diff --git a/.RData b/.RData
index 36897f1..a25024f 100644
Binary files a/.RData and b/.RData differ
diff --git a/.Rhistory b/.Rhistory
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--- a/.Rhistory
+++ b/.Rhistory
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+#select models with head mass
+pgls_todo_hm<-pgls_todo_nogeomet[seq(2,length(pgls_todo_nogeomet),2)]
+library(phytools)
+library(ggalt)
+library(ggrepel)
+#get residuals from pgls of head mass vs each ear measure
+source("Extract pgls residuals.R")
+#Plotting adapted from:
+#https://thackl.github.io/ggtree-composite-plots
+library(patchwork)
+library(viridis)
+#color palettes
+# The palette with grey:
+cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
+# The palette with black:
+cbbPalette <- c(	"#FFFFFF","#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
+barplot(1:5, col=cbbPalette)
+#subset the df with resids dataframe to include only the residuals
+#run the PCA scripts to create the dfwith resids data frame
+names(dfwithresids)
+#input column numbers that have residuals
+residseach<-dfwithresids[,c(37:48)]
+names(residseach)
+#add
+residseach$order<-dfwithresids$Order
+residseach$Binomial<-dfwithresids$Binomial
+residseach$Category<-dfwithresids$Category
+residseach$divescore<-dfwithresids$divescore
+residseach$plungedistinct<-dfwithresids$plungedistinct
+residseach$waterbirds<-dfwithresids$waterbirds
+residseach$superorder<-dfwithresids$superorder
+residseach$IAC<-dfwithresids$IAC_detail
+residseach$IBP<-dfwithresids$IBP_detail
+residseach$PC1<-dfwithresids$PC1
+residseach$plungedistinct<-relevel(as.factor(residseach$plungedistinct),"Terrestrial")
+#residseach$Category<-relevel(as.factor(residseach$Category),"Terrestrial")
+#put in long format
+longdfplotting<-gather(residseach,key = "earmeasuresresid", value = "earmeasureval",
+-c(order,Binomial,Category,divescore,plungedistinct,IAC,IBP))#waterbirds,superorder,
+longdfplotting$earmeasuresresid<-as.factor(longdfplotting$earmeasuresresid)
+longdfplotting$earmeasureval<-as.numeric(longdfplotting$earmeasureval)
+#longdfplotting$label<-longdfplotting$order
+#longdfplotting$label<-longdfplotting$waterbirds
+#longdfplotting$label<-longdfplotting$superorder
+longdfplotting$label<-longdfplotting$order
+longdfplotting$earmeasuresresid<-as.character(longdfplotting$earmeasuresresid)
+longdfplotting$Terr<-longdfplotting$Category
+longdfplotting$Terr<-ifelse(longdfplotting$Category=="Terrestrial","Terrestrial",NA)
+#make list of ear measures to plot
+yvarnames<-c(
+"RES_logTMtotalarealogHeadmassg"            ,
+"RES_logFPtotalarealogHeadmassg"            ,
+"RES_logarearatiologHeadmassg"              ,
+"RES_logdiscoltipTMcentroidlogHeadmassg"    ,
+"RES_logUmbodistancetoTMplanelogHeadmassg",
+"RES_logmeanTManglelogHeadmassg"            ,
+"RES_logtotalEClengthlogHeadmassg"          ,
+"RES_logRWtotalarealogHeadmassg"            ,
+"RES_logCAtotalarealogHeadmassg"            ,
+"RES_logBehindTMlogHeadmassg"              ,
+"RES_logColumellalengthmmlogHeadmassg"      ,
+"RES_logColumellavolumemm3logHeadmassg"     ,"PC1")
+#create functions for plotting
+source("Tblog.R")
+#add medians
+#source("add median.R")
+#############make the order-level cladogram for aligning the residuals###########
+source("Order_level_cladogram.R")
+###
+ggtree(orderPhy)+
+geom_text(aes(label = node))
+gg_tr <- ggtree(orderPhy, branch.length = "none") +
+geom_tiplab(align=TRUE) +
+#scale_x_continuous(expand=expand_scale(0.2)) + # make more room for the labels
+scale_y_tree()+
+xlim(0,40)+
+ylim(0.5,38)+
+annotate("text", x = 13,y = 36,label = "Terrestrial")+
+annotate("text", x = 13,y = 33.5,label = "Surface-foraging")+
+annotate("text", x = 13,y = 31,label = "Plunge-diving")+
+annotate("text", x = 13,y = 28.5,label = "Underwater-pursuit")+
+annotate("text", x = 1,y = 38,label = "A")+
+annotate("text", x = 1,y = 26,label = "B")
+gg_tr
+#reversed phylogenetic tree
+gg_tr_rev <- ggtree(orderPhy, branch.length = "none", col = "white") +
+geom_tiplab(align=TRUE) +
+scale_x_continuous(expand=expand_scale(0.2)) + # make more room for the labels
+scale_y_tree()+
+xlim(10,20)+
+ylim(0.5,38)+
+scale_x_reverse()+
+annotate("text", x = 11,y = 36,label = "Terrestrial")+
+annotate("text", x = 11,y = 33.5,label = "Surface-foraging")+
+annotate("text", x = 11,y = 31,label = "Plunge-diving")+
+annotate("text", x = 11,y = 28.5,label = "Underwater-pursuit")
+gg_tr_rev
+###############scatterplot function###########
+gg_plungedistinct<-function(index2, letter, box = "yes"){
+ggtreeplot(gg_tr, subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[index2]), aes(y=earmeasureval), flip=TRUE)  +{
+if(box == "yes")   annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 5)
+else annotate("text",x = Inf, y = Inf, label = "", hjust = 2, vjust = 1.25)
+} +
+#geom_label(aes(x=Inf,y=-Inf,vjust = 1,
+#              hjust = -1,label=letter, lineheight = 0))+
+geom_vline(xintercept = 1:26,col = "black")+
