This code chunk can be used to explore your data, but remember to eventually comment out (#) these code lines if you do not want these outputs in your final report.
## view the first ten rows of data
head(linelist_cleaned, n = 10)## number case_number sex age_years agegroup dateentry epiquestdate team
## 1 1 1001 F 35 3 2016-09-01 <NA> <NA>
## 2 2 1002 F 21 3 2016-09-06 <NA> <NA>
## 3 3 1003 F 18 3 2016-09-09 <NA> <NA>
## 4 4 1004 F 25 3 2016-09-12 2016-09-12 <NA>
## 5 5 1005 F 20 3 2016-09-19 2016-09-27 <NA>
## 6 6 1006 M 8 2 2016-09-19 <NA> <NA>
## 7 7 1007 M 14 2 2016-09-20 <NA> <NA>
## 8 8 1008 M 10 2 2016-09-21 <NA> <NA>
## 9 9 1009 F 5 2 2016-09-21 2016-09-27 <NA>
## 10 10 1010 F 15 2 2016-09-21 2016-09-26 <NA>
## chw patient_origin_free_text hh detected_by patient_origin
## 1 <NA> <NA> <NA> <NA> Rassalfil
## 2 <NA> <NA> <NA> <NA> Anfandock
## 3 <NA> <NA> <NA> <NA> Al-Hougna
## 4 <NA> <NA> <NA> <NA> Dinguess
## 5 <NA> <NA> <NA> <NA> Taradona 2
## 6 <NA> <NA> <NA> <NA> Albayadi
## 7 <NA> <NA> <NA> <NA> Salamat
## 8 <NA> <NA> <NA> <NA> Al-Hougna
## 9 <NA> <NA> <NA> <NA> Commercant
## 10 <NA> <NA> <NA> <NA> Taradona 2
## interviewee hhpers hhmale hhfemale hhu5 hpreferral hprefpos
## 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 Parent <NA> <NA> <NA> <NA> <NA> <NA>
## 5 Patient 3 2 1 1 <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 9 Parent 9 5 4 1 <NA> <NA>
## 10 Parent 15 8 7 0 <NA> <NA>
## patientpresent ptjaundice ptvomit mtmental ptpregnant ptu1 referring
## 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> <NA>
## 5 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 9 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 10 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## otherajs otherajsnum borehole comtap river citywater otherwater
## 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> Oui <NA> <NA> <NA>
## 5 Non <NA> Oui <NA> <NA> <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 9 Non <NA> <NA> <NA> <NA> Oui <NA>
## 10 Non <NA> <NA> <NA> <NA> Oui <NA>
## otherwatersp watersourcefreq ceramicjar jerrycan oildrum reserother
## 1 <NA> <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA> <NA> <NA>
## 4 <NA> <NA> Oui Oui <NA> <NA>
## 5 <NA> <NA> Oui <NA> <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA> <NA>
## 9 <NA> <NA> Oui <NA> <NA> <NA>
## 10 <NA> <NA> Oui <NA> <NA> <NA>
## reserothersp resertype chlorination volumreser handreser hweating
## 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> <NA>
## 6 <NA> <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA> <NA>
## 9 <NA> <NA> <NA> <NA> <NA> <NA>
## 10 <NA> <NA> <NA> <NA> <NA> <NA>
## hwwater hwsoap treatwater tptreatwater tptreatwaterother
