DGobj.rawdata {StrainRanking}

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.

Note

Demographic measurements, say Y_i(t_1) and Y_i(t_2), made at sampling sites i\in\{1,\ldots,I\} and at the first and second sampling times, respectively, are transformed into the values Z_i=\log\left(\frac{1+Y_i(t_2)}{1+Y_i(t_1)}\right) characterizing the temporal growth of the epidemic in space. The growth variable Z_i is given in the thrid column of the demographic slot of the returned DG object.

Author(s)

Soubeyrand, S., Tollenaere, C., Haon-Lasportes, E. and Laine, A.-L.

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

## 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)