add SMA-allometries.R

GeneralAllometry/SMA-allomtries.R

@@ -0,0 +1,49 @@
+### This script builds a table of allometry predictions (L~D, D~M)
+### at branch levels for cherry and apples. The results are reported in the
+### manuscript.
+
+library('smatr')
+
+test_slope <- function(name, formulas, data){  
+  sma_row <- c(name)
+  for (i in 1:length(formulas)) {
+      test <- sma(formulas[i][[1]], log = 'xy', data = data)
+      sma_row <- c(sma_row, params_out(test))
+  }
+  return(sma_row)
+}
+
+params_out <- function(sma_data){
+  return (paste("a: ", round(sma_data$coef[[1]][2,1],2), " [ ", 
+                round(sma_data$coef[[1]][2,2],2), " , ", 
+                round(sma_data$coef[[1]][2,3],2), " ]; b: ",
+                round(sma_data$coef[[1]][1,1],2), " [ ", 
+                round(sma_data$coef[[1]][1,2],2), " , ", 
+                round(sma_data$coef[[1]][1,3],2), " ]; ", 
+                round(sma_data$r2[[1]], 3), sep = ""))
+} 
+
+branch_size <- read.csv("BranchSegments.csv", sep = ',', header = T)
+group_data <- list()
+group_data[[1]] <- branch_size[branch_size$species=="cherry",]
+group_data[[2]] <- branch_size[branch_size$species=="apple",]
+
+groups <- c("cherry", "apple")
+relationships <- c("L~D (Segment)", "(Path)", "(Subtree)", 
+                   "M~D (Segment)", "(Path)", "(Subtree)")
+branch_formulas <- c(length_cm   ~ diameter_mm, 
+                     path_length ~ diameter_mm, 
+                     tot_length  ~ diameter_mm,
+                     stem_m      ~ diameter_mm,
+                     path_stem_m ~ diameter_mm,
+                     tot_stem_m  ~ diameter_mm)
+
+output <- c()
+for (i in 1:2){
+  output <- rbind(output, test_slope(groups[i], branch_formulas, 
+                                     group_data[[i]]))
+}
+
+colnames(output) <- c('group', relationships)
+
+write.csv(output, "allometries.csv")

GeneralAllometry/allometries.csv

@@ -0,0 +1,3 @@
+"","group","L~D (Segment)","(Path)","(Subtree)","M~D (Segment)","(Path)","(Subtree)"
+"1","cherry","a: 0.83 [ 0.76 , 0.91 ]; b: 0.51 [ 0.4 , 0.62 ]; 0.006","a: 0.99 [ 0.93 , 1.05 ]; b: 0.64 [ 0.56 , 0.73 ]; 0.605","a: 1.53 [ 1.45 , 1.62 ]; b: 0.08 [ -0.05 , 0.2 ]; 0.613","a: 2.09 [ 2.01 , 2.17 ]; b: -0.75 [ -0.87 , -0.64 ]; 0.825","a: 2.33 [ 2.27 , 2.4 ]; b: -0.9 [ -0.99 , -0.81 ]; 0.92","a: 2.49 [ 2.43 , 2.55 ]; b: -1.05 [ -1.14 , -0.96 ]; 0.926"
+"2","apple","a: -1.15 [ -1.27 , -1.04 ]; b: 3.63 [ 3.45 , 3.82 ]; 0.024","a: 1.1 [ 1.02 , 1.19 ]; b: 0.32 [ 0.19 , 0.46 ]; 0.442","a: 1.65 [ 1.54 , 1.76 ]; b: -0.43 [ -0.61 , -0.26 ]; 0.577","a: 2.11 [ 1.99 , 2.23 ]; b: -0.67 [ -0.87 , -0.48 ]; 0.688","a: 2.36 [ 2.28 , 2.45 ]; b: -0.93 [ -1.07 , -0.79 ]; 0.867","a: 2.57 [ 2.49 , 2.66 ]; b: -1.21 [ -1.35 , -1.07 ]; 0.892"