Description Usage Arguments Value Note Author(s) References See Also Examples
View source: R/DGobj.rawData.R
Construction of a DG object from raw demographic and genetic data.
1 2 | DGobj.rawdata(demographic.coord, demographic.measures, genetic.coord,
genetic.frequencies)
|
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. |
An object from the DG class.
Demographic measurements, say Y_i(t_1) and Y_i(t_2), made at sampling sites i\in\{1,…,I\} and at the first and second sampling times, respectively, are transformed into the values Z_i=\log≤ft(\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.
Soubeyrand, S., Tollenaere, C., Haon-Lasportes, E. and Laine, A.-L.
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.
DGobj-class, DGobj.simul.mechanistic, DGobj.simul.regression
1 2 3 4 5 6 7 8 9 10 | ## 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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