+#geom_vline(xintercept = -4:30, col = "black")+
+#geom_rect(aes(xmin = -3.5, xmax = 26.5, ymin = -Inf, ymax = -Inf), col = "black", fill = "white", alpha = 0.1)+
+#geom_rect(aes(xmin = -3.5, xmax = 26.5, ymin = Inf, ymax = Inf), col = "black", fill = "white", alpha = 0.1)+
+#geom_line(aes(xmin = -3.5, xmax = 26.5, ymin = 0, ymax = 0), col = "black", size = 1)+
+geom_segment(aes(x = 0.5,xend = 38, y = 0, yend = 0), col = "black")+
+#geom_segment(aes(x = 28,xend = 36, y = 0, yend = 0), col = "black")+
+geom_point(aes(fill = plungedistinct), size = 3,shape = 21, col = "black")+
+scale_fill_manual(values = cbbPalette)+
+#geom_vline(xintercept = 27,col = "black")+
+coord_flip() + no_y_axis()+
+ylab("")+
+xlim(0.5,38)+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+#axis.text.x.left = element_text(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 5, r = 5, b = 0, l = 0, unit = "pt"))+
+geom_boxplot(data = subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[index2]&
+longdfplotting$plungedistinct=="Terrestrial"),
+aes(x = 36, y = earmeasureval),fill= "white", col = "black", outlier.size = 3,
+outlier.colour = "black", width = 2.25, outlier.fill = "white",
+outlier.shape = 21)+
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 5)
+}
+gg_plungedistinct(1, letter = "aa", box = "no")
+gg_plungedistinct(1, letter = "aa", box = "yes")
+annotate("text",x = Inf, y = -Inf, label = "a")
+addbxplt(1,1,"a")
+gg_plungedistinct(1, box = "no")+
+geom_text(aes(x=Inf,y=-Inf,vjust = 1,
+hjust = -1,label="i"))
+gg_plungedistinct(1, letter = "K", box = "yes")
+gg_tr|addbxplt(1,1,"i")
+############function to add boxplots at bottom################
+addbxplt<-function(j,index2,letter,box = "yes"){
+d<-gg_plungedistinct(index2,letter,box)+
+geom_boxplot(data = subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[j]&
+longdfplotting$plungedistinct=="Plunging"),
+aes(x = 31, y = earmeasureval),fill= "black",col = "black", outlier.size = 3,
+outlier.fill = "#000000", outlier.shape = 21, width = 2.25, outlier.color = "black")+
+geom_boxplot(data = subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[j]&
+longdfplotting$plungedistinct=="Underwater pursuit"),
+aes(x = 28.5, y = earmeasureval),fill ="#56B4E9",col = "black", outlier.size = 3,
+outlier.fill = "#56B4E9", outlier.shape = 21, width = 2.25, outlier.color = "black")+
+geom_boxplot(data = subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[j]&
+longdfplotting$plungedistinct=="Surface"),
+mapping = aes(x = 33.5, y = earmeasureval), fill = "#E69F00",col = "black",
+outlier.size = 3, outlier.fill = "#E69F00", width = 2.25, outlier.shape = 21, outlier.color = "black")
+d
+}
+#####################plots for interaural canal an interbullar passage#######
+#data for plotting by order
+summ2<-avgdf %>% group_by(Order,IBP_detail) %>% count(na.omit = T)
+summ2$IBP_detail<-ifelse(summ2$IBP_detail=="Pneumaticity present"|
+summ2$IBP_detail=="Pneumaticity absent"|
+summ2$IBP_detail=="Y",summ2$IBP_detail,NA)
+summ2$label<-summ2$Order
+summ2$number<-summ2$n
+summ2<-as.data.frame(summ2)
+names(summ2)
+summb<-summ2[which(!is.na(summ2$IBP_detail)),]
+#data for plotting by ecology
+summpl<-avgdf %>% group_by(IBP_detail,plungedistinct) %>% count(na.omit = T)
+summpl$IBP_detail<-ifelse(summpl$IBP_detail=="Pneumaticity present"|
+summpl$IBP_detail=="Pneumaticity absent"|
+summpl$IBP_detail=="Y",summpl$IBP_detail,NA)
+summpl$number<-summpl$n
+summpl<-as.data.frame(summpl)
+names(summpl)
+summpl_<-summpl[which(!is.na(summpl$IBP_detail)),]
+IBP<-function(letter){
+d<-ggtreeplot(gg_tr, summb, aes(y = number), flip=TRUE) +
+geom_bar(aes(fill = as.factor(IBP_detail)), position = "fill",
+color = "black",stat = "identity")+
+scale_fill_manual(values = c("black","grey","white"))+
+#no_legend()+
+xlim(0.5,38)+
+coord_flip() + no_y_axis()+
+theme(axis.text.x = element_text(angle = 90))+
+ylab("")+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "pt"))+
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25)
+d
+}
+IBP("d")
+IBPfull<-function(letter){
+IBP(letter)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Underwater pursuit",],
+aes(x = 28.5, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Terrestrial",],
+aes(x = 36, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Plunging",],
+aes(x = 31, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Surface",],
+aes(x = 33.5, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25)
+}
+IBPfull("l")
+###
+summ<-avgdf %>% group_by(Order,IAC_detail) %>% count(na.omit = T)
+summ$IAC_detail<-ifelse(summ$IAC_detail=="Pneumaticity present"|
+summ$IAC_detail=="Pneumaticity absent"|
+summ$IAC_detail=="Y",summ$IAC_detail,NA)
+summ$label<-summ$Order
+summ$number<-summ$n
+summ<-as.data.frame(summ)
+summa<-summ[which(!is.na(summ$IAC_detail)),]
+summpl2<-avgdf %>% group_by(IAC_detail,plungedistinct) %>% count(na.omit = T)
+summpl2$IAC_detail<-ifelse(summpl2$IAC_detail=="Pneumaticity present"|
+summpl2$IAC_detail=="Pneumaticity absent"|
