| 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 ofoutcomeindicated 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 \longrightarrow \mbox{Flowering} \longrightarrow \mbox{Flowers} \longrightarrow \mbox{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
Examples
data(radish)