setwd("/Users/akimmitt/Documents/MaleChoice/MaleChoice-Paper/Data") d<-read.csv("Kimmittetal_DataFile_MaleChoice2016-ESM.csv",header=TRUE) ######## LOAD PACKAGES ######## require(car) require(MASS) require(lme4) require(emmeans) #replacement for lsmeans require(ggplot2) # add 1 to get rid of zeroes d$SRS <-d$SRS+1 d$TS <-d$TS+1 d$PT <-d$PT+1 d$WIN5 <-d$WIN5+1 d$LRS <-d$LRS+1 #Box-Cox Test of Transformation summary(powerTransform(lm(SRS ~ LureSubsp, data=d))) # advocates for the log transform summary(powerTransform(lm(TS ~ LureSubsp, data=d))) # advocates for the log transform (estimated lambda is close to 0) summary(powerTransform(lm(PT ~ LureSubsp, data=d))) # estimated lambda is close to 0.5, sqrt transformation is better summary(powerTransform(lm(WIN5 ~ LureSubsp, data=d))) # estimated lambda is between 0 and 0.5, so log or sqrt possible; based on histogram, sqrt will be best transformation summary(powerTransform(lm(LRS ~ LureSubsp, data=d))) # estimated lambda is close to 0, so log transform ###### Models ###### ######################## ######### SRS ########## ######################## srs.m1<-glmer(SRS~(1|LureID)+ LureSubsp, data=d, family="gaussian"(link="log")) Anova(srs.m1) emm.srs<-emmeans(srs.m1,"LureSubsp") emm.srs ### Boxplot Code-SRS ### srs.box1<-ggplot(d, aes(x=LureSubsp,y=SRS))+geom_boxplot()+geom_point() srs.box1 srs.box2<-srs.box1+ theme(axis.title.x = element_text(vjust=-.3, face="bold", size=25),axis.text.x  = element_text(vjust=0.5, size=25)) + theme(axis.title.y = element_text(vjust=1.1, face="bold", size=25),axis.text.y  = element_text(vjust=.5, size=25)) srs.box2 srs.box3<-srs.box2+ylab("Short-range song (seconds)") + xlab("Female Migratory Strategy") + scale_color_manual(values = cols,cols <- c("blue3","red1")) srs.box3 ######################## ########## TS ########## ######################## ts.m1<-glmer(TS~(1|LureID)+ LureSubsp, data=d,family="gaussian"(link="log")) Anova(ts.m1) emm.ts<-emmeans(ts.m1, ~LureSubsp) emm.ts ### Boxplot Code- TS ### ts.box1<-ggplot(d, aes(x=LureSubsp,y=TS))+geom_boxplot()+geom_point() ts.box1 ts.box2<-ts.box1+ theme(axis.title.x = element_text(vjust=-.3, face="bold", size=25),axis.text.x  = element_text(vjust=0.5, size=25)) + theme(axis.title.y = element_text(vjust=1.1, face="bold", size=25),axis.text.y  = element_text(vjust=.5, size=25)) ts.box2 ts.box3<-ts.box2+ylab("Tail Spread (seconds)") + xlab("Female Migratory Strategy") + scale_color_manual(values = cols,cols <- c("blue3","red1")) ts.box3 ######################## ########## PT ########## ######################## pt.m1<-glmer(d$PT~(1|LureID)+ LureSubsp, data=d,family="gaussian"(link="sqrt")) Anova(pt.m1) emm.pt<- emmeans(pt.m1,~LureSubsp) emm.pt ### Boxplot Code- PT ### pt.box1<-ggplot(d, aes(x=LureSubsp,y=PT))+geom_boxplot()+geom_point() pt.box1 pt.box2<-pt.box1+ theme(axis.title.x = element_text(vjust=-.3, face="bold", size=25),axis.text.x  = element_text(vjust=0.5, size=25)) + theme(axis.title.y = element_text(vjust=1.1, face="bold", size=25),axis.text.y  = element_text(vjust=.5, size=25)) pt.box2 pt.box3<-pt.box2+ylab("Ptiloerection (seconds)") + xlab("Female Migratory Strategy") + scale_color_manual(values = cols,cols <- c("blue3","red1")) pt.box3 ######################## ######## WIN5 ########## ######################## win5.m1<-glmer(WIN5~(1|LureID)+ LureSubsp, data=d, family="gaussian"(link="sqrt")) Anova(win5.m1) emm.win5<-emmeans(win5.m1, ~LureSubsp) emm.win5 ### Boxplot Code-Win5 ### win.box1<-ggplot(d, aes(x=LureSubsp,y=WIN5))+geom_boxplot()+geom_point() win.box1 win.box2<-win.box1+ theme(axis.title.x = element_text(vjust=-.3, face="bold", size=25),axis.text.x  = element_text(vjust=0.5, size=25)) + theme(axis.title.y = element_text(vjust=1.1, face="bold", size=25),axis.text.y  = element_text(vjust=.5, size=25)) win.box2 win.box3<-win.box2+ylab("Time Spent within 5 meters (seconds)") + xlab("Female Migratory Strategy") + scale_color_manual(values = cols,cols <- c("blue3","red1")) win.box3 ######################## ########## LRS ########## ######################## lrs.m1<-glmer(LRS~(1|LureID)+ LureSubsp, data=d,family="gaussian"(link="log")) Anova(lrs.m1) emm.lrs<-emmeans(lrs.m1, ~LureSubsp) emm.lrs ### Boxplot Code- LRS ### lrs.box1<-ggplot(d, aes(x=LureSubsp,y=LRS))+geom_boxplot()+geom_point() lrs.box1 lrs.box2<-lrs.box1+ theme(axis.title.x = element_text(vjust=-.3, face="bold", size=25),axis.text.x  = element_text(vjust=0.5, size=25)) + theme(axis.title.y = element_text(vjust=1.1, face="bold", size=25),axis.text.y  = element_text(vjust=.5, size=25)) lrs.box2 lrs.box3<-lrs.box2+ylab("Long-range song (count)") + xlab("Female Migratory Strategy") + scale_color_manual(values = cols,cols <- c("blue3","red1")) lrs.box3