R Under development (unstable) (2024-01-24 r85824 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options(warn=1)
> library(compositions)
Welcome to compositions, a package for compositional data analysis.
Find an intro with "? compositions"


Attaching package: 'compositions'

The following objects are masked from 'package:stats':

    anova, cor, cov, dist, var

The following object is masked from 'package:graphics':

    segments

The following objects are masked from 'package:base':

    %*%, norm, scale, scale.default

> #library(compositions,lib.loc="../../compositions.Rcheck")
> par(pch=20)
> data(SimulatedAmounts)
> 
> geomSetA <- acomp(rbind(c(1,2,3),c(1,1,1)))
> geomSetA
     [,1]        [,2]        [,3]       
[1,] "0.1666667" "0.3333333" "0.5000000"
[2,] "0.3333333" "0.3333333" "0.3333333"
attr(,"class")
[1] "acomp"
> plot(geomSetA)
> ellipses(acomp(geomSetA[1,]),ilrvar2clr(clrvar2ilr(diag(3))))
> 
> geomSetA <- acomp(rbind(c(a=1,b=2,c=3,d=4),c(1,1,1,1)))
> geomSetA
     a      b      c      d     
[1,] "0.10" "0.20" "0.30" "0.40"
[2,] "0.25" "0.25" "0.25" "0.25"
attr(,"class")
[1] "acomp"
> plot(geomSetA,col=1:2,axes=list(side=-1:-3,pos=0.5))
> 
> 
> ellipses(acomp(geomSetA[1,]),ilrvar2clr(clrvar2ilr(diag(4))))
> ellipses(acomp(geomSetA[1,]),ilrvar2clr(clrvar2ilr(diag(4))),thinRatio=1)
> ellipses(acomp(geomSetA[1,]),ilrvar2clr(clrvar2ilr(diag(4))),thinRatio=0)
> 
> plot(geomSetA,col=1:2,margin="b")
> ellipses(acomp(geomSetA[1,]),ilrvar2clr(clrvar2ilr(diag(4))))
> 
> plot(rcomp(geomSetA),col=1:2,margin="b")
> 
> # In this file we suppress unnecessary warnings targeting end-users
> # Human: if you want to see them, replace suppressWarnings() by I()
> suppressWarnings( ellipses(rcomp(geomSetA[1,]),ilrvar2clr(clrvar2ilr(diag(4)))) )
> 
> 
> geomSetA <- acomp(rbind( c(2,1,1),c(1,2,1),c(1,1,2),c(1,1,1)))
> delta <- acomp(c(0.4,0.9,3))
> plot(geomSetA+delta)
> straight(acomp(c(2,1,1))+delta,acomp(c(1,2,1))-acomp(c(2,1,1)))
> rr = norm(acomp(c(1,1,2))-acomp(c(1,1,1)))
> ellipses(acomp(c(1,1,2))+delta,var=diag(3),r=rr)
> ellipses(mean(geomSetA+delta),var=var(geomSetA+delta),r=2)
> 
> 
> plot(rcomp(geomSetA+delta))
> straight(rcomp(acomp(c(2,1,1))+delta),rcomp(acomp(c(1,2,1))+delta)-rcomp(acomp(c(2,1,1))+delta))
> ellipses(rcomp(acomp(c(1,1,2)+delta)),var=diag(3)-1/3,r=norm(rcomp(acomp(c(1,1,2))+delta)-rcomp(acomp(c(2,1,1))+delta)))
> ellipses(mean(rcomp(geomSetA+delta)),var=var(rcomp(geomSetA+delta)),r=2)
> 
> geomSetA <- acomp(rbind( c(2,1,1,1),c(1,2,1,1),c(1,1,2,1),c(1,1,1,2),c(1,1,1,1)))
