caper: Comparative Analyses of Phylogenetics and Evolution in R

系統学および進化学における比較解析ツール

> library(caper)

バージョン: 0.5.2

関数名 概略
BritishBirds Conservation status of British birds (Thomas 2008)
IsaacEtAl Example dataset for the caper package
VCV.array Create a 2D or 3D variance-covariance matrix from a phylogeny
anova.caic Anova and model checking methods for independent contrast models.
anova.pgls Anova and AIC tables for 'pgls' models.
brunch Comparative analysis using the brunch algorithm.
caic-class The 'caic' S3 object class and methods
caic.diagnostics Diagnostic tools for independent contrasts models
caper-benchmarks Datasets used for benchmarking caper
caper-package Comparative analysis of phylogenetics and evolution in R (caper)
clade.matrix Create a clade matrix from a phylogeny
clade.members Identify tips descended from a node
coef.pgls Generic model methods for 'pgls' models.
comparative.data Comparative dataset creation
crunch Comparative analysis using the crunch algorithm.
fusco.test Imbalance statistics using Fusco and Cronk's method.
fuscoBirdData Example dataset for Fusco imbalance calculations
growTree Tree simulation with traits.
macrocaic Comparative analysis using independent contrasts on species richness data.
pd.calc Calculate and bootstrap phylogenetic diversity measurements.
perissodactyla Example dataset for the CAIC package
pgls Phylogenetic generalized linear models
pgls.profile Likelihood profiles and confidence intervals for 'pgls' models.
phylo.d Calculates the phylogenetic D statistic
phylo.d.subset Calculates the phylogenetic D statistic across clades within a phylogeny
plot.pgls Diagnostic plots for 'pgls' models.
shorebird Example dataset for the caper package
summary.caic Summarize a crunch, brunch or macrocaic analysis
syrphidae The syrphidae dataset of Katzourakis et al. 2001

comparative.data

比較解析用データセットの生成

Arguments

  • data
  • phy
  • names.col
  • vcv.dim
  • na.omit
  • force.root
  • warn.dropped
  • scope
  • x
  • object
  • select
  • order
  • i, j
  • ...
> data(shorebird)
> shorebird <- comparative.data(phy = shorebird.tree, data = shorebird.data, 
+                               names.col = 'Species')
> print(shorebird)

Comparative dataset of 71 taxa:
Phylogeny: shorebird.tree 
   71 tips, 62 internal nodes
   chr [1:71] "Catoptrophorus_semipalmatus" "Tringa_ochropus" ...
Data: shorebird.data 
   $ M.Mass  : num [1:71] 273 75 67.1 80 172 123 142 164 62 50.2 ...
   $ F.Mass  : num [1:71] 301.4 85 76 83.7 175 ...
   $ Egg.Mass: num [1:71] 39.5 15.5 14 17.4 30.5 22.3 24.5 27.9 13.5 9.4 ...
   $ Cl.size : num [1:71] 4 3.9 4 4 3.9 4 4 3.7 4 4 ...
   $ Mat.syst: Factor w/ 3 levels "MO","PA","PG": 1 1 1 1 1 1 1 1 1 2 ...

pgls

系統的一般化最小二乗法

> data(shorebird)
> shorebird <- comparative.data(shorebird.tree, shorebird.data, Species, vcv = TRUE, vcv.dim = 3)
> mod1 <- pgls(log(Egg.Mass) ~ log(M.Mass) * log(F.Mass), shorebird, lambda = 'ML')
> mod2 <- pgls(log(Egg.Mass) ~ log(M.Mass), data = shorebird, lambda = 'ML', delta = 'ML')

plot.pgls

> # usage_pgls
> plot(mod1)
> plot(mod2)

shorebird

Lislevand and Thomas (2006)の記録した卵のサイズデータセット

> data(shorebird)
> class(shorebird)

[1] "comparative.data"

> names(shorebird)

[1] "phy"       "data"      "data.name" "phy.name"  "dropped"   "vcv"      
[7] "vcv.dim"