## 1 <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA> <NA>
## 4 <NA> <NA> Non <NA> <NA>
## 5 <NA> <NA> Non <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA> <NA>
## 9 <NA> <NA> Oui JAVELLE <NA>
## 10 <NA> <NA> Oui JAVELLE <NA>
## nottreatwhy defecriver defecair defeclatrine
## 1 <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA>
## 4 <NA> <NA> <NA> Oui
## 5 L'EAU C'EST TRAITE DANS LE FORAGE <NA> <NA> Oui
## 6 <NA> <NA> <NA> <NA>
## 7 <NA> <NA> <NA> <NA>
## 8 <NA> <NA> <NA> <NA>
## 9 <NA> <NA> <NA> Oui
## 10 <NA> <NA> <NA> Oui
## numlatrine date_of_consultation_admission treatment_facility_site
## 1 <NA> 2016-09-01 633
## 2 <NA> 2016-09-06 643
## 3 <NA> 2016-09-09 649
## 4 <NA> 2016-09-12 656
## 5 <NA> 2016-09-19 72
## 6 <NA> 2016-09-19 1875
## 7 <NA> 2016-09-20 5230
## 8 <NA> 2016-09-21 5254
## 9 <NA> 2016-09-21 5255
## 10 <NA> 2016-09-21 78
## outreachscreened evaljaundice jaundiceid referredbychw jaundiceid2
## 1 <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA> <NA>
## 4 N <NA> <NA> <NA> <NA>
## 5 N <NA> <NA> <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA>
## 7 <NA> Oui 1007 Oui 1007
## 8 <NA> <NA> <NA> <NA> <NA>
## 9 N <NA> <NA> <NA> <NA>
## 10 N <NA> <NA> <NA> <NA>
## medjaundice date_of_onset fever nausea_anorexia vomiting
## 1 <NA> <NA> Oui Non Non
## 2 <NA> <NA> Oui Oui Oui
## 3 <NA> <NA> Non Oui Oui
## 4 <NA> <NA> Non Oui Non
## 5 <NA> 2016-09-15 Oui Oui Oui
## 6 <NA> 2016-09-14 Oui Oui Non
## 7 Oui 2016-08-28 Oui Non Non
## 8 <NA> 2016-09-14 Oui Oui Oui
## 9 <NA> 2016-08-18 Non Non Non
## 10 <NA> 2016-10-09 Non Oui Oui
## epigastric_pain_heartburn generalized_itch headache joint_pains
## 1 Non Non Oui Non
## 2 Oui Non Oui Oui
## 3 Oui Non Oui Non
## 4 Oui Non Oui Non
## 5 Oui Non Oui Oui
## 6 Oui Non Oui Oui
## 7 Non Non Non Oui
## 8 Oui Non Oui Non
## 9 Non Oui Non Non
## 10 Oui Non Oui Non
## diarrhoea bleeding medfev38 mental_state other_symptoms
## 1 Oui Non Non Normal <NA>
## 2 Oui Non Oui Normal <NA>
## 3 Non Oui Oui Confus/somnolent <NA>
## 4 Non Non Non Confus/somnolent <NA>
## 5 Non Non Non Normal <NA>
## 6 Oui Non Oui Normal <NA>
## 7 Non Non Non Normal <NA>
## 8 Non Non Oui Normal <NA>
## 9 Non Non Non Normal Non
## 10 Non Non Non Normal Non
## other_cases_in_hh medothhhajsnum othercaseid pregnant trimester medpp
## 1 Non <NA> <NA> Non <NA> Oui
## 2 Unknown <NA> <NA> Oui 1 Non
## 3 Non <NA> <NA> Oui 3 Non
## 4 Non <NA> <NA> Oui 2 Non
## 5 Non <NA> <NA> Non <NA> Non
## 6 Oui <NA> <NA> Non <NA> Non
## 7 Non <NA> <NA> Non <NA> Non
## 8 Non <NA> <NA> Non <NA> Non
## 9 Non <NA> <NA> Non <NA> Non
## 10 Non <NA> <NA> Non <NA> Non
## medppdays pregnancy_outcome_at_exit matdeathdt medppga medblood
## 1 5 