#Examples of models used in Klein et al. Sleep Maps study. Not every subset or model was used in our analyses.

subset(bees,bees$d_n=="d")->dbees				#d = day; n = night
subset(bees,bees$d_n=="n")->nbees
subset(bees,bees$Year=="first")->first          #first year, entire dataset
subset(bees,bees$Year=="second")->second        #second year, entire dataset
subset(bees,bees$Caste=="f")->foragers          #only have forager data for first year
subset(bees,bees$Caste=="n")->nurses 
subset(bees,bees$Caste=="fs")->storers
subset(bees,bees$Caste=="c")->cleaners
subset(cleaners,cleaners$Year=="first")->firstyearcleaners 
subset(cleaners,cleaners$Year=="second")->secondyearcleaners 
subset(bees,bees$Beh=="awake")->awakebees       #both years, awake bees (important for 2006, when T is the response variable & want to analyze across castes; only have data for awake condition; sleep data insufficient for non-foragers  
subset(bees,bees$Beh=="asleep")->asleepbees
subset(awakebees,awakebees$Caste=="f")->awakeforagers
subset(awakebees,awakebees$Caste=="n")->awakenurses
subset(awakebees,awakebees$Caste=="fs")->awakestorers
subset(awakebees,awakebees$Caste=="c")->awakecleaners
subset(asleepbees,asleepbees$Caste=="f")->asleepforagers
subset(asleepbees,asleepbees$Caste=="n")->asleepnurses
subset(asleepbees,asleepbees$Caste=="fs")->asleepstorers
subset(asleepbees,asleepbees$Caste=="c")->asleepcleaners
subset(awakebees,awakebees$Year=="first")->firstyearawakebees      #first year, analysis T of awake bees across castes
subset(awakebees,awakebees$Year=="second")->secondyearawakebees
subset(firstyearawakebees,firstyearawakebees$Caste=="c")->firstyearawakecleaners
subset(secondyearawakebees,secondyearawakebees$Caste=="c")->secondyearawakecleaners
subset(bees,bees$Behav=="0")->zerobees   
subset(zerobees,zerobees$Caste=="f")->zeroforagers      
subset(zerobees,zerobees$Caste=="n")->zeronurses   
subset(zerobees,zerobees$Caste=="fs")->zerostorers 
subset(zerobees,zerobees$Caste=="c")->zerocleaners       
subset(zerobees,zerobees$Year=="first")->firstyearzerobees
subset(zerobees,zerobees$Year=="second")->secondyearzerobees
subset(firstyearzerobees,firstyearzerobees$Caste=="c")->firstyearzerocleaners
subset(secondyearzerobees,secondyearzerobees$Caste=="c")->secondyearzerocleaners
subset(bees,bees$Behav=="dv")->dvbees 
subset(dvbees,dvbees$Year=="first")->firstyeardvbees
subset(dvbees,dvbees$Year=="second")->secondyeardvbees
subset(bees,bees$Behav=="awake")->Behavawakebees       
subset(Behasleepcleaners,Behasleepcleaners$Year=="first")->firstyearBehasleepcleaners
subset(Behasleepcleaners,Behasleepcleaners$Year=="second")->secondyearBehasleepcleaners
rbind(zerobees,Behavawakebees)->zeroawake       #comparing 0 vs. awake, both years 
rbind(firstyearzerobees,firstyearBehavawakebees)->firstyearzeroawake
rbind(firstyearzeroforagers,firstyearBehavawakeforagers)->firstyearzeroawakeforagers    #compare foragers 0 vs. awake
subset(firstyearzeroawakeforagers ,firstyearzeroawakeforagers$Newforager=="no")->firstyearzeroawakeforagers_nonewforagers    #compare foragers 0 vs. awake, but only after removing added foragers (added in 2006 when sample was dwindling)
rbind(secondyearzerobees,secondyearBehavawakebees)->secondyearzeroawake
rbind(dvbees,Behavawakebees)->dvawake       #comparing dv vs. awake, both years 
rbind(firstyeardvbees,firstyearBehavawakebees)->firstyeardvawake
rbind(secondyeardvbees,secondyearBehavawakebees)->secondyeardvawake
subset(bees,bees$Newforager=="no")->nonewbees       #yes & no only in rows for 2006 data, but can be used for entire dataset (all castes), eliminates all extra foragers, added during 2006 to supplement dwindling sample
subset(nonewbees,nonewbees$Caste=="f")->nonewbees_foragers
subset(nonewbees_foragers,nonewbees_foragers$Behav=="awake")->nonewbees_foragers_awake


