Add bookdown index and chapter ordering

Chapter_2.Rmd

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-A simple model for allel fixation

Chapter_3.Rmd

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+---
+title: "Chapter 3"
+---
+
+Figure 3.5
+
+Pueblo lineage 
+```{r}
+```
+
+A simple model for allel fixation
+
+Figure 3.13
+```{r}
+# drift vs selection
+set.seed(1)
+N <- 10000          # population size
+gens <- 200       # generations
+p0 <- 0.2         # initial allele frequency
+s <- .1            # selection advantage (fitness of A is 1+s, a is 1)
+
+drift <- sel <- numeric(gens + 1)
+drift[1] <- p0
+sel[1] <- p0
+
+for (g in 1:gens) {
+  # neutral drift
+  drift[g + 1] <- rbinom(1, N, drift[g]) / N
+  
+  # selection then drift (haploid fitness model)
+  p_after_sel <- (1 + s) * sel[g] / ((1 + s) * sel[g] + (1 - sel[g]))
+  sel[g + 1] <- rbinom(1, N, p_after_sel) / N
+}
+aá
+matplot(
+  cbind(0:gens, 0:gens),
+  cbind(drift, sel),
+  type = "l", lty = 1, lwd = 4, xlab = "Generation", ylab = "Allele A frequency",
+  col = c("grey50", "firebrick"), main = "Neutral drift vs. positive selection"
+)
+abline(h = c(0, 1), lty = 2, col = "gray70")
+legend("topright", c("drift", "selected"), col = c("grey50", "firebrick"), lwd = 2, bty = "n")
+```
+
+We will see later how this can be adapte to represent change in frequency of cultural traits under different cultrural transmission regimes
+

Chapter_4.Rmd

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+---
+title: "Chapter 4"
+---

Chapter_5.Rmd

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+---
+title: "Chapter 5"
+---
+
+Figure 5.3
+```{r}
+```
+Figure 5.8
+```{r}
+```
+
+Figure 5.9
+```{r}
+```
+
+Figure 5.11
+```{r}
+```
+

Chapter_6.Rmd

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+---
+title: "Chapter 6"
+---
+
+CV transmission etc..
+
+Figure 6.4
+
+```{r}
+plot(1,1)
+```
+

Chapter_9.Rmd

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+---
+title: "Chapter 9"
+---
+
+Figure 9.13
+```{r}
+```
+

_bookdown.yml

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+rmd_files: [
+  "index.Rmd",
+  "Chapter_3.Rmd",
+  "Chapter_4.Rmd",
+  "Chapter_5.Rmd",
+  "Chapter_6.Rmd",
+  "Chapter_9.Rmd"
+]

index.Rmd

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+---
+title: "EA Companion"
+author: "CE Book Team"
+date: "`r Sys.Date()`"
+site: bookdown::bookdown_site
+output:
+  bookdown::gitbook:
+    split_by: section
+---
+
+# EA Companion
+
+This is the front page for the Bookdown project.
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+