R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("ouch-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('ouch')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "anolis.ssd"
> 
> ### * anolis.ssd
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: anolis.ssd
> ### Title: Greater Antillean anolis lizard sexual size dimorphism data.
> ### Aliases: anolis.ssd
> ### Keywords: models
> 
> ### ** Examples
> 
> data(anolis.ssd)
> attach(anolis.ssd)
> tree.plot(node,ancestor,time,species,OU.7)
> brown.fit(log.SSD,node,ancestor,time)
$sigma
[1] 0.1181802

$theta.0
[1] 0.1430728

$u
[1] -38.35443

$aic
[1] -34.35443

$sic
[1] -32.08344

$df
[1] 2

> hansen.fit(log.SSD,node,ancestor,time,OU.1)
$alpha
[1] 0.3414213

$sigma
[1] 0.1335365

$theta
   theta.0   theta.ns 
0.18163910 0.07391728 

$u
[1] -38.44080

$aic
[1] -30.44080

$sic
[1] -25.89882

$df
[1] 4

> hansen.fit(log.SSD,node,ancestor,time,OU.7)
$alpha
[1] 1.436713

$sigma
[1] 0.08852319

$theta
    theta.0   theta.anc    theta.tw    theta.cg    theta.tc    theta.gb 
 0.22802416  0.46847578 -0.07403442 -0.06046253  0.13423525 -0.01286922 
   theta.tg    theta.tr 
 0.32715384 -0.05126040 

$u
[1] -72.71001

$aic
[1] -52.71001

$sic
[1] -41.35507

$df
[1] 10

> 
> 
> 
> cleanEx(); ..nameEx <- "bimac"
> 
> ### * bimac
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: bimac
> ### Title: Anolis bimaculatus lizard size data.
> ### Aliases: bimac
> ### Keywords: models
> 
> ### ** Examples
> 
> data(bimac)
> attach(bimac)
> tree.plot(node,ancestor,time,names=species,regimes=OU.LP)
> brown.fit(log(size),node,ancestor,time/max(time))
$sigma
[1] 0.2076296

$theta.0
[1] 2.948075

$u
[1] -34.66257

$aic
[1] -30.66257

$sic
[1] -28.39158

$df
[1] 2

> hansen.fit(log(size),node,ancestor,time/max(time),OU.1)
$alpha
[1] 0.001000000

$sigma
[1] 0.2076905

$theta
    theta.0    theta.ns 
2.951050015 0.002952527 

$u
[1] -34.65802

$aic
[1] -26.65802

$sic
[1] -22.11604

$df
[1] 4

> hansen.fit(log(size),node,ancestor,time/max(time),OU.3)
$alpha
[1] 0.3154043

$sigma
[1] 0.196042

$theta
     theta.0 theta.medium  theta.small  theta.large 
   3.9940480    0.1785914   -1.4032215    2.7056768 

$u
[1] -40.06191

$aic
[1] -28.06191

$sic
[1] -21.24894

$df
[1] 6

> hansen.fit(log(size),node,ancestor,time/max(time),OU.4)
$alpha
[1] 14.67051

$sigma
[1] 0.4747051

$theta
     theta.0    theta.anc  theta.small  theta.large theta.medium 
5.024086e-06 2.827655e+00 2.582593e+00 3.297562e+00 3.105650e+00 

$u
[1] -47.22319

$aic
[1] -33.22319

$sic
[1] -25.27473

$df
[1] 7

> hansen.fit(log(size),node,ancestor,time/max(time),OU.LP)
$alpha
[1] 2.490477

$sigma
[1] 0.2216015

$theta
     theta.0 theta.medium  theta.small  theta.large 
   0.8628386    3.2376820    2.7531639    3.5582111 

$u
[1] -49.69484

$aic
[1] -37.69484

$sic
[1] -30.88188

$df
[1] 6

> 
> 
> 
> cleanEx(); ..nameEx <- "tree"
> 
> ### * tree
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: tree.plot
> ### Title: Validating and plotting phylogenetic trees.
> ### Aliases: tree.plot is.valid.ouch.tree
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(bimac)
> attach(bimac)
> is.valid.ouch.tree(node,ancestor,time,OU.LP)
[1] TRUE
> tree.plot(node,ancestor,time,species,OU.LP)
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  2.82 0.03 2.87 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')