Multifractals in ecology using R - Day 2

Posgraduate course, University of Maringá, 2013

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)
          ps <- read.table("patch1968.dat",header=T)
          ps$r <- rank(-ps$pSize)
          plot(r ~ pSize,data=ps)
          lm0 <- lm(log(r)~log(pSize),data=ps)

Cumulative distributions and fractal dimension 1

  • If $B$ is the exponent then $H = 2 - 2B$
          slope0 <- coef(lm0)[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.

    we can draw a grid to determine the break point.


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.

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

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


  • 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")
  • We can use the functions:
          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


		p <- ggplot(data=ps,aes(x=log(pSize),y=log(r),

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")