+summpl2$IAC_detail=="Y",summpl2$IAC_detail,NA)
+summpl2$number<-summpl2$n
+summpl2<-as.data.frame(summpl2)
+names(summpl2)
+summpl2_<-summpl2[which(!is.na(summpl2$IAC_detail)),]
+#IAC
+IAC<-function(letter){
+d<-ggtreeplot(gg_tr, summa, aes(y = number), flip=TRUE) +
+geom_bar(aes(fill = as.factor(IAC_detail)), position = "fill",
+color = "black",stat = "identity")+
+scale_fill_manual(values = c("black","grey","white"))+
+#no_legend()+
+xlim(0.5,38)+
+coord_flip() + no_y_axis()+
+theme(axis.text.x = element_text(angle = 90))+
+ylab("")+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "pt"))  +
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 5)
+# geom_text(aes(x=Inf,y=-Inf,vjust = 1,
+#               hjust = -1,label=letter))
+d
+}
+IAC("d")
+IACfull<-function(letter){
+IAC(letter)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Underwater pursuit",],
+aes(x = 28.5, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Terrestrial",],
+aes(x = 36, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Plunging",],
+aes(x = 31, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Surface",],
+aes(x = 33.5, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 5)
+}
+IACfull("m")
+###################Plot all together#######################
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi"))
+#umbo height and TM angle
+(gg_tr|addbxplt(8,8,"vii")+addbxplt(9,9,"viii", box = "no")|#ESlength & RW
+addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
+addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
+IACfull("xiii")+IBPfull("xiv"))
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi"))|addbxplt(8,8,"vii")+addbxplt(9,9,"viii", box = "no")|#ESlength & RW
+addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
+addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
+IACfull("xiii")+IBPfull("xiv"))
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi")|
+addbxplt(8,8,"vii")+addbxplt(9,9,"viii", box = "no")|#ESlength & RW
+addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
+addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
+IACfull("xiii")+IBPfull("xiv"))
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi"))
+gg_plungedistinct<-function(index2, letter, box = "yes"){
+ggtreeplot(gg_tr, subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[index2]), aes(y=earmeasureval), flip=TRUE)  +{
+if(box == "yes")   annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 7)
+else annotate("text",x = Inf, y = Inf, label = "", hjust = 2, vjust = 1.25)
+} +
+#geom_label(aes(x=Inf,y=-Inf,vjust = 1,
+#              hjust = -1,label=letter, lineheight = 0))+
+geom_vline(xintercept = 1:26,col = "black")+
+#geom_vline(xintercept = -4:30, col = "black")+
+#geom_rect(aes(xmin = -3.5, xmax = 26.5, ymin = -Inf, ymax = -Inf), col = "black", fill = "white", alpha = 0.1)+
+#geom_rect(aes(xmin = -3.5, xmax = 26.5, ymin = Inf, ymax = Inf), col = "black", fill = "white", alpha = 0.1)+
+#geom_line(aes(xmin = -3.5, xmax = 26.5, ymin = 0, ymax = 0), col = "black", size = 1)+
+geom_segment(aes(x = 0.5,xend = 38, y = 0, yend = 0), col = "black")+
+#geom_segment(aes(x = 28,xend = 36, y = 0, yend = 0), col = "black")+
+geom_point(aes(fill = plungedistinct), size = 3,shape = 21, col = "black")+
+scale_fill_manual(values = cbbPalette)+
+#geom_vline(xintercept = 27,col = "black")+
+coord_flip() + no_y_axis()+
+ylab("")+
+xlim(0.5,38)+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+#axis.text.x.left = element_text(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 5, r = 5, b = 0, l = 0, unit = "pt"))+
+geom_boxplot(data = subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[index2]&
+longdfplotting$plungedistinct=="Terrestrial"),
+aes(x = 36, y = earmeasureval),fill= "white", col = "black", outlier.size = 3,
+outlier.colour = "black", width = 2.25, outlier.fill = "white",
+outlier.shape = 21)+
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 7)
+}
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi"))
+###############scatterplot function###########
+gg_plungedistinct<-function(index2, letter, box = "yes"){
+ggtreeplot(gg_tr, subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[index2]), aes(y=earmeasureval), flip=TRUE)  +{
+if(box == "yes")   annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 8)
+else annotate("text",x = Inf, y = Inf, label = "", hjust = 2, vjust = 1.25)
+} +
+#geom_label(aes(x=Inf,y=-Inf,vjust = 1,
+#              hjust = -1,label=letter, lineheight = 0))+
+geom_vline(xintercept = 1:26,col = "black")+
+#geom_vline(xintercept = -4:30, col = "black")+
+#geom_rect(aes(xmin = -3.5, xmax = 26.5, ymin = -Inf, ymax = -Inf), col = "black", fill = "white", alpha = 0.1)+
+#geom_rect(aes(xmin = -3.5, xmax = 26.5, ymin = Inf, ymax = Inf), col = "black", fill = "white", alpha = 0.1)+
+#geom_line(aes(xmin = -3.5, xmax = 26.5, ymin = 0, ymax = 0), col = "black", size = 1)+
+geom_segment(aes(x = 0.5,xend = 38, y = 0, yend = 0), col = "black")+
+#geom_segment(aes(x = 28,xend = 36, y = 0, yend = 0), col = "black")+
