update comments, readme, Fig 4, supplemental file naming

Audiograms linked to anatomy.R

@@ -1,5 +1,6 @@
-#run up until line 185, proceed to pgls_resids re headmass
-#otherwise unadjusted for head mass proceed past line 185
+#For analysis which is adjusted for head mass, run up until line 180,
+#then proceed to 'pgls_resids re headmass.R'
+#Otherwise, analysis unadjusted for head mass proceeds past line 185
 
 library(ggrepel)
 library(ggplot2)
@@ -151,12 +152,6 @@ limits$binomial[limits$Species=="Mallard duck"]<-"Anas_georgica_georgica"
 limits$binomial[limits$Species=="Rock dove"]<-"Columba_livia"#
 limits$binomial[limits$Species=="Zebra finch"]<-"Taeniopygia_guttata"
 
-#limits$binomial[limits$Species=="Orange fronted conure"]<-"Aratinga_canicularis"
-#limits$binomial[limits$Species=="Lesser scaup"]<-"Aythya_affinis"
-#limits$binomial[limits$Species=="Japanese quail"]<-"Coturnix_japonica"
-#limits$binomial[limits$Species=="Blue Jay"]<-"Cyanocitta_cristata"
-#limits$binomial[limits$Species=="Kea parrot"]<-"Nestor_notabilis"
-
 
 ##################add anatomical data from anatomy df############
 limits$TM<-avgdf$TM[match(limits$binomial,avgdf$Binomial)]

README.md

@@ -7,7 +7,7 @@ Start with _**"Set up data_scl.R".**_ This loads the data and phylogeny. This al
 
 ## **To run the pgls between ear structures and audiometric measurements:**  
 
-First,  _**"Set up data_scl.R"**_ also has to be run to get the data prepared (minus the pgls from those scripts). Next, the scripts in _**"Audiograms linked to anatomy.R"**_ can be run. This creates a 'limits' dataframe with the audiogram metrics, which will be joined with the anatomy dataframes for analysis. Once the limits df is created the _**"pgls_resids re headmass.R"**_ can be used to run the pgls analyses with head mass-corrected values.  
+First,  _**"Set up data_scl.R"**_ also has to be run (up to line 70) to get the data prepared. Next, the scripts in _**"Audiograms linked to anatomy.R"**_ can be run to create a  dataframe ('limits') containing the audiogram metrics which will be joined with the morphological data.  Once the dataframe is created is created, _**"pgls_resids re headmass.R"**_ can be used to run the pgls analyses with head mass-corrected values. Note that for running analyses at different cut-off levels (35 or 60 dB), the cutoff is specified in the 'Audiograms linked to anatomy.R' file. When switching cut-off levels it is recommended to to empty the environment, modify the cut-off level, and re-rerun all relevant scripts with updated cut-off 
 
 <br>
 

Set up data_scl.R

@@ -8,7 +8,7 @@ library(tidyr)
 library(purrr)
 
 
-#########Line 73 - scaling intraear##########
+#########Line 73 - scaling between ear structures##########
 #########Line 173 - scaling vs head mass########
 
 ################Set up data############

pgls_audiogram_bh.R

@@ -4,8 +4,6 @@
 #modellist<-pgls_todo_hm
 pgls_models_list_bh<-lapply(modellist_bh,pgls_models)#run pgls
 
