DGobj.rawdata

0th

Percentile

Construction of a DG object from raw data

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

Keywords
datagen
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.

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

Aliases
  • DGobj.rawdata
Examples
# 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)
# }
Documentation reproduced from package StrainRanking, version 1.2, License: GPL (>= 2.0) | file LICENSE

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