radish {aster}R Documentation

Life History Data on Raphanus sativus

Description

Data on life history traits for the invasive California wild radish Raphanus sativus

Usage

data(radish)

Format

A data frame with records for 286 plants. Data are already in “long” format; no need to reshape.

resp

Response vector.

varb

Categorical. Gives node of graphical model corresponding to each component of resp. See details below.

root

All ones. Root variables for graphical model.

id

Categorical. Indicates individual plants.

Site

Categorical. Experimental site where plant was grown. Two sites in this dataset.

Block

Categorical. Block nested within site.

Region

Categorical. Region from which individuals were obtained: northern, coastal California (N) or southern, inland California (S).

Pop

Categorical. Wild population nested within region.

varbFlowering

Indicator (zero or one). Shorthand for as.numeric(radish$varb == "Flowering").

varbFlowers

Indicator (zero or one). Shorthand for as.numeric(radish$varb == "Flowers").

fit

Indicator (zero or one). Shorthand for as.numeric(radish$varb == "Fruits"). So-called because the components of outcome indicated are the best surrogate of Darwinian fitness in these data.

Details

The levels of varb indicate nodes of the graphical model to which the corresponding elements of the response vector resp belong. This is the typical “long” format produced by the R reshape function. For each individual, there are several response variables. All response variables are combined in one vector resp. The variable varb indicates which “original” variable the number was for. The variable id indicates which individual the number was for. The levels of varb, which are the names of the “original” variables are

Flowering

Indicator (zero or one). Bernoulli, One if individual survived to produce flowers.

Flowers

Integer. Zero-truncated Poisson, number of flowers observed.

Fruits

Integer. Poisson, number of fruits observed.

Graphical model is

1 -> Flowering -> Flowers -> Fruits.

Source

Caroline Ridley

References

These data are a subset of data previously analyzed using fixed effect aster methods (R function aster) in the following.

Ridley, C. E. and Ellstrand, N. C. (2010). Rapid evolution of morphology and adaptive life history in the invasive California wild radish (Raphanus sativus) and the implications for management. Evolutionary Applications, 3, 64–76.

These data are a subset of data previously analyzed using random effect aster methods (R function reaster) in the following.

Geyer, C. J., Ridley, C. E., Latta, R. G., Etterson, J. R., and Shaw, R. G. (2013) Local Adaptation and Genetic Effects on Fitness: Calculations for Exponential Family Models with Random Effects. Annals of Applied Statistics, 7, 1778–1795. doi: 10.1214/13-AOAS653.

See Also

pickle

Examples

data(radish)

[Package aster version 1.1-2 Index]