StrainRanking (version 1.2)

DGobj.rawdata: Construction of a DG object from raw data

Description

Construction of a DG object from raw demographic and genetic data.

Usage

DGobj.rawdata(demographic.coord, demographic.measures, genetic.coord, 
 genetic.frequencies)

Arguments

demographic.coord

[2-column matrix] Coordinates of sites where demographic measurements were made.

demographic.measures

[2-column matrix] Demographic measurements (e.g. pathogen intensity). The first column contains measurements at the first sampling time. The second column contains measurements at the second sampling time.

genetic.coord

[2-column matrix] Coordinates of sites where genetic samples were collected.

genetic.frequencies

[Matrix] with frequencies of genetic samples from all sampled strains. Each column corresponds to a given strain.

Value

An object from the DG class.

References

Soubeyrand S., Tollenaere C., Haon-Lasportes E. & Laine A.-L. (2014). Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics. PLOS ONE 9(1): e86591.

See Also

DGobj-class, DGobj.simul.mechanistic, DGobj.simul.regression

Examples

Run this code
# NOT RUN {
## load the powdery mildew data set
data(powderymildew)

## create a DG object from this data set
DGdata=DGobj.rawdata(demographic.coord=powderymildew$demographic.coord,
 genetic.coord=powderymildew$genetic.coord,
 demographic.measures=powderymildew$demographic.measures,
 genetic.frequencies=powderymildew$genetic.frequencies)

summary(DGdata)
# }

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