> delta <- acomp(c(0.4,0.9,3,1.2))
> #delta <- acomp(c(1,1,1,1))
> plot(geomSetA+delta,col=1:5,pch=1:5)
> straight(acomp(c(2,1,1,1))+delta,acomp(c(1,2,1,1))-acomp(c(2,1,1,1)),steps=100)
> #straight(acomp(c(2,1,1,1))+delta,acomp(c(1,2,1,1))-acomp(c(2,1,1,1)),steps=10)
> #ellipses(acomp(c(1,1,2,1))+delta,var=diag(4)-1/4,r=norm(acomp(c(1,1,2,1))-acomp(c(1,1,1,1))))
> replot(onlyPanel=c(3,1))
> segments.acomp(acomp(c(2,1,1,1))+delta,acomp(c(1,2,1,1))+delta,col="red")
> 
> ellipses(acomp(c(1,1,1,1))+delta,var=diag(4)-1/4,r=norm(acomp(c(1,1,2,1))-acomp(c(1,1,1,1))),col="blue")
> ellipses(mean(geomSetA+delta),var=var(geomSetA+delta),r=2,col="red")
> 
> ellipses(mean(geomSetA+delta),var=var(geomSetA+delta),r=2,col="red",thinRatio=0.1)
> 
> plot(rcomp(geomSetA+delta),col=1:5,pch=1:5)
> straight(rcomp(acomp(c(2,1,1,1))+delta),rcomp(acomp(c(1,2,1,1))+delta)-rcomp(acomp(c(2,1,1,1))+delta))
> ellipses(rcomp(acomp(c(1,1,2,1)+delta)),var=diag(4)-1/4,r=norm(rcomp(acomp(c(1,1,2,1))+delta)-rcomp(acomp(c(2,1,1,1))+delta)))
> ellipses(mean(rcomp(geomSetA+delta)),var=var(rcomp(geomSetA+delta)),r=2)
> 
> geomSetA <- aplus(rbind( c(2,1,1),c(1,2,1),c(1,1,2),c(1,1,1),c(1.5,1.5,1.5)))
> delta <- aplus(c(0.4,0.9,3))
> #delta <- aplus(c(1,1,1))
> plot(geomSetA+delta,xlim=c(0.1,10),ylim=c(0.1,10),logscale=TRUE)
> straight(aplus(c(2,1,1))+delta,aplus(c(1,2,1))-aplus(c(2,1,1)))
> ellipses(aplus(c(1.5,1.5,1.5))+delta,var=diag(3),r=norm(aplus(c(1,1,2))-aplus(c(1,1,1))))
> ellipses(aplus(c(1,1,1))+delta,var=diag(3),r=norm(aplus(c(1,1,2))-aplus(c(1,1,1))))
> ellipses(mean(geomSetA+delta),var=var(geomSetA+delta),r=2)
> lines(geomSetA+delta)
> geomSetA <- rplus(rbind( c(2,1,1),c(1,2,1),c(1,1,2),c(1,1,1),c(1.5,1.5,1.5)))
> delta <- rplus(c(0.4,0.9,3))
> plot(geomSetA+delta,xlim=c(0.1,10),ylim=c(0.1,10))
> #straight(aplus(c(2,1,1))+delta,aplus(c(1,2,1))-aplus(c(2,1,1)))
> ellipses(rplus(c(1.5,1.5,1.5))+delta,var=diag(3),r=norm(rplus(c(1,1,2))-rplus(c(1,1,1))))
> ellipses(mean(geomSetA+delta),var=var(geomSetA+delta),r=2)
> 
> plot(rcomp(sa.lognormals))
> ternaryAxis(side=1:3,pos=0,col.axis="red",col.lab="green")
> ternaryAxis(side=1:3,at=1:9/10,labels=expression(9:1,4:1,7:3,3:2,1:1,2:3,3:7,1:4,1:9),pos=0,col.axis="red",col.lab="green")
> ternaryAxis(side=rep(-1:-3,3),labels=paste(seq(20,80,by=20),"%"),
+             pos=rep(c(0,0.5,1),each=3),col.axis=1:3,col.lab="green")
> ternaryAxis(side=rep(1:3,3),at=1:9/10,labels=expression(9:1,4:1,7:3,3:2,1:1,2:3,3:7,1:4,1:9),pos=rep(c(0,0.5,1),each=3))
> 
> proc.time()
   user  system elapsed 
   3.67    0.56    4.23