adjusting the bttleship plot

Chapter_6.Rmd

@@ -7,7 +7,79 @@ title: "Chapter 6"
 CV transmission etc..
 
 Figure 6.4
+kroeber seriation:
+
+```{r battleship-seriation, fig.width=7.2, fig.height=4.8, fig.cap=""}
+dt <- data.frame(
+  "Black-on-Red" = c(1,2, 2, 2, 3, 4, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0),
+  "Three-Color" = c(0,0, 0, 0, 0, 0, 1, 1, 3, 4, 3, 2, 0, 0, 0, 0),
+  "Corrugated" = c(1,1, 0, 1, 2, 3, 2, 7, 4, 7, 9, 10, 11, 10, 15, 20),
+  check.names = FALSE
+)
+rownames(dt) <- 
+ c( "Zuni",
+"Towway",
+"Kolliwa",
+"Shunnte",
+"Wimmay",
+"Mattsak",
+"Kyakki",
+"Pinnawa",
+"Site W",
+"Hattsina",
+"Kyakki W",
+"Shoptlu",
+"Hawwik B",
+"Te\\'alla",
+"Site X",
+"Tetlnat"
+)
+ship_cols <- c("#8c6bb1", "#1f77b4", "#ff7f0e")
+series_col <- ncol(dt)
+n_phase <- nrow(dt)
+
+dt_pct <- sweep(as.matrix(dt), 2, colSums(as.matrix(dt)), "/") * 100
+
+par(mfrow = c(1, 3), las = 1, bty = "n", mar = c(0,0, 3,0), oma = c(0, 6, 0, 0),xpd=NA)
+phase_axis <- seq_len(n_phase)
+phase_labels <- rownames(dt)
+
+for (s in seq_len(series_col)) {
+  plot(
+    NA,
+    xlim = c(-(max(dt_pct[,s]/2)),max(dt_pct[,s]/2)),
+    ylim = c(0.5, n_phase + 0.5),
+    axes = FALSE,
+    xlab = "Width = relative frequency (%)",
+    ylab = ifelse(s == 1, "Phase", ""),
+    main = colnames(dt)[s]
+  )
+
+  for (r in phase_axis) {
+    chip_bottom <- (n_phase - r) + 0.55
+    chip_top <- (n_phase - r) + 1.45
+    chip_width <- dt_pct[r, s]
+
+    rect(
+      -chip_width / 2,
+      chip_bottom,
+      chip_width / 2,
+      chip_top,
+      col = ship_cols[s],
+      border = "white"
+    )
+  }
+
+  if(s==1) 
+      text(-(max(dt_pct[,s]/2)),seq((0.55+1.45)/2, (0.55+1.45)/2*n_phase ,length.out=n_phase),phase_labels,pos=2,font=2,,cex=2)
+}
+```
+
+A more common wa to represent tht would be to plot the freuecny through time, using 
 
 ```{r}
-plot(1,1)
+  matplot(cbind(1:nrow(dt) ,1:nrow(dt) ,1:nrow(dt)) ,dt,type="l",lwd=3,col=ship_cols,lty=1)
 ```
+
+This should remind you of the plot about chnges in allele frquency seen in Chapter 3, we will see later how we cna use these describption of the dt to test hypothese about the cultural transmission process
+