#FORAGERS: Tbody & d_n (only data for 2006)
model1a1 = lmer(Tbody~(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model1a2 = lmer(Tbody~d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model11 = lmer(Tbody~Beh+d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model1a4 = lmer(Tbody~Beh*d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model11 = lmer(Tbody~Behav+d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model1d = lmer(Tbody~d_n+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model1e = lmer(Tbody~d_n+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model12 = lmer(Tbody~d_n+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)
model2a = lmer(Tbodysurr~d_n+(1|Bee), data=foragers, na.action=na.omit)
model2b = lmer(Tbodysurr~Beh*d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model2c = lmer(Tbodysurr~Behav*d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model2d = lmer(Tbodysurr~d_n+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model2e = lmer(Tbodysurr~d_n+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model2f = lmer(Tbodysurr~d_n+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)

#FORAGERS: Tbody & UnderColor_majority (only data for 2006)
model3b = lmer(Tbody~Beh*UnderColor_majority+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model3c = lmer(Tbody~Behav*UnderColor_majority+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model3d = lmer(Tbody~UnderColor_majority+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model3e = lmer(Tbody~UnderColor_majority+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model3f = lmer(Tbody~UnderColor_majority+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)
model4b = lmer(Tbodysurr~Beh*UnderColor_majority+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model4c = lmer(Tbodysurr~Behav*UnderColor_majority+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model4d = lmer(Tbodysurr~UnderColor_majority+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model4e = lmer(Tbodysurr~UnderColor_majority+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model4f = lmer(Tbodysurr~UnderColor_majority+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)

#FORAGERS: Tbody & UnderColor_white (only data for 2006)
model5b = lmer(Tbody~Beh*UnderColor_white+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model5c = lmer(Tbody~Behav*UnderColor_white+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model5d = lmer(Tbody~UnderColor_white+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model5e = lmer(Tbody~UnderColor_white+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model5f = lmer(Tbody~UnderColor_white+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)
model6b = lmer(Tbodysurr~Beh*UnderColor_white+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model6c = lmer(Tbodysurr~Behav*UnderColor_white+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model6d = lmer(Tbodysurr~UnderColor_white+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model6e = lmer(Tbodysurr~UnderColor_white+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model6f = lmer(Tbodysurr~UnderColor_white+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)

#FORAGERS: Tbody & cm_edge (only data for 2006)
model7b = lmer(Tbody~Beh*cm_edge+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model7c = lmer(Tbody~Behav*cm_edge+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model7d = lmer(Tbody~cm_edge+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model7e = lmer(Tbody~cm_edge+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model7f = lmer(Tbody~cm_edge+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)
model8a = lmer(Tbodysurr~cm_edge+(1|Bee), data=foragers, na.action=na.omit)
model8b = lmer(Tbodysurr~Beh*cm_edge+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model8c = lmer(Tbodysurr~Behav*cm_edge+(1|Bee), data=subset(bees,bees$Caste=="f"), na.action=na.omit)
model8d = lmer(Tbodysurr~cm_edge+(1|Bee), data=subset(awakebees,awakebees$Caste=="f"), na.action=na.omit)
model8e = lmer(Tbodysurr~cm_edge+(1|Bee), data=subset(zerobees,zerobees$Caste=="f"), na.action=na.omit)
model8f = lmer(Tbodysurr~cm_edge+(1|Bee), data=subset(Behasleepbees, Behasleepbees$Caste=="f"), na.action=na.omit)

#Repeat above with other castes (n, fs, & c = nurse bees, food storers, & cell cleaners, respectively)

#Beh~Tsurr [NOTE that family=binomial because Beh is categorical, not continuous (default; family=gaussian)]
mod9a = lmer(Beh~Tsurr*cm_edge+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
mod9b = lmer(Beh~Tsurr*d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
mod9c = lmer(Beh~Tsurr*UnderColor_majority+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
mod9d = lmer(Beh~Tsurr*UnderColor_white+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
#Behav~Tsurr
mod9e = lmer(Behav~Tsurr*cm_edge+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
mod9f = lmer(Behav~Tsurr*d_n+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
mod9g = lmer(Behav~Tsurr*UnderColor_majority+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)
mod9h = lmer(Behav~Tsurr*UnderColor_white+(1|Bee), data=subset(bees,bees$Caste=="f"), family = binomial, na.action=na.omit)

#Repeat with other castes

#mean(na.omit(bees$cm_edge[bees$Caste=="f"]))             #Mean

#binary logistic regression: 
#arbitrary name(e.g., g) = glm(DEPENDENT VAR~INDEPvar+INDEPvar2, family=binomial)