Migration_model/MigVsStat.html at master · sjpeacock/Migration_model · GitHub

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<html>
<head>
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	<title>Parasite dynamics of migratory and non-migratory host populations</title>
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	<div class="scianimator" style="width: 800px; text-align: left"><pre><code class="r">## Simulations for two scenarios - a stationary population (dashed lines) and a migratory host
##   population (solid lines) - illustrating the influence of migration on disease dynamics.
##   Spatial dynamics are on the left and the changes in time at the location of peak host
##   population density are on the right. Parameters for the simulation are: beta=0, mu=0,
##   alpha=0.1, sigma = 5, rho = 0, omega = 0, gamma = 0, theta = 0, c = 10000, kappa = 10, lambda
##   = 0.01 and mu_L = 5.
library(animation)
for (j in plot.ind) {
    layout(matrix(1:8, 4, 2, byrow = TRUE))
    par(mar = c(1, 2, 1, 0), oma = c(4, 3, 3, 1), mgp = c(3,
        1, 0))
    migInd <- c(mean.start + 2 * dx + params["c."] * dt *
        j)/dx
    for (i in 1:4) {
        y1 <- V[[1]][c(4:7)[i], x.ind, j]
        y1.all <- y1
        if (i < 4)
            y1[which(round(V[[1]][4, x.ind, j]) <= 1)] <- NA
        y2 <- V[[2]][c(1:3, 7)[i], x.ind, j]
        y2.all <- y2
        if (i < 4)
            y2[which(round(V[[2]][1, x.ind, j]) <= 1)] <- NA
        plot(x[x.ind], y1, "l", bty = "l", xaxt = "n", xlab = "",
            ylab = "", las = 1, ylim = range(c(V[[1]][c(4:7)[i],
              , ], V[[2]][c(1:3, 7)[i], , ])), las = 1, col = col.mig[1],
            lwd = 1.2, yaxt = "n")
        if (i == 4) {
            axis(side = 2, at = c(0, 1000, 2000, 3000), labels = c(0,
              1, 2, 3), las = 1, cex = big)
        }
        else if (i == 1) {
            axis(side = 2, at = c(0, 500, 1000), labels = c(0,
              0.5, 1), las = 1, cex = big)
        }
        else if (i == 3) {
            axis(side = 2, at = c(2, 4, 6), las = 1, cex = big)
        }
        else {
            axis(side = 2, las = 1)
        }
        if (i < 4)
            lines(x[x.ind], y1.all, col = col.mig[1], lty = 3)
        lines(x[x.ind], y2, col = col.mig[2], lwd = 1.2)
        if (i < 4)
            lines(x[x.ind], y2.all, col = col.mig[2], lty = 3)
        points(x[migInd], V[[1]][c(4:7)[i], migInd, j], pch = 19,
            cex = 0.8, col = col.mig[1])
        points(x[c(mean.start + 2 * dx)/dx], V[[2]][c(1:3,
            7)[i], c(mean.start + 2 * dx)/dx, j], pch = 19,
            col = col.mig[2], cex = 0.8)
        if (i == 4)
            axis(side = 1, cex = big)
        else axis(side = 1, labels = FALSE, cex = big)
        mtext(side = 2, line = 3, c("Host population\n(thousands)",
            "Parasite burden", "VMR", "Free-living parasites\n(thousands)")[i],
            cex = big)
        if (i == 4)
            mtext(side = 1, "Distance", cex = big, line = 3)
        mtext(side = 3, adj = 0, paste(" ", letters[(i -
            1) * 2 + 1]), cex = big)
        Ind <- cbind(rep(c(4:7)[i], j), round(c(mean.start +
            2 * dx + params["c."] * dt * c(1:j))/dx), 1:j)
        plot(c(1:j) * dt, V[[1]][Ind], "l", bty = "l", xaxt = "n",
            xlab = "", ylab = "", las = 1, ylim = range(c(V[[1]][c(4:7)[i],
              , ], V[[2]][c(1:3, 7)[i], , ])), xlim = c(0,
              n.t * dt), yaxt = "n", col = col.mig[1], lwd = 1.2)
        if (i == 4) {
            axis(side = 2, at = c(0, 1000, 2000, 3000), labels = FALSE)
        }
        else if (i == 1) {
            axis(side = 2, at = c(0, 500, 1000), labels = FALSE)
        }
        else if (i == 3) {
            axis(side = 2, at = c(2, 4, 6), labels = FALSE)
        }
        else {
            axis(side = 2, labels = FALSE)
        }
        if (i == 4)
            axis(side = 1, cex = big)
        else axis(side = 1, labels = FALSE)
        lines(c(1:j) * dt, V[[2]][c(1:3, 7)[i], c(mean.start +
            2 * dx)/dx, 1:j], col = col.mig[2], lwd = 1.2)
        points(j * dt, V[[1]][Ind[dim(Ind)[1], 1], Ind[dim(Ind)[1],
            2], Ind[dim(Ind)[1], 3]], pch = 19, cex = 0.8,
            col = col.mig[1])
        points(j * dt, V[[2]][c(1:3, 7)[i], c(mean.start +
            2 * dx)/dx, j], pch = 19, col = col.mig[2], cex = 0.8)
        if (i == 4)
            mtext(side = 1, "Time", cex = big, line = 3)
        mtext(side = 3, adj = 0, paste(" ", letters[(i -
            1) * 2 + 2]), cex = big)
    }
    reset()
    legend("top", lwd = 1.2, col = col.mig, ncol = 2, c("Migratory",
        "Non-migratory"), xpd = NA, bty = "n", cex = big)
}
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Other packages: animation 2.4</code></pre></div>
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