spaMM (version 2.0.0)

arabidopsis:

Description

For 948 “accessions” from European Arabidopsis thaliana populations, this data set merges the genotypic information at four single nucleotide polmorphisms (SNP) putatively involved in adaptation to climate (Fournier-Level et al, 2011, Table 1), with 13 climatic variables from Hancock et al. (2011).

Usage

data(arabidopsis)

Format

The data frame includes 948 observations on the following variables:

pos1046738, pos5510910, pos6235221, pos8132698

Genotypes at four SNP loci

LAT

latitude

LONG

longitude

seasonal, tempWarmest, tempColdest, preciWettest, preciDriest, preciCV, PAR_SPRING,

growingL, conseqCold, conseqFrFree, RelHumidSp, dayLSp, aridity

Thirteen climatic variables. See Hancock et al. (2011) for details about these variables.

Details

The response is binary so “HLmethod="PQL/L"” seems warranted (see Rousset and Ferdy, 2014).

References

Fournier-Level A, Korte A., Cooper M. D., Nordborg M., Schmitt J., Wilczek AM (2011). A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89.

Hancock, A. M., Brachi, B., Faure, N., Horton, M. W., Jarymowycz, L. B., Sperone, F. G., Toomajian, C., Roux, F., and Bergelson, J. 2011. Adaptation to climate across the Arabidopsis thaliana genome, Science 334: 83-86.

Rousset F., Ferdy, J.-B. (2014) Testing environmental and genetic effects in the presence of spatial autocorrelation. Ecography, 37: 781-790. http://dx.doi.org/10.1111/ecog.00566

Examples

data(arabidopsis)
if (spaMM.getOption("example_maxtime")>15) {
  HLCor(cbind(pos1046738,1-pos1046738)~seasonal+Matern(1|LAT+LONG),
        ranPars=list(rho=0.1192889,nu=0.2369864,lambda=8.599),
        family=binomial(),HLmethod="PQL/L",data=arabidopsis)
}
## The above ranPars are deduced from the following fit:
if (spaMM.getOption("example_maxtime")>220) {
  opt <- spaMM.options("matrix_method")
  # Selecting a slightly faster algorithm for this computation:
  spaMM.options(matrix_method="def_sXaug_EigenDense_QRP_scaled")
  SNPfit <- fitme(cbind(pos1046738,1-pos1046738)~seasonal+Matern(1|LAT+LONG),
              family=binomial(),method="PQL/L",data=arabidopsis)
  spaMM.options(opt)
  summary(SNPfit)
}