radish: Life History Data on Raphanus sativus
In aster: Aster Models

Description Usage Format Details Source References See Also Examples

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

1	data(radish)

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.

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.

Caroline Ridley

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.

pickle