-
-
 #make list of dataframes with the PGLS outputs.
 tbllist_audiogram<-list()
 for (i in seq_along(pgls_models_list_bh)){#change th 'Model' colume in this as appropriate
@@ -26,18 +24,8 @@ for(i in seq_along(tbllist_audiogram)){
   #identify numeric cols and character cols to apply the significant digits function
   character_cols<-unlist(lapply(tbllist_audiogram[[i]], is.character))
   numeric_cols <- unlist(lapply(tbllist_audiogram[[i]], is.numeric))# Identify numeric columns
-  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 2))
-  #tbllist_audiogram[[i]] <- tbllist_audiogram[[i]][, c(6,11,8:10,7,5,1:4)]#change order of columns
-  #dplyr::select_if(tbllist_audiogram[[i]], is.numeric)#select only numeric data
+  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 3))
   colnames(tbllist_audiogram[[i]])[6]<-"P.val"#rename b/c flextable doesn't work will with the '>' sign
-  #tbllist_audiogram[[i]]$Fstat[2:nrow(tbllist_audiogram[[i]])]<-""
-  #tbllist_audiogram[[i]]$Fstat_numdf[2:nrow(tbllist_audiogram[[i]])]<-""
-  #tbllist_audiogram[[i]]$Fstat_dendf[2:nrow(tbllist_audiogram[[i]])]<-" "
-  #tbllist_audiogram[[i]]$Model[2:nrow(tbllist_audiogram[[i]])]<-""
-  #tbllist_audiogram[[i]]$Lambda[2:nrow(tbllist_audiogram[[i]])]<-""
-  #tbllist_audiogram[[i]]$Adj_Rsquared[2:nrow(tbllist_audiogram[[i]])]<-""
-  #tbllist_audiogram[[i]]$AICc[2:nrow(tbllist_audiogram[[i]])]<-""
-  #row.names(tbllist_audiogram[[i]])<-c()#remove row names
   print(tbllist_audiogram[[i]])
 }
 

pgls_audiogram_bs.R

@@ -3,7 +3,6 @@
 #Head mass only
 #modellist<-pgls_todo_hm
 
-options(scipen = 1000)
 pgls_models_list_bs<-lapply(modellist_bs,pgls_models)#run pgls
 
 
@@ -27,7 +26,7 @@ for(i in seq_along(tbllist_audiogram)){
   #identify numeric cols and character cols to apply the significant digits function
   character_cols<-unlist(lapply(tbllist_audiogram[[i]], is.character))
   numeric_cols <- unlist(lapply(tbllist_audiogram[[i]], is.numeric))# Identify numeric columns
-  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 2))
+  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 3))
   colnames(tbllist_audiogram[[i]])[6]<-"P.val"#rename b/c flextable doesn't work will with the '>' sign
   row.names(tbllist_audiogram[[i]])<-c()#remove row names
   print(tbllist_audiogram[[i]])
@@ -42,7 +41,7 @@ flexall<-flextable(audiogrampgls_bs) %>% add_header_lines(
   values = "Table X. Models for selection") %>%
   bold(i = ~ P.val < 0.05) %>% # select columns add: j = ~ Coefficients + P.val
   autofit()
-flexall 
+flexall
 
 #pgls diagnostics
 

pgls_audiogram_hf.R

@@ -25,7 +25,7 @@ for(i in seq_along(tbllist_audiogram)){
   #identify numeric cols and character cols to apply the significant digits function
   character_cols<-unlist(lapply(tbllist_audiogram[[i]], is.character))
   numeric_cols <- unlist(lapply(tbllist_audiogram[[i]], is.numeric))# Identify numeric columns
-  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 2))
+  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 3))
   #tbllist_audiogram[[i]] <- tbllist_audiogram[[i]][, c(6,11,8:10,7,5,1:4)]#change order of columns
   #dplyr::select_if(tbllist_audiogram[[i]], is.numeric)#select only numeric data
   colnames(tbllist_audiogram[[i]])[6]<-"P.val"#rename b/c flextable doesn't work will with the '>' sign

pgls_audiogram_lf.R

@@ -26,7 +26,7 @@ for(i in seq_along(tbllist_audiogram)){
   #identify numeric cols and character cols to apply the significant digits function
   character_cols<-unlist(lapply(tbllist_audiogram[[i]], is.character))
   numeric_cols <- unlist(lapply(tbllist_audiogram[[i]], is.numeric))# Identify numeric columns
-  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 2))
+  tbllist_audiogram[[i]]<-cbind(tbllist_audiogram[[i]][,which(character_cols)],signif(tbllist_audiogram[[i]][,which(numeric_cols)], digits = 3))
   #tbllist_audiogram[[i]] <- tbllist_audiogram[[i]][, c(6,11,8:10,7,5,1:4)]#change order of columns
   #dplyr::select_if(tbllist_audiogram[[i]], is.numeric)#select only numeric data
   colnames(tbllist_audiogram[[i]])[6]<-"P.val"#rename b/c flextable doesn't work will with the '>' sign