+geom_point(aes(fill = plungedistinct), size = 3,shape = 21, col = "black")+
+scale_fill_manual(values = cbbPalette)+
+#geom_vline(xintercept = 27,col = "black")+
+coord_flip() + no_y_axis()+
+ylab("")+
+xlim(0.5,38)+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+#axis.text.x.left = element_text(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 5, r = 5, b = 0, l = 0, unit = "pt"))+
+geom_boxplot(data = subset(longdfplotting,
+longdfplotting$earmeasuresresid==yvarnames[index2]&
+longdfplotting$plungedistinct=="Terrestrial"),
+aes(x = 36, y = earmeasureval),fill= "white", col = "black", outlier.size = 3,
+outlier.colour = "black", width = 2.25, outlier.fill = "white",
+outlier.shape = 21)+
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 8)
+}
+###################Plot all together#######################
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi"))
+gg_tr <- ggtree(orderPhy, branch.length = "none") +
+geom_tiplab(align=TRUE) +
+#scale_x_continuous(expand=expand_scale(0.2)) + # make more room for the labels
+scale_y_tree()+
+xlim(0,40)+
+ylim(0.5,38)+
+annotate("text", x = 13,y = 36,label = "Terrestrial")+
+annotate("text", x = 13,y = 33.5,label = "Surface-foraging")+
+annotate("text", x = 13,y = 31,label = "Plunge-diving")+
+annotate("text", x = 13,y = 28.5,label = "Underwater-pursuit")+
+annotate("text", x = 1,y = 38,label = "A", size = 8)+
+annotate("text", x = 1,y = 26,label = "B", siz = 8)
+gg_tr
+gg_tr <- ggtree(orderPhy, branch.length = "none") +
+geom_tiplab(align=TRUE) +
+#scale_x_continuous(expand=expand_scale(0.2)) + # make more room for the labels
+scale_y_tree()+
+xlim(0,40)+
+ylim(0.5,38)+
+annotate("text", x = 13,y = 36,label = "Terrestrial")+
+annotate("text", x = 13,y = 33.5,label = "Surface-foraging")+
+annotate("text", x = 13,y = 31,label = "Plunge-diving")+
+annotate("text", x = 13,y = 28.5,label = "Underwater-pursuit")+
+annotate("text", x = 1,y = 38,label = "A", size = 8)+
+annotate("text", x = 1,y = 26,label = "B", size = 8)
+gg_tr
+(gg_tr|addbxplt(8,8,"vii")+addbxplt(9,9,"viii", box = "no")|#ESlength & RW
+addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
+addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
+IACfull("xiii")+IBPfull("xiv"))
+IBP<-function(letter){
+d<-ggtreeplot(gg_tr, summb, aes(y = number), flip=TRUE) +
+geom_bar(aes(fill = as.factor(IBP_detail)), position = "fill",
+color = "black",stat = "identity")+
+scale_fill_manual(values = c("black","grey","white"))+
+#no_legend()+
+xlim(0.5,38)+
+coord_flip() + no_y_axis()+
+theme(axis.text.x = element_text(angle = 90))+
+ylab("")+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "pt"))+
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 8)
+d
+}
+IBP("d")
+IBPfull<-function(letter){
+IBP(letter)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Underwater pursuit",],
+aes(x = 28.5, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Terrestrial",],
+aes(x = 36, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Plunging",],
+aes(x = 31, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl_[summpl_$plungedistinct=="Surface",],
+aes(x = 33.5, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
+annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 8)
+}
+IBPfull("l")
+###
+summ<-avgdf %>% group_by(Order,IAC_detail) %>% count(na.omit = T)
+summ$IAC_detail<-ifelse(summ$IAC_detail=="Pneumaticity present"|
+summ$IAC_detail=="Pneumaticity absent"|
+summ$IAC_detail=="Y",summ$IAC_detail,NA)
+summ$label<-summ$Order
+summ$number<-summ$n
+summ<-as.data.frame(summ)
+summa<-summ[which(!is.na(summ$IAC_detail)),]
+summpl2<-avgdf %>% group_by(IAC_detail,plungedistinct) %>% count(na.omit = T)
+summpl2$IAC_detail<-ifelse(summpl2$IAC_detail=="Pneumaticity present"|
+summpl2$IAC_detail=="Pneumaticity absent"|
+summpl2$IAC_detail=="Y",summpl2$IAC_detail,NA)
+summpl2$number<-summpl2$n
+summpl2<-as.data.frame(summpl2)
+names(summpl2)
+summpl2_<-summpl2[which(!is.na(summpl2$IAC_detail)),]
+#IAC
+IAC<-function(letter){
+d<-ggtreeplot(gg_tr, summa, aes(y = number), flip=TRUE) +
+geom_bar(aes(fill = as.factor(IAC_detail)), position = "fill",
+color = "black",stat = "identity")+
+scale_fill_manual(values = c("black","grey","white"))+
+#no_legend()+
+xlim(0.5,38)+
+coord_flip() + no_y_axis()+
+theme(axis.text.x = element_text(angle = 90))+
+ylab("")+
+theme_test() +
+theme(axis.line.y = element_blank(),
+axis.title.y = element_blank(),
+axis.text.y = element_blank(),
+axis.ticks.y = element_blank(),
+axis.text.x = element_text(angle = 90, colour = "black"),
+legend.position = "none",
+plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "pt"))  +
+annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 8)
+# geom_text(aes(x=Inf,y=-Inf,vjust = 1,
+#               hjust = -1,label=letter))
+d
+}
+IAC("d")
+IACfull<-function(letter){
+IAC(letter)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Underwater pursuit",],
