Saved modified PlotPanel.r with all cat() calls added for full data e…

…xtraction

.Rproj.user/DFCA1C7C/sources/prop/INDEX

@@ -1,8 +1,10 @@
 C%3A%2FUsers%2FMeloMan%2FAppData%2FLocal%2FTemp%2FTemp1_RTaxometrics-master.zip%2FRTaxometrics-master%2FR%2FPlotPanel.R="3DCCC88D"
+D%3A%2FRProjects%2FHability_Taxon%2FPlotPanel_modified.R="33C8D1B8"
 D%3A%2FRProjects%2FHability_Taxon%2Fconsistency.R="7ADF8CD9"
 D%3A%2FRProjects%2FHability_Taxon%2Fdemographics.R="AE710784"
 D%3A%2FRProjects%2FHability_Taxon%2Fdistributions.R="663AA20D"
 D%3A%2FRProjects%2FHability_Taxon%2Fhability_taxon_data_prep.R="421CC383"
 D%3A%2FRProjects%2FHability_Taxon%2Fhability_taxon_data_prep_report.Rmd="E6AC997F"
+D%3A%2FRProjects%2FHability_Taxon%2FplotPanel_modified.R="9384B192"
 D%3A%2FRProjects%2FHability_Taxon%2Fplots.R="08424B45"
 D%3A%2F_TEMP%2FRTaxometrics-master%2FR%2FPlotPanel.R="00ED1479"

.Rproj.user/shared/notebooks/paths

@@ -1,4 +1,6 @@
 C:/Users/MeloMan/AppData/Local/Temp/Temp1_RTaxometrics-master.zip/RTaxometrics-master/R/PlotPanel.R="A713BB77"
+D:/RProjects/Hability_Taxon/PlotPanel_modified.R="8BCE7E95"
 D:/RProjects/Hability_Taxon/hability_taxon_data_prep_report.Rmd="5FF27526"
+D:/RProjects/Hability_Taxon/plotPanel_modified.R="F913FFAF"
 D:/RProjects/Hability_Taxon/plots.R="7E8D510D"
 D:/_TEMP/RTaxometrics-master/R/PlotPanel.R="4A083566"