pgls_resids re headmass.R

@@ -1,8 +1,10 @@
+###Note the dataframe 'limits', created from 'Audiograms linked to anatomy.R'
+###is required to run this code
+
+
 library(patchwork)
 library(ggrepel)
 
-###note the dataframe 'limits', created from 'Audiograms linked to anatomy.R'
-###is required to run this code
 
 #ensure phylogeny matches dataframe
 #remake comparative data frame object with averaged congeners

plots/Fig 3. phylogeny all species plot.R

@@ -1,3 +1,5 @@
+#run 'set up data_scl.R up to line 70 before running this script
+
 library(ggplot2)
 library(RColorBrewer)
 library(ggtree)
@@ -104,9 +106,6 @@ avgdf %>% dplyr::select(aud_rel) %>%
   scale_fill_manual(values = c("white","grey","black"), na.value = "#FFFFFF")
 
 
-#order level plot
-
-
 
 
 #open up the circle
@@ -115,64 +114,3 @@ l
 
 ggsave("D:/Analysis_plots/ecolcircle.pdf", width=10, height=10)
 
-
-#############plot heatmap showing sampling of all auditory traits (supplemental materials)#####333
-avgdf$Binomial2<-avgdf$Binomial
-
-avgdf$Binomial3<-gsub("_"," ",avgdf$Binomial2)
-
-
-library(ggtext)
-a<-ggtree(birdtreels) %<+% avgdf + ###########, layout = "circular"
-  geom_tiplab(aes(label= aud_rel), linesize = 0.01, offset = 30)+
-  #geom_tiplab(aes(label=paste0('italic(', Binomial2,')')),
-  #          parse=TRUE, linesize = 0.01, offset = 30)+
-  #geom_text(aes(label = node))+
-  xlim(NA, 160) +
-  ylim(NA,140)
-a
-
-
-
-avgdf$IACN<-ifelse(avgdf$IAC_detail=="",0,1)
-avgdf$IBPN<-ifelse(avgdf$IBP_detail=="",0,1)
-names(avgdf)
-
-sampled<-avgdf[,c("Head.mass..g.",
-                  "TMtotalarea"  ,
-                  "FPtotalarea"  ,
-                  "dis_coltip_TMcentroid",
-                  "meanTMangle"  ,
-                  "Umbo_distancetoTMplane",
-                  "CAtotalarea"  ,
-                  "RWtotalarea"  ,
-                  "totalEClength",
-                  "Columella.length.mm"   ,
-                  "Columella.volume.mm3" ,
-                  "Behind.TM"  ,
-                  "IACN","IBPN"  )]/avgdf[,c("Head.mass..g.",
-                                             "TMtotalarea"  ,
-                                             "FPtotalarea"  ,
-                                             "dis_coltip_TMcentroid",
-                                             "meanTMangle"  ,
-                                             "Umbo_distancetoTMplane",
-                                             "CAtotalarea"  ,
-                                             "RWtotalarea"  ,
-                                             "totalEClength",
-                                             "Columella.length.mm"   ,
-                                             "Columella.volume.mm3" ,
-                                             "Behind.TM"  ,
-                                             "IACN","IBPN"   )]
-colnames(sampled)
-colnames(sampled)<-seq(1:length(colnames(sampled)))
-#current sampling
-k2<-gheatmap(a,sampled,
-             width = 0.4, offset = 0,
-             color = "black",
-             low = "white",  high = "blue",
-             colnames = T,
-             colnames_position = "top",
-             colnames_angle = 0,
-             colnames_offset_x = 0,
-             colnames_offset_y = 5)
-k2