R/AJS_linelist_internal.R
AJS_linelist_internal.RdData from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the Chadian town of Am Timan between October 2016 and April 2017. The Chadian Ministry of Health (MoH) has approved the use of this data for training purposes. Please note, that some data has been adapted in order to best achieve training objectives. Also, the GPS coordinates included in the dataset do not correspond to real cases identified during this outbreak. They have been generated exclusively for training purposes.
data(AJS_linelist_internal)An object of class "cross"; see read.cross.
None (PLoS)
data(AJS_linelist_internal)
head(AJS_linelist_internal)
#> Number HEVID Sex Age Agegroup dateentry epiquestdate team chw block hh
#> 1 1 1001 F 35 3 2016-09-01 <NA> <NA> <NA> <NA> <NA>
#> 2 2 1002 F 21 3 2016-09-06 <NA> <NA> <NA> <NA> <NA>
#> 3 3 1003 F 18 3 2016-09-09 <NA> <NA> <NA> <NA> <NA>
#> 4 4 1004 F 25 3 2016-09-12 2016-09-12 <NA> <NA> <NA> <NA>
#> 5 5 1005 F 20 3 2016-09-19 2016-09-27 <NA> <NA> <NA> <NA>
#> 6 6 1006 M 8 2 2016-09-19 <NA> <NA> <NA> <NA> <NA>
#> referredby quartier interviewee hhpers hhmale hhfemale hhu5 hpreferral
#> 1 <NA> Rassalfil <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> Anfandock <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> Al-Hougna <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> Dinguess Parent <NA> <NA> <NA> <NA> <NA>
#> 5 <NA> Taradona 2 Patient 3 2 1 1 <NA>
#> 6 <NA> Albayadi <NA> <NA> <NA> <NA> <NA> <NA>
#> hprefpos patientpresent ptjaundice ptvomit mtmental ptpregnant ptu1 referring
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> otherajs otherajsnum borehole comtap river citywater otherwater otherwatersp
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> Oui <NA> <NA> <NA> <NA>
#> 5 Non <NA> Oui <NA> <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> watersourcefreq ceramicjar jerrycan oildrum reserother reserothersp resertype
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> Oui Oui <NA> <NA> <NA> <NA>
#> 5 <NA> Oui <NA> <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> chlorination volumreser handreser hweating hwwater hwsoap treatwater
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA> <NA> <NA> Non
#> 5 <NA> <NA> <NA> <NA> <NA> <NA> Non
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> tptreatwater tptreatwaterother nottreatwhy defecriver
#> 1 <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> L'EAU C'EST TRAITE DANS LE FORAGE <NA>
#> 6 <NA> <NA> <NA> <NA>
#> defecair defeclatrine numlatrine dtmedical hpid outreachscreened
#> 1 <NA> <NA> <NA> 2016-09-01 633 <NA>
#> 2 <NA> <NA> <NA> 2016-09-06 643 <NA>
#> 3 <NA> <NA> <NA> 2016-09-09 649 <NA>
#> 4 <NA> Oui <NA> 2016-09-12 656 N
#> 5 <NA> Oui <NA> 2016-09-19 72 N
#> 6 <NA> <NA> <NA> 2016-09-19 1875 <NA>
#> evaljaundice jaundiceid referredbychw jaundiceid2 medjaundice dtjaundice