PlotPanel_modified.R

@@ -0,0 +1,128 @@
+function (x.results, x.dim.results, x.cat.results, parameters, 
+          procedure) 
+{
+  if (procedure == "MAMBAC") {
+    n <- parameters$n.cuts
+    x.values <- 1:n
+    y.values <- apply(x.results$MAMBAC, 2, mean)
+    x.label <- "Cut"
+    y.label <- "Mean Difference"
+  }
+  if (procedure == "MAXEIG") {
+    n <- parameters$windows
+    x.values <- apply(x.results$MAXEIG.x, 2, mean)
+    y.values <- apply(x.results$MAXEIG.y, 2, mean)
+    x.label <- "Score"
+    y.label <- "Eigenvalue"
+  }
+  if (procedure == "MAXSLOPE") {
+    n <- parameters$n - 1
+    x.values <- apply(x.results$MAXSLOPE.x, 2, mean)
+    y.values <- apply(x.results$MAXSLOPE.y, 2, mean)
+    x.label <- "Score"
+    y.label <- "LOWESS Slope"
+  }
+  if (procedure == "LMode") {
+    n <- 512
+    x.values <- x.results$LMode.x
+    y.values <- x.results$LMode.y
+    x.label <- "Factor Score"
+    y.label <- "Density"
+  }
+  cat.sum <- matrix(0, nrow = 6, ncol = n)
+  dim.sum <- matrix(0, nrow = 6, ncol = n)
+  for (i in 1:n) {
+    if (procedure == "MAMBAC") {
+      cat.sum[, i] <- summary(x.cat.results$MAMBAC[, i])
+      dim.sum[, i] <- summary(x.dim.results$MAMBAC[, i])
+    }
+    if (procedure == "MAXEIG") {
+      cat.sum[, i] <- summary(x.cat.results$MAXEIG.y[, 
+                                                     i])
+      dim.sum[, i] <- summary(x.dim.results$MAXEIG.y[, 
+                                                     i])
+    }
+    if (procedure == "MAXSLOPE") {
+      cat.sum[, i] <- summary(x.cat.results$MAXSLOPE.y[, 
+                                                       i])
+      dim.sum[, i] <- summary(x.dim.results$MAXSLOPE.y[, 
+                                                       i])
+    }
+    if (procedure == "LMode") {
+      cat.sum[, i] <- summary(x.cat.results$LMode.y[, 
+                                                    i])
+      dim.sum[, i] <- summary(x.dim.results$LMode.y[, 
+                                                    i])
+    }
+  }
+  y.range <- c(min(c(y.values, cat.sum[1, ], dim.sum[1, ])), 
+               max(c(y.values, cat.sum[6, ], dim.sum[6, ])))
+  main.title <- paste(procedure, "\nCategorical Comparison Data")
+  plot(x.values, y.values, type = "l", ylim = y.range, xlab = x.label, 
+       ylab = y.label, main = main.title, cex.main = 0.75, 
+       cex.axis = 0.75, cex.lab = 0.75)
+  n <- length(x.values)
+  cat(main.title)
+  cat("\nx.values\n")
+  cat(x.values)
+  cat("\ny.values\n")
+  cat(y.values)
+  cat("\ny.range\n")
+  cat(y.range)
+  cat("\npolygon.x\n")
+  cat(c(x.values[1:n], x.values[n:1]))
+  cat("\npolygon.y\n")
+  cat(c(cat.sum[5, 1:n], cat.sum[2, n:1]))
+  cat("\nline 1.y\n")
+  cat(cat.sum[1, ])
+  cat("\nline 2.y\n")
+  cat(cat.sum[6, ])
+  polygon(x = c(x.values[1:n], x.values[n:1]), y = c(cat.sum[5, 
+                                                             1:n], cat.sum[2, n:1]), col = 8, lty = 0)
+  lines(x.values, cat.sum[1, ])
+  lines(x.values, cat.sum[6, ])
+  lines(x.values, y.values, lwd = 3)
+  if (procedure == "LMode") {
+    max.l <- max(smooth(y.values)[x.values <= parameters$mode.l])
+    loc.l <- (1:n)[smooth(y.values) == max.l]
+    if (length(loc.l) > 1) {
+      loc.l <- loc.l[1]
+    }
+    max.r <- max(smooth(y.values)[x.values >= parameters$mode.r])
+    loc.r <- (1:n)[smooth(y.values) == max.r]
+    if (length(loc.r) > 1) {
+      loc.r <- loc.r[1]
+    }
+    cat("lmode.line1.x")
+    cat(rep(x.values[loc.l], 2))
+    cat("lmode.line1.y")
+    cat(c(0, y.values[loc.l]))
+    cat("lmode.line2.x")
+    cat(rep(x.values[loc.r], 2))
+    cat("lmode.line2.y")
+    cat(c(0, y.values[loc.r]))
+    lines(x = rep(x.values[loc.l], 2), y = c(0, y.values[loc.l]))
+    lines(x = rep(x.values[loc.r], 2), y = c(0, y.values[loc.r]))
+  }
+  main.title <- paste(procedure, "\nDimensional Comparison Data")
+  plot(x.values, y.values, type = "l", ylim = y.range, xlab = x.label, 
+       ylab = y.label, main = main.title, cex.main = 0.75, 
+       cex.axis = 0.75, cex.lab = 0.75)
+  n <- length(x.values)
+  cat(main.title)
+  cat("\npolygon.y\n")
+  cat(c(dim.sum[5, 1:n], dim.sum[2, n:1]))
+  cat("\nline 1.y\n")
+  cat(dim.sum[1, ])
+  cat("\nline 2.y\n")
+  cat(dim.sum[6, ])
+  polygon(x = c(x.values[1:n], x.values[n:1]), y = c(dim.sum[5, 
+                                                             1:n], dim.sum[2, n:1]), col = 8, lty = 0)
+  lines(x.values, dim.sum[1, ])
+  lines(x.values, dim.sum[6, ])
+  lines(x.values, y.values, lwd = 3)
+  if (procedure == "LMode") {
+    lines(x = rep(x.values[loc.l], 2), y = c(0, y.values[loc.l]))
+    lines(x = rep(x.values[loc.r], 2), y = c(0, y.values[loc.r]))
+  }
+}