grey_cloud_2015: Life History Data on Chamaecrista fasiculata

In aster: Aster Models

Life History Data on Chamaecrista fasiculata

Description

Data on life history traits for the partridge pea Chamaecrista fasiculata

Usage

data(grey_cloud_2015)

Format

Loads 3 R objects.

redata

A data frame with records for 3658 plants. Data are already in “long” format; no need to reshape. Variables contained include

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.

fit

Bernoulli. Indicates terminal node (fitness) of the graph. Same as as.numeric(varb == "totalseeds").

id

Categorical. Indicates individual plants.

block

Categorical. Indicates block in experimental design.

paternalID

Categorical. Indicates father.

maternalID

Categorical. Indicates mother.

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 the following.

Germ

Bernoulli, one indicates individual germinated.

flw

Conditionally Bernoulli given germ, one indicates individual flowered.

total.pods

Conditionally Poisson given flw, counts number of seed pods produced.

total.pods.collected

Conditionally Bernoulli given total.pods, size of the subsample of the total.pods counted by the scientists.

totalseeds

Conditionally Poisson given total.pods.collected, total number of seeds found in the subsample of pods.

References

These data were published in the following.

Kulbaba, M. W., Sheth, S. N., Pain, R. E., Eckhart, V. M. and Shaw, R. G. (2019) Additive genetic variance for lifetime fitness and the capacity for adaptation in an annual plant Evolution, 73, 1746–1758. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/evo.13830")}.

Geyer, C. J., Kulbaba, M. W., Sheth, S. N., Pain, R. E., Eckhart, V. M. and Shaw, R. G. (2022) Correction for Kulbaba et al. (2019). Evolution, 76, 3074. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/evo.14607")}. Supplementary material, version 2.0.1. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.7013098")}.

Shaw, R. G., Geyer, C. J., Kulbaba, M. W., Sheth, S. N., Eckhart, V. M. and Pain, R. E. (in preparation). Realization of ongoing evolutionary adaptation in the field. Supplementary material (all of the data analysis) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.17093288")}.

Examples

data(grey_cloud_2015)
## Not run: 
# takes too long for CRAN
modmat.sire <- model.matrix(~ 0 + fit:paternalID, redata)
modmat.dam <- model.matrix(~ 0 + fit:maternalID, redata)
modmat.siredam <- cbind(modmat.sire, modmat.dam)
rout <- reaster(resp ~ fit + varb,
    list(parental = ~ 0 + modmat.siredam, block = ~ 0 + fit:block),
    pred, fam, varb, id, root, data = redata)

## End(Not run)

aster documentation built on Dec. 8, 2025, 9:06 a.m.