$notes == "gazelle?, skin, lion present" &
!is.na(lh.indvbehav.behav$notes),]$size_cat <- "scrap"
nrow(filter(lh.indvbehav.behav, is.na(size_cat) & behav_cat == "fd")) #0
nrow(filter(lh.indvbehav.behav, !is.na(size_cat) & behav_cat != "fd")) #0
########## 5.8 Assign final food size in mobbing sessions ##########
lh.indvbehav.behav$food_size <- NA
summary(as.factor(lh.indvbehav.behav$carc_cat))
summary(as.factor(lh.indvbehav.behav$size_cat))
#Clear size_cat and behav_cat for t78815 "old hardened piece of hide" - not real food
lh.indvbehav.behav[is.na(lh.indvbehav.behav$prey_type) & is.na(lh.indvbehav.behav$carc_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat),]$size_cat <- NA
lh.indvbehav.behav[is.na(lh.indvbehav.behav$prey_type) & is.na(lh.indvbehav.behav$carc_cat) &
lh.indvbehav.behav$behav_cat == "fd" & !is.na(lh.indvbehav.behav$behav_cat),]$behav_cat <- NA
#Assign food_size based on this table
# Carcass size: small medium large extra-large
# Scraps xs xs xs xs
# Pieces xs s s m
# Carcass s m l xl
for(i in 1:nrow(lh.indvbehav.behav)){
#Extra-large carcasses (buffalo, giraffe, hippo of all ages)
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "xl" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "carcass"){
lh.indvbehav.behav$food_size[i] <- "xl"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "xl" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "piece"){
lh.indvbehav.behav$food_size[i] <- "m"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "xl" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "scrap"){
lh.indvbehav.behav$food_size[i] <- "xs"
}
#Large carcasses (cow, topi, wildebeest, zebra)
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "l" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "carcass"){
lh.indvbehav.behav$food_size[i] <- "l"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "l" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "piece"){
lh.indvbehav.behav$food_size[i] <- "s"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "l" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "scrap"){
lh.indvbehav.behav$food_size[i] <- "xs"
}
#Medium carcasses (gazelle, impala, shoat, warthog; also juvenile: cow, topi, wildebeest, zebra)
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "m" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "carcass"){
lh.indvbehav.behav$food_size[i] <- "m"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "m" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "piece"){
lh.indvbehav.behav$food_size[i] <- "s"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "m" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "scrap"){
lh.indvbehav.behav$food_size[i] <- "xs"
}
#Small carcasses (juvenile: gazelle, impala, shoat, warthog)
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "s" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "carcass"){
lh.indvbehav.behav$food_size[i] <- "s"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "s" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "piece"){
lh.indvbehav.behav$food_size[i] <- "xs"
}
if(!is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$carc_cat[i] == "s" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "scrap"){
lh.indvbehav.behav$food_size[i] <- "xs"
}
#Unknown carcasses (assume carc_cat = m)
if(is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$prey_type[i] == "unknown" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "carcass"){
lh.indvbehav.behav$food_size[i] <- "m"
}
if(is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$prey_type[i] == "unknown" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "piece"){
lh.indvbehav.behav$food_size[i] <- "s"
}
if(is.na(lh.indvbehav.behav$carc_cat[i]) & lh.indvbehav.behav$prey_type[i] == "unknown" &
!is.na(lh.indvbehav.behav$size_cat[i]) & lh.indvbehav.behav$size_cat[i] == "scrap"){
lh.indvbehav.behav$food_size[i] <- "xs"
}
}
########## 5.9 Create final dataset lh.indvbehav.food ##########
#Clean and create final dataset
lh.indvbehav.food <- lh.indvbehav.behav[,c(1:11,17:18,12:13,16,19:20)]
colnames(lh.indvbehav.food)[1] <- "event"
colnames(lh.indvbehav.food)[2] <- "session"
colnames(lh.indvbehav.food)[3] <- "hyena"
colnames(lh.indvbehav.food)[4] <- "time"
colnames(lh.indvbehav.food)[5] <- "order"
colnames(lh.indvbehav.food)[6] <- "behavior"
colnames(lh.indvbehav.food)[7] <- "target"
colnames(lh.indvbehav.food)[8] <- "distance"
colnames(lh.indvbehav.food)[9] <- "leader"
colnames(lh.indvbehav.food)[10] <- "food"
colnames(lh.indvbehav.food)[11] <- "notes"
lh.indvbehav.food$behav_cat <- as.factor(lh.indvbehav.food$behav_cat)
lh.indvbehav.food$prey_type <- as.factor(lh.indvbehav.food$prey_type)
lh.indvbehav.food$prey_age <- as.factor(lh.indvbehav.food$prey_age)
lh.indvbehav.food$carc_cat <- as.factor(lh.indvbehav.food$carc_cat)
lh.indvbehav.food$carc_cat <- ordered(lh.indvbehav.food$carc_cat, levels = c("s", "m", "l", "xl"))
lh.indvbehav.food$size_cat <- as.factor(lh.indvbehav.food$size_cat)
lh.indvbehav.food$food_size <- as.factor(lh.indvbehav.food$food_size)
lh.indvbehav.food$food_size <- ordered(lh.indvbehav.food$food_size, levels = c("xs", "s", "m", "l", "xl"))
summary(lh.indvbehav.food)
summary(filter(lh.indvbehav.food, behav_cat == "fd"))
save(file = "06.lh_data_behav_food.Rdata", list = c("lh.sessions.food", "lh.indvbehav.food"))