+aes(x = 28.5, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Terrestrial",],
+aes(x = 36, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Plunging",],
+aes(x = 31, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+geom_col(data = summpl2_[summpl2_$plungedistinct=="Surface",],
+aes(x = 33.5, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
+annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 8)
+}
+IACfull("m")
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+addbxplt(5,5,"v")+addbxplt(6,6,"vi"))
+#umbo height and TM angle
+(gg_tr|addbxplt(8,8,"vii")+addbxplt(9,9,"viii", box = "no")|#ESlength & RW
+addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
+addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
+IACfull("xiii")+IBPfull("xiv"))
diff --git a/Eardata.csv b/Eardata.csv
index bedc659..350e91b 100644
--- a/Eardata.csv
+++ b/Eardata.csv
@@ -4,11 +4,11 @@ Spheniscus demersus,Spheniscus_demersus,Sphenisciformes,Spheniscidae,African pen
 Larus hartlaubii,Chroicocephalus_hartlaubii,Charadriiformes,Laridae,Hartlaub's gull,H414,Surface foraging,Scanned,Other,Y,Pneumaticity present,22.17,21.49,0.6387115,,1.6285463,399.42,3.7292626,17.7525684,12.8811013,0.4708316,0.4603956,1.4555714,1.0448887,1.8047,0.142,27.35819197
 Puffinus griseus,Ardenna_grisea,Procellariiformes,Procellariidae,Sooty shearwater,SW01,Pursuit diving,Scanned,Other,Pneumaticity present,Pneumaticity present,30.52,NA,0.5687735,,1.7550923,231.33,4.14108,14.8505159,14.1101799,0.8797251,3.0077953,2.6428105,1.1576382,2.9779,0.37039,16.0393058
 Larus dominicanus,Larus_dominicanus,Charadriiformes,Laridae,Kelp gull,K151,Surface foraging,Scanned,Other,Y,Y,40.95,62.3,1.017922,,2.537805,3236.84,5.237897,16.261305,36.053742,0.97365,1.818927,2.394297,2.027716,3.8787,0.430434,37.02946849
-Morus capensis,Morus_capensis,Suliformes,Sulidae,Gannet,G045,Pursuit diving,Scanned,Poor LF,Y,Y,47.58,275,0.592118,,1.5276351,7067.93,6.6173265,12.0753945,27.8116976,1.1589345,3.511894,2.2928683,1.0647901,8.6,1.029,23.99764404
-Phalacrocorax capensis,Phalacrocorax_capensis,Suliformes,Phalacrocoridae,Cape Cormorant,CC209,Pursuit diving,Scanned,Poor LF,Y,Pneumaticity absent,27,71.26,0.3453295,,0.79324334,372.35,5.08996474,13.0261082,9.22449752,0.44051429,2.72894333,2.03706372,0.45345296,3.8696,0.266328,20.94029122
+Morus capensis,Morus_capensis,Suliformes,Sulidae,Cape gannet,G045,Pursuit diving,Scanned,Poor LF,Y,Y,47.58,275,0.592118,,1.5276351,7067.93,6.6173265,12.0753945,27.8116976,1.1589345,3.511894,2.2928683,1.0647901,8.6,1.029,23.99764404
+Phalacrocorax capensis,Phalacrocorax_capensis,Suliformes,Phalacrocoridae,Cape cormorant,CC209,Pursuit diving,Scanned,Poor LF,Y,Pneumaticity absent,27,71.26,0.3453295,,0.79324334,372.35,5.08996474,13.0261082,9.22449752,0.44051429,2.72894333,2.03706372,0.45345296,3.8696,0.266328,20.94029122
 Phoenicopterus roseus,Phoenicopterus_roseus,Phoenicopteriformes,Phoenicopteridae,Greater flamingo,Flamingo01,Surface foraging,Scanned,Other,Y,Pneumaticity present,32.43,NA,0.897117,,2.1548053,1379.64,5.7269092,18.206483,23.9107099,1.114212,4.407708,3.3531699,1.706508,3.31,0.448037,21.45974904
 Procellaria aequinoctialis,Procellaria_aequinoctialis,Procellariiformes,Procellariidae,White-chinned petrel,WCP03,Pursuit diving,Scanned,Other,Pneumaticity present,Pneumaticity present,43.39,NA,0.6965724,fluid filled,2.3398132,NA,6.2084629,15.854649,19.97404,1.0531436,3.1105181,2.7006765,2.0672644,4.7777,0.612506,18.9661125
-Chionis minor,Chionis_minor,Charadriiformes,Chionidae,Lesser Sheathbill,SB-01-2019,Terrestrial,Scanned,Other,Y,Y,21.72,NA,0.487271,,1.5954347,751.71,4.6720255,13.9758777,12.2568029,0.4497441,2.3852071,1.5378967,1.2606874,1.75,0.104,27.25283756
+Chionis minor,Chionis_minor,Charadriiformes,Chionidae,Lesser sheathbill,SB-01-2019,Terrestrial,Scanned,Other,Y,Y,21.72,NA,0.487271,,1.5954347,751.71,4.6720255,13.9758777,12.2568029,0.4497441,2.3852071,1.5378967,1.2606874,1.75,0.104,27.25283756
 Macronectes halli,Macronectes_halli,Procellariiformes,Procellariidae,Northern giant petrel,NGP-01-2019,Surface foraging,Scanned,Other,Y,Y,53.82,271.5,0.5378209,,1.8362029,5937.11,6.5958948,7.9291175,43.0391185,1.3891691,6.155614,3.6991239,1.7127285,5.6,0.851,30.98191466
 Bucorvus abyssinicus,Bucorvus_leadbeateri,Bucerotiformes,Bucorvidae,Southern ground hornbill,GHB01,Terrestrial,Scanned,Other,,,69.06,NA,0.8311657,fluid filled,3.9816637,NA,8.3393286,8.9851082,88.3744713,1.9769213,0.3481421,10.2280263,3.5247887,6.267897,0.897199875,44.70308014
 Aethopyga siparaja,Cinnyris_chalybeus,Passeriformes, Nectariniidae,Southern double-collared sunbird,DCSB01,Terrestrial,Scanned,Poor LF,Y,Y,11,NA,0.31907899,,0.61324873,47.16,1.99507714,13.58151162,5.35102153,0.21222748,0.03260038,0.3605546,0.61367124,0.895437,0.018883125,25.21361291
diff --git a/Plot PCA.R b/Plot PCA.R
index 30aaf9f..ceefe11 100644
--- a/Plot PCA.R	
+++ b/Plot PCA.R	
@@ -19,7 +19,7 @@ p<-ggplot(d, aes(x = reorder(PC1,-percentexplained), y = percentexplained))+
   ylab("Percent variance \n explained")
 p
 
