hagelloch.obk: Converted Hagelloch 1861 measles outbreak into obkData...
In Hackout2/incidence: Computation and Visualisation of Incidence from Line Lists

Description Usage Format Details Author(s)

The hagelloch.df data.frame available in the surveillance package is converted into an object of obkData. Only the individuals slot of the obkData object is populated.

1	hagelloch.obk

Formal class 'obkData' [package "OutbreakTools"] with 6 slots
  ..@ individuals:'data.frame':	187 obs. of  26 variables:
  .. ..$ NAME          : Factor w/ 27 levels "Aberle","Buerker",..: 15 15 15 23 14 14 21 21 21 21 ...
  .. ..$ FN            : int [1:187] 41 41 41 61 42 42 26 44 44 29 ...
  .. ..$ HN            : int [1:187] 61 61 61 62 63 63 23 69 69 31 ...
  .. ..$ AGE           : num [1:187] 7 6 4 13 8 12 6 10 13 7 ...
  .. ..$ SEX           : Factor w/ 2 levels "male","female": 2 2 2 1 2 1 1 1 1 2 ...
  .. ..$ PRO           : Date[1:187], format: "1861-11-21" "1861-11-23" ...
  .. ..$ ERU           : Date[1:187], format: "1861-11-25" "1861-11-27" ...
  .. ..$ CL            : Factor w/ 3 levels "preschool","1st class",..: 2 2 1 3 2 3 1 2 3 2 ...
  .. ..$ DEAD          : Date[1:187], format: NA NA ...
  .. ..$ IFTO          : int [1:187] 45 45 172 180 45 180 42 45 182 45 ...
  .. ..$ SI            : int [1:187] 10 12 9 10 11 9 9 10 11 10 ...
  .. ..$ C             : Factor w/ 6 levels "no complicatons",..: 1 1 1 1 1 2 1 2 1 2 ...
  .. ..$ PR            : int [1:187] 4 4 4 1 5 3 4 5 4 4 ...
  .. ..$ CA            : int [1:187] 4 4 4 1 3 3 3 3 3 5 ...
  .. ..$ NI            : int [1:187] 3 3 3 1 2 2 1 2 2 1 ...
  .. ..$ GE            : int [1:187] 1 1 2 1 1 1 1 1 1 1 ...
  .. ..$ TD            : int [1:187] NA 3 1 3 NA 2 2 6 1 11 ...
  .. ..$ TM            : num [1:187] NA 40.3 40.5 40.7 NA 40.7 39.3 39.9 40.7 38.4 ...
  .. ..$ x.loc         : num [1:187] 142 142 142 165 145 ...
  .. ..$ y.loc         : num [1:187] 100 100 100 102 120 ...
  .. ..$ tPRO          : num [1:187] 22.7 24.2 29.6 28.1 23.1 ...
  .. ..$ tERU          : num [1:187] 26.2 28.8 33.7 29 28.4 ...
  .. ..$ tDEAD         : num [1:187] NA NA NA NA NA NA NA NA NA NA ...
  .. ..$ tR            : num [1:187] 29.2 31.8 36.7 32 31.4 ...
  .. ..$ tI            : num [1:187] 21.7 23.2 28.6 27.1 22.1 ...
  .. ..$ locationFactor: Factor w/ 56 levels "125-187.5","127.5-147.5",..: 5 5 5 13 7 7 47 56 56 37 ...
  ..@ records    :List of 3
  .. ..$ timePRO :'data.frame':	187 obs. of  2 variables:
  .. .. ..$ individualID: chr [1:187] "1" "2" "3" "4" ...
  .. .. ..$ date        : Date[1:187], format: "1861-11-21" ...
  .. ..$ timeERU :'data.frame':	187 obs. of  2 variables:
  .. .. ..$ individualID: chr [1:187] "1" "2" "3" "4" ...
  .. .. ..$ date        : Date[1:187], format: "1861-11-25" ...
  .. ..$ timeDEAD:'data.frame':	187 obs. of  2 variables:
  .. .. ..$ individualID: chr [1:187] "1" "2" "3" "4" ...
  .. .. ..$ date        : Date[1:187], format: NA ...
  ..@ dna        : NULL
  ..@ contacts   : NULL
  ..@ context    : NULL
  ..@ trees      : NULL

See the surveillance package Hagelloch data hagelloch for a description of the data. For developers: The conversion is done by a conversion function hagelloch.obk.R found in the develop directory of the package.

Michael H<c3><b6>hle <http://www.math.su.se/~hoehle>

Hackout2/incidence documentation built on May 6, 2019, 9:47 p.m.