demos/phases_plots.R

In cboettig/AdaptiveDynamics: Waiting Times for Evolutionary Branching in Adaptive Dynamics

colVars <- function(X) sapply(1:dim(X)[2], function(i) var(X[,i]))
library(Hmisc)
##
# plot the output of waiting_times.R
# all is one of vary_mu, vary_sigma_mu, etc

plot_phases <- function(all, parameter, xlab){


	sigma_c2 <- parameter
	K<- length(all)
	reps <- all[[1]]$reps

	phase1_attempts <- sapply(1:K, function(i)
		sapply(1:reps, function(j) all[[i]]$data[[j]]$dimorph_fails)
	)

	phase2_attempts <- sapply(1:K, function(i)
		sapply(1:reps, function(j) all[[i]]$data[[j]]$trimorph_fails)
	)

	phase1_times <-  sapply(1:K, function(i)
		sapply(1:reps, function(j) all[[i]]$data[[j]]$pos_time[1,1])
	)
	phase2_times <-  sapply(1:K, function(i)
		sapply(1:reps, function(j) all[[i]]$data[[j]]$pos_time[2,1])
	)
	phase3_times <-  sapply(1:K, function(i)
		sapply(1:reps, function(j) all[[i]]$data[[j]]$pos_time[3,1])
	)


	plot_err <- function(phase, xlab, add=F, col="black", ylab=ylab, ...){
		cm1 <- colMeans(phase)
		cv1 <- sqrt(colVars(phase))
			errbar(parameter, cm1, cm1+cv1, cm1-cv1, xlab=xlab, ylab=ylab, add=add, col=col, ...)
			lines(parameter, cm1, col=col, ...)
	}

	plottries <- function(){
		plot_err(phase1_attempts, xlab, ylab="Num. of attempts")
		plot_err(phase2_attempts, add=T, col="blue")
		legend("topleft", c("phase 1", "phase 2"), col=c("black", "blue"), lty=1)
	}

	
	plottimes <- function(){
		plot_err(phase3_times, xlab, ylab="Time to phase", lwd=3)
		plot_err(phase2_times, xlab, add=T, col="blue")
		plot_err(phase1_times, xlab, add=T, col="green")
		legend("topleft", c("phase 3", "phase 2", "phase 1"), col=c("black", "blue", "green"), lty=1)
	}

social_plot(plottries(), file="attempts.png", tags="adaptivedynamics", comment="Number of attempts", mention="cboettig")
social_plot(plottimes(), file="times.png", tags="adaptivedynamics", comment="times")

}
#social_plot(errbar(sigma_c2, cm1/cm2, cm1/cm2+(cv1+cv2), cm1/cm2-(cv1+cv2)),
#	file="sigma_c2.png", tags="adaptivedynamics", comment="ratio")