-#remove lavels for inset plot
+#remove labels for inset plot
 p<-ggplot(d[1:6,], aes(x = reorder(PC1,-percentexplained), y = percentexplained))+
   geom_bar(stat = "identity")+
   theme_classic()+
@@ -32,19 +32,6 @@ p<-ggplot(d[1:6,], aes(x = reorder(PC1,-percentexplained), y = percentexplained)
 p
 
 
-themejz<-function (base_size = 11, base_family = "", base_line_size = base_size/22, 
-                   base_rect_size = base_size/22) 
-{
-  theme_grey(base_size = base_size, base_family = base_family, 
-             base_line_size = base_line_size, base_rect_size = base_rect_size) %+replace% 
-    theme(panel.background = element_blank(), panel.border = element_rect(), panel.grid = element_line(), 
-          panel.grid.minor = element_blank(), 
-          strip.background = element_rect(fill = "grey85", 
-                                          colour = "grey20"), legend.key = element_rect(fill = "white", 
-                                                                                        colour = NA), complete = TRUE)
-}
-
-
 
 ################Make a grouping of orders that includes species with one underwater-pursuit species#####################
 speciesPCAvalues$Order<-as.character(speciesPCAvalues$Order)
@@ -285,7 +272,7 @@ loadings2<-loadings1 + annotation_custom(ggplotGrob(p),
                        ymin = 0, ymax = 1)
 loadings2
 