#> 1 <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> <NA> <NA> <NA> 2016-09-15
#> 6 <NA> <NA> <NA> <NA> <NA> 2016-09-14
#> medfever mednausea medvomit medepigastric meditching medheadache
#> 1 Oui Non Non Non Non Oui
#> 2 Oui Oui Oui Oui Non Oui
#> 3 Non Oui Oui Oui Non Oui
#> 4 Non Oui Non Oui Non Oui
#> 5 Oui Oui Oui Oui Non Oui
#> 6 Oui Oui Non Oui Non Oui
#> medarthralgia meddiar medbleeding medfev38 medmental medother
#> 1 Non Oui Non Non Normal <NA>
#> 2 Oui Oui Non Oui Normal <NA>
#> 3 Non Non Oui Oui Confus/somnolent <NA>
#> 4 Non Non Non Non Confus/somnolent <NA>
#> 5 Oui Non Non Non Normal <NA>
#> 6 Oui Oui Non Oui Normal <NA>
#> medothhhajs medothhhajsnum othercaseid medpreg medpregtri medpp medppdays
#> 1 Non <NA> <NA> Non <NA> Oui 5
#> 2 Unknown <NA> <NA> Oui 1 Non <NA>
#> 3 Non <NA> <NA> Oui 3 Non <NA>
#> 4 Non <NA> <NA> Oui 2 Non <NA>
#> 5 Non <NA> <NA> Non <NA> Non <NA>
#> 6 Oui <NA> <NA> Non <NA> Non <NA>
#> medppoutcome matdeathdt medppga medblood
#> 1 Naissance, enfant toujours vivant NA <NA> Non
#> 2 Sortie, enceinte NA <NA> Non
#> 3 Naissance, enfant toujours vivant NA <NA> Non
#> 4 Avortement/mort.né NA 30 Oui
#> 5 <NA> NA - Oui
#> 6 <NA> NA <NA> Oui
#> medblooddt medmalrdt medhepb medhepc medhevrdt medhevelisa hevrecent
#> 1 No Neg <NA> <NA> <NA> <NA> <NA>
#> 2 No Pos <NA> <NA> <NA> <NA> <NA>
#> 3 Yes but not sent Neg Neg Neg Neg <NA> <NA>
#> 4 2016-09-14 Neg Neg Neg Pos IgG+/IgM+ 1
#> 5 2016-09-19 Neg Neg Neg Neg IgG-/IgM- 0
#> 6 2016-09-19 Pos Neg Neg Pos IgG+/IgM+ 1
#> hevpcr hevgenotest hevgenotype medhavelisa medhbvelisa medhcvelisa arbovpcr
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
#> 4 Pos <NA> <NA> Neg Neg Neg <NA>
#> 5 Neg <NA> <NA> Neg Neg Neg Neg
#> 6 Neg <NA> <NA> Neg Neg Neg <NA>
#> yf zika dengue wnv rvf chik hospitalised
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> Oui
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> Oui
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> Oui
#> 4 <NA> <NA> <NA> <NA> <NA> <NA> Oui
#> 5 IgG-/IgM- IgG-/IgM- IgG-/IgM- IgG+/IgM- IgG-/IgM- IgG-/IgM- Non
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> Oui
#> dthospitalisation outcomehp dtdeath epiwajs epiwhevelisa epiwoutreach
#> 1 2016-09-01 Déchargé/Guéri <NA> <NA> <NA> 2016_35
#> 2 2016-09-06 Déchargé/Guéri <NA> <NA> <NA> 2016_36
#> 3 2016-09-09 Décédé 2016-09-13 <NA> <NA> 2016_36
#> 4 2016-09-12 Décédé 2016-09-14 <NA> <NA> 2016_37
#> 5 <NA> <NA> <NA> 2016_37 <NA> 2016_38
#> 6 2016-09-19 Déchargé/Guéri <NA> 2016_37 2016_37 2016_38
#> epiwmed epiwepiquest epiwhp epiwdeath caseclass Latitude Longitude
#> 1 2016_35 <NA> 2016_35 <NA> Suspect NA NA
#> 2 2016_36 <NA> 2016_36 <NA> Suspect NA NA
#> 3 2016_36 <NA> 2016_36 2016_37 Not a case NA NA
#> 4 2016_37 2016_37 2016_37 2016_37 Confirmed 11.01991 20.28088
#> 5 2016_38 2016_39 <NA> <NA> Not a case 11.05434 20.27419
#> 6 2016_38 <NA> 2016_38 <NA> Confirmed NA NA