Description Usage Format References See Also Examples
This is a comparative dataset on Perissodactyla taken from the examples include with the original CAIC program.
1 |
The datafile contains a phylogeny (perissodactyla.tree
) of 18 perissodactyl species as a 'phylo' object from the ape
library. The tip names are the binomial names of the species. The file also contains a data frame (perissodactyla.data
) of variables 5 variables for 13 of those species:
The species binomial name.
Log female weight
Log gestation length
Log neonatal weight
A factor indicating whether or not the species displays territorial behaviour.
The dataset is incomplete - it does not include data for each species in the phylogeny and contains missing values. See the examples for the behaviour of the 'comparative.data' function in handling missing data.
Purvis, A. and Rambaut, A. (1995). Comparative Analysis by Independent Contrasts (CAIC) User's Guide.
caic, pgls
1 2 3 4 5 6 | data(perissodactyla)
# default behaviour is to omit incomplete data rows
(perisso <- comparative.data(perissodactyla.tree, perissodactyla.data, Binomial))
# but this can be turned off
(perisso <- comparative.data(perissodactyla.tree, perissodactyla.data, Binomial, na.omit=FALSE))
na.omit(perisso)
|
Loading required package: ape
Loading required package: MASS
Loading required package: mvtnorm
Comparative dataset of 9 taxa:
Phylogeny: perissodactyla.tree
9 tips, 7 internal nodes
chr [1:9] "Rhinoceros unicornis" "Diceros bicornis" "Ceratotherium simum" ...
Data: perissodactyla.data
$ log.female.wt : num [1:9] 6.24 6.18 6.26 5.46 5.65 ...
$ log.gestation.length: num [1:9] 2.68 2.65 2.69 2.6 2.59 ...
$ log.neonatal.wt : num [1:9] 4.84 4.7 4.9 3.92 4.6 ...
$ Territoriality : Factor w/ 2 levels "No","Yes": 2 1 2 2 2 1 1 2 2
Dropped taxa:
perissodactyla.tree { 9 ( 9 } 0 ) perissodactyla.dataComparative dataset of 13 taxa:
Phylogeny: perissodactyla.tree
13 tips, 11 internal nodes
chr [1:13] "Dicerorhinus sumatrensis" "Rhinoceros sondaicus" ...
Data: perissodactyla.data
$ log.female.wt : num [1:13] 5.91 6.15 6.24 6.18 6.26 ...
$ log.gestation.length: num [1:13] 2.6 2.68 2.68 2.65 2.69 ...
$ log.neonatal.wt : num [1:13] 4.54 4.7 4.84 4.7 4.9 ...
$ Territoriality : Factor w/ 2 levels "No","Yes": NA NA 2 1 2 NA NA 2 2 1 ...
Dropped taxa:
perissodactyla.tree { 5 ( 13 } 0 ) perissodactyla.dataComparative dataset of 9 taxa:
Phylogeny: perissodactyla.tree
9 tips, 7 internal nodes
chr [1:9] "Rhinoceros unicornis" "Diceros bicornis" "Ceratotherium simum" ...
Data: perissodactyla.data
$ log.female.wt : num [1:9] 6.24 6.18 6.26 5.46 5.65 ...
$ log.gestation.length: num [1:9] 2.68 2.65 2.69 2.6 2.59 ...
$ log.neonatal.wt : num [1:9] 4.84 4.7 4.9 3.92 4.6 ...
$ Territoriality : Factor w/ 2 levels "No","Yes": 2 1 2 2 2 1 1 2 2
Dropped taxa:
perissodactyla.tree { 9 ( 9 } 0 ) perissodactyla.data
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