Cumulative distributions - Day 2

Cumulative distributions and ranks

  • We want to make a plot of the cumulative distribution of a function $P(x)$ the frequency of words in a text.

  • The cumulative distribution of the frequency is defined such that $P(x)$ is the fraction of words with frequency greater than or equal to $x$.

  • If $x$ is the frequency of the most frequent word, usually “the”, then there is exactly one word with frequency greater than or equal to $x$.

    Similarly for the second most frequent word, usually “of”, there are two words with frequency greater than or equal: “of” and “the”.

Cumulative distributions and ranks 1

  • In general if we rank the words in descending order then by definition there are n words with frequency greater than or equal than that of the nth most commond word.

    Thus the cumulative distribution $P(x)$ is proportional to the rank n of a word.

    Then to plot $P(x)$ we only need to plot the ranks as a function of the frequency.

Cumulative distributions and fractal dimension

  • We can analyze the data from Metzler (1992)
		rm(list=ls())

		ps <- read.table("patch1968.dat",header=T)

		ps$r <- rank(-ps$pSize)

		plot(r ~ pSize,data=ps)

		plot(log(r)~log(pSize),data=ps)		

		lm0 <- lm(log(r)~log(pSize),data=ps)

		summary(lm0)

		abline(lm0)

Cumulative distributions and fractal dimension 1

  • If $B$ is the exponent then $H = 2 - 2B$
		slope0 <- coef(lm0)[2]
		
		2+slope0*2
The patches are persistent because H=1.18 > 0.5
  • We need to install the package “car” to test for autocorrelation with the Durbin-Watson statistic. We can do this using the RStudio menu Tools/Install Packages.
		require(car)

		dwt(lm0)
we can draw a grid to determine the break point.
		grid()

Exercise 1

  • Split the data in two to obtain two fractal dimensions without correlation

  • There is a shorcut for doing this: the package “segmented” fits a broken line and finds the break point.

		require(segmented)

		ps$logr <- log(ps$r)
		ps$logpSize <- log(ps$pSize)
		lm0 <- lm(logr~logpSize,data=ps)
		seg <- segmented(lm0, seg.Z = ~logpSize, psi=4)
		summary(seg)
		slope(seg)

Exercise 1 (Cont.)

  • Let’s do a function to calculate H

  • small patches are persistent

		calcH <- function(B) { 2-2*abs(B)}

		calcH(.1550) # H = 1.69
Big patches are anti-persistent
		calcH(.9036) # H = 0.19
  • What is the breakpoint value in ha? Let’s do another function.

  • A possible answer:

		calcBreak <- function(B) { 0.1*exp(B)*0.65 } 

		calcBreak(3.35) # 1.85 ha

Conclusion

  • small patches: if they are growing they keep growing, if they are reducing they vanish.

  • big patches: if they are growing they will reduce, if they are reducing they will grow.

  • Thus big patches are more stable, small patches appear and disappear.

Exercise 2

  • Let’s do the same thing using segmented with the 1985 data: “patch1985.dat”

  • We can do a plot with the segmented object

		plot(seg,col="green",xlab="Log Patch Size"
				,ylab="Acum Freq")
		
		points(log(r)~log(pSize),data=ps,pch=2,cex=.5)
  • We can use the functions:
		summary(seg)
		slope(seg)

		calcH(0.2676)
		calcH(1.26)

		calcBreak(2.708) # 0.97 ha

A different graphic analysis

  • Using graphics package “ggplot2”. We need to add both datasets in one data frame
		ps <- read.table("patch1985.dat",header=T)
		ps$r <- rank(-ps$pSize)
		ps$Year <- "1985"

		ps1 <- read.table("patch1968.dat",header=T)
		ps1$r <- rank(-ps1$pSize)
		ps1$Year <- "1968"

		ps <- rbind(ps,ps1)

Gramar of graphics ggplot2

		require(ggplot2)
		ggplot(data=ps,aes(x=pSize,y=r,color=Year))
					+geom_point()

		p <- ggplot(data=ps,aes(x=log(pSize),y=log(r),
				color=Year))+geom_point(aes(shape=Year))

More questions

  • This seems a fragmentation process the frequency of small patches increases but the scaling of big patches seems similar, have big patches different scalings?
		ps$logpSize <- log(ps$pSize)
		
		ps1 <- ps[ps$logpSize>3.35,]

		p + geom_smooth(data=ps1,method="lm")

		ggsave("patch_Breaks.png",width=2)
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