update to selection to allow multiple conditions to be plotted on the…

… same graph

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PopGen
-Version: 0.4
-Date: 2017-10-06
+Version: 0.5
+Date: 2018-02-13
 Title: Population genetic simulations & numerical analysis
 Author: Liam J. Revell
 Maintainer: Liam J. Revell <liam.revell@umb.edu>
@@ -11,6 +11,6 @@ ZipData: no
 Description: conducts various numerical analyses and simulations in population genetics and evolutionary theory.
 License: GPL (>= 2)
 URL: http://github.com/liamrevell/PopGen
-Packaged: 2017-10-06 21:00:00 EST
+Packaged: 2018-02-13 12:00:00 EST
 Repository: 
-Date/Publication: 2017-10-06 21:00:00 EST
+Date/Publication: 2018-02-13 12:00:00 EST

R/popgen.R

@@ -1,48 +1,53 @@
-# functions by Liam Revell 2012 (some small updates 2017)
+# functions by Liam Revell 2012 (some small updates 2017, 2018)
 
-selection<-function(p0=0.01,w=c(1.0,0.9,0.8),time=100,show="p",pause=0){
+selection<-function(p0=0.01,w=c(1.0,0.9,0.8),time=100,show="p",pause=0,...){
+	if(hasArg(add)) add<-list(...)$add
+	else add<-FALSE
+	if(hasArg(color)) color<-list(...)$color
+	else color<-"black"
 	if(show=="surface"){
 		p<-0:100/100
 		wbar<-p^2*w[1]+2*p*(1-p)*w[2]+(1-p)^2*w[3]
-		plot(p,wbar,type="l",ylim=c(0,1),main="mean fitness")
+		plot(p,wbar,type="l",ylim=c(0,1),main="mean fitness",col=color)
 	}
 	else if(show=="deltap"){
 		p<-0:100/100
 		wbar<-p^2*w[1]+2*p*(1-p)*w[2]+(1-p)^2*w[3]
 		deltap<-(p/wbar)*(p*w[1]+(1-p)*w[2]-wbar)
-		plot(p,deltap,type="l",main="delta p")
+		plot(p,deltap,type="l",main="delta p",col=color)
 		lines(c(0,1),c(0,0),lty=2)
 	} else {
 		if(show=="cobweb"){
 			p<-0:100/100
 			wbar<-p^2*w[1]+2*p*(1-p)*w[2]+(1-p)^2*w[3]
 			p2<-(p/wbar)*(p*w[1]+(1-p)*w[2]-wbar)+p
-			plot(p,p2,type="l",xlab="p(t)",ylab="p(t+1)")
+			plot(p,p2,type="l",xlab="p(t)",ylab="p(t+1)",col=color)
 			lines(c(0,1),c(0,1),lty=2)
 			dev.flush()
 		}
-		p<-wbar<-vector(); p[1]<-p0
+		p<-wbar<-vector()
+		p[1]<-p0
 		wbar[1]<-p[1]^2*w[1]+2*p[1]*(1-p[1])*w[2]+(1-p[1])^2*w[3]
 		for(i in 2:time){
 			p[i]<-p[i-1]
 			p[i]<-(p[i]^2*w[1]+p[i]*(1-p[i])*w[2])/wbar[i-1]
 			wbar[i]<-p[i]^2*w[1]+2*p[i]*(1-p[i])*w[2]+(1-p[i])^2*w[3]
 			ii<-(i-1):i
 			if(show=="p"){
-				if(i==2) plot(1:i,p,type="l",xlim=c(0,time),ylim=c(0,1),xlab="time",
-					main="frequency of A")
-				else lines(ii,p[ii],type="l")
-			} else if(show=="q"){
+				if(i==2 && !add) plot(1:i,p,type="l",xlim=c(0,time),ylim=c(0,1),xlab="time",
+					main="frequency of A",col=color)
+				else lines(ii,p[ii],type="l",col=color)
+			} else if(show=="q" && !add){
 				if(i==2) plot(1:i,1-p,type="l",xlim=c(0,time),ylim=c(0,1),xlab="time",
-					ylab="q",main="frequency of a")
-				else lines(ii,1-p[ii],type="l")
-			} else if(show=="fitness"){
+					ylab="q",main="frequency of a",col=color)
+				else lines(ii,1-p[ii],type="l",col=color)
+			} else if(show=="fitness" && !add){
 				if(i==2) plot(1:i,wbar/max(w),type="l",xlim=c(0,time),ylim=c(0,1),
-					xlab="time",main="mean fitness")
-				else lines(ii,wbar[ii]/max(w),type="l")
+					xlab="time",main="mean fitness",col=color)
+				else lines(ii,wbar[ii]/max(w),type="l",col=color)
 			} else if(show=="cobweb"){
-				lines(c(p[i-1],p[i-1]),c(p[i-1],p[i]))
-				lines(c(p[i-1],p[i]),c(p[i],p[i]))
+				lines(c(p[i-1],p[i-1]),c(p[i-1],p[i]),col=color)
+				lines(c(p[i-1],p[i]),c(p[i],p[i]),col=color)
 			} else {
 				message("not a recognized option")
 				break

man/selection.Rd

@@ -2,14 +2,15 @@
 \alias{selection}
 \title{Numerical analysis of biallelic locus frequency independent selection}
 \usage{
-	selection(p0=0.01,w=c(1.0,0.9,0.8),time=100,show="p",pause=0)
+	selection(p0=0.01,w=c(1.0,0.9,0.8),time=100,show="p",pause=0,...)
 }
 \arguments{
 	\item{p0}{Starting frequency for the A allele.}
 	\item{w}{Fitnesses for the three genotypes in the following order: AA, Aa, aa.}
 	\item{time}{Number of generations to run the analysis.}
 	\item{show}{Various options for plotting. \code{"p"} shows the frequency of A through time; \code{"surface"} plots the mean fitness as a function of p; \code{"deltap"} shows the change in p as a function of p; \code{"cobweb"} creates a cobweb plot showing p(t) by p(t+1). The default is \code{show="p"}.}
 	\item{pause}{Pause between generations. \code{pause=0.01} (for instance) might smooth animation.}
+	\item{...}{optional arguments.}
 }
 \description{
 	This function performs numerical analysis of a simple biallelic selection model.