-ggarrange(loadings2,plunge,divescore, order,
+ggarrange(loadings1,plunge,divescore, order,
           labels = c("A","B","C","D"))
 
 ggsave("D:/00_Manuscripts/0Avian aquatic hearing project/___Oct 1 version/PCAOct 4_noair.pdf",width = 10, height = 10)
diff --git a/Residualphylogplots_a panel top.R b/Residualphylogplots_a panel top.R
index 8ec6508..da2379d 100644
--- a/Residualphylogplots_a panel top.R	
+++ b/Residualphylogplots_a panel top.R	
@@ -1,5 +1,4 @@
-#Plotting adapted from:
-#https://thackl.github.io/ggtree-composite-plots
+#Plotting adapted from: https://thackl.github.io/ggtree-composite-plots
 library(patchwork)
 library(viridis)
 
@@ -85,8 +84,8 @@ annotate("text", x = 13,y = 36,label = "Terrestrial")+
   annotate("text", x = 13,y = 33.5,label = "Surface-foraging")+
   annotate("text", x = 13,y = 31,label = "Plunge-diving")+
   annotate("text", x = 13,y = 28.5,label = "Underwater-pursuit")+
-  annotate("text", x = 1,y = 38,label = "A")+
-  annotate("text", x = 1,y = 26,label = "B")
+  annotate("text", x = 1,y = 38,label = "A", size = 8)+
+  annotate("text", x = 1,y = 26,label = "B", size = 8)
 gg_tr
 
 #reversed phylogenetic tree
@@ -108,7 +107,7 @@ gg_plungedistinct<-function(index2, letter, box = "yes"){
   ggtreeplot(gg_tr, subset(longdfplotting,
                            longdfplotting$earmeasuresresid==yvarnames[index2]), aes(y=earmeasureval), flip=TRUE)  +{
     
-    if(box == "yes")   annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 5)
+    if(box == "yes")   annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 8)
  else annotate("text",x = Inf, y = Inf, label = "", hjust = 2, vjust = 1.25)
     } +
    #geom_label(aes(x=Inf,y=-Inf,vjust = 1,
@@ -142,7 +141,7 @@ gg_plungedistinct<-function(index2, letter, box = "yes"){
                  aes(x = 36, y = earmeasureval),fill= "white", col = "black", outlier.size = 3,
                  outlier.colour = "black", width = 2.25, outlier.fill = "white",
                  outlier.shape = 21)+
-    annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 5)
+    annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 8)
   
   }
 
@@ -231,7 +230,7 @@ IBP<-function(letter){
           axis.text.x = element_text(angle = 90, colour = "black"),
           legend.position = "none",
           plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "pt"))+
-    annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25)
+    annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 8)
   
   
   d
@@ -249,7 +248,7 @@ IBPfull<-function(letter){
              aes(x = 31, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
     geom_col(data = summpl_[summpl_$plungedistinct=="Surface",],
              aes(x = 33.5, fill = IBP_detail),col = "black", position = "fill",width = 2.25)+
-    annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25)
+    annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 8)
 }
 IBPfull("l")
 
@@ -296,7 +295,7 @@ IAC<-function(letter){
           axis.text.x = element_text(angle = 90, colour = "black"),
           legend.position = "none",
           plot.margin = margin(t = 0, r = 0, b = 0, l = 0, unit = "pt"))  +
-    annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 5)
+    annotate("text",x = Inf, y = -Inf, label = letter,hjust = -1,vjust = 1.25, size = 8)
    # geom_text(aes(x=Inf,y=-Inf,vjust = 1,
    #               hjust = -1,label=letter))
   
@@ -316,7 +315,7 @@ IACfull<-function(letter){
              aes(x = 31, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
     geom_col(data = summpl2_[summpl2_$plungedistinct=="Surface",],
              aes(x = 33.5, fill = IAC_detail),col = "black", position = "fill",width = 2.25)+
-    annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 5)
+    annotate("text",x = Inf, y = Inf, label = "*", hjust = 2, vjust = 1.25, size = 8)
   
 }
 IACfull("m")
@@ -332,3 +331,11 @@ IACfull("m")
   addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
   addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
   IACfull("xiii")+IBPfull("xiv"))
+
+(gg_tr|addbxplt(1,1,"i")+addbxplt(2,2,"ii")|
+    addbxplt(3,3,"iii")+addbxplt(4,4,"iv")|#
+    addbxplt(5,5,"v")+addbxplt(6,6,"vi")|
+    addbxplt(8,8,"vii")+addbxplt(9,9,"viii", box = "no")|#ESlength & RW 
+    addbxplt(7,7,"ix")+addbxplt(11,11,"x")|#CA and collenght
+    addbxplt(12,12,"xi", box = "no")+addbxplt(10,10,"xii")|#colvol and air
+    IACfull("xiii")+IBPfull("xiv"))
diff --git a/Run PGLS and AIC.R b/Run PGLS and AIC.R
index f1b8f9d..e50361c 100644
--- a/Run PGLS and AIC.R	
+++ b/Run PGLS and AIC.R	
@@ -84,8 +84,8 @@ body_add_flextable(toprint,flexall)#add pgls output table
 body_end_section_landscape(toprint)
 
 #print to file
-print(toprint,target = "D:/Analysis_plots/AIC best model Dec 9 no terr.docx")
-print(toprint,target = "D:/Analysis_plots/AIC Dec 1 compare_terr.docx")
+print(toprint,target = "E:/Analysis_plots/AIC best model Mar31 no terr.docx")
+print(toprint,target = "E:/Analysis_plots/AIC Mar 31 compare_terr.docx")
 
 
 ########(2)Get model details for best model###########
@@ -122,6 +122,6 @@ toprint<-read_docx() #create word doc object
 body_add_flextable(toprint,flexall)#add pgls output table
 body_end_section_landscape(toprint)
 
-print(toprint,target = "D:/Analysis_plots/AIC Details Dec 9 no terr.docx")
-print(toprint,target = "D:/Analysis_plots/DetailsNov 12 terr compare.docx")
+print(toprint,target = "E:/Analysis_plots/AIC Details Dec 31 no terr.docx")
+print(toprint,target = "E:/Analysis_plots/DetailsMar 31 terr compare.docx")