Naissance, enfant toujours vivant NA <NA> Non
## 2 <NA> Sortie, enceinte NA <NA> Non
## 3 <NA> Naissance, enfant toujours vivant NA <NA> Non
## 4 <NA> Avortement/mort.né NA 30 Oui
## 5 <NA> <NA> NA - Oui
## 6 <NA> <NA> NA <NA> Oui
## 7 <NA> <NA> NA <NA> Oui
## 8 <NA> <NA> NA <NA> Oui
## 9 <NA> <NA> NA - Oui
## 10 <NA> <NA> NA - Oui
## date_lab_sample_taken malaria_rdt_at_admission hep_b_rdt hep_c_rdt
## 1 No Neg <NA> <NA>
## 2 No Pos <NA> <NA>
## 3 Yes but not sent Neg Neg Neg
## 4 2016-09-14 Neg Neg Neg
## 5 2016-09-19 Neg Neg Neg
## 6 2016-09-19 Pos Neg Neg
## 7 2016-09-20 Neg Neg Neg
## 8 2016-09-21 Pos Neg Neg
## 9 2016-09-21 Neg Neg Neg
## 10 2016-09-21 Neg Neg Neg
## hep_e_rdt test_hepatitis_e_virus test_hepatitis_e_igm hevpcr
## 1 <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA>
## 3 Neg <NA> <NA> <NA>
## 4 Pos IgG+/IgM+ 1 Pos
## 5 Neg IgG-/IgM- 0 Neg
## 6 Pos IgG+/IgM+ 1 Neg
## 7 Neg IgG-/IgM- 0 Neg
## 8 Pos IgG+/IgM+ 1 Pos
## 9 Pos IgG+/IgM+ 1 Pos
## 10 Neg IgG+/IgM- 0 Neg
## hevgenotest test_hepatitis_e_genotype test_hepatitis_a test_hepatitis_b
## 1 <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA>
## 4 <NA> <NA> Neg Neg
## 5 <NA> <NA> Neg Neg
## 6 <NA> <NA> Neg Neg
## 7 <NA> <NA> Neg Neg
## 8 <NA> <NA> Neg Neg
## 9 <NA> <NA> Neg Neg
## 10 <NA> <NA> Neg Neg
## test_hepatitis_c other_arthropod_transmitted_virus yellow_fever
## 1 <NA> <NA> <NA>
## 2 <NA> <NA> <NA>
## 3 <NA> <NA> <NA>
## 4 Neg <NA> <NA>
## 5 Neg Neg IgG-/IgM-
## 6 Neg <NA> <NA>
## 7 Neg Neg IgG+/IgM-
## 8 Neg <NA> <NA>
## 9 Neg Neg IgG-/IgM-
## 10 Neg Neg IgG-/IgM-
## zika dengue wnv rvf chikungunya_onyongnyong
## 1 <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA> <NA>
## 4 <NA> <NA> <NA> <NA> <NA>
## 5 IgG-/IgM- IgG-/IgM- IgG+/IgM- IgG-/IgM- IgG-/IgM-
## 6 <NA> <NA> <NA> <NA> <NA>
## 7 IgG+/IgM- IgG+/IgM- IgG+/IgM+ IgG-/IgM- IgG-/IgM-
## 8 <NA> <NA> <NA> <NA> <NA>
## 9 IgG-/IgM- IgG+/IgM- IgG+/IgM- IgG-/IgM- IgG-/IgM-
## 10 IgG-/IgM- IgG-/IgM- IgG+/IgM- IgG-/IgM- IgG-/IgM-
## patient_facility_type dthospitalisation exit_status dtdeath
## 1 Oui 2016-09-01 Déchargé/Guéri <NA>
## 2 Oui 2016-09-06 Déchargé/Guéri <NA>
## 3 Oui 2016-09-09 Décédé 2016-09-13
## 4 Oui 2016-09-12 Décédé 2016-09-14
## 5 Non <NA> <NA> <NA>
## 6 Oui 2016-09-19 Déchargé/Guéri <NA>
## 7 Non <NA> <NA> <NA>
## 8 Non <NA> <NA> <NA>
## 9 Non <NA> <NA> <NA>
## 10 Non <NA> <NA> <NA>
## epiwajs epiwhevelisa epiwoutreach epiwmed epiwepiquest epiwhp
## 1 <NA> <NA> 2016_35 2016_35 <NA> 2016_35
## 2 <NA> <NA> 2016_36 2016_36 <NA> 2016_36
## 3 <NA> <NA> 2016_36 2016_36 <NA> 2016_36
## 4 <NA> <NA> 2016_37 2016_37 2016_37 2016_37
## 5 2016_37 <NA> 2016_38 2016_38 2016_39 <NA>
## 6 2016_37 2016_37 2016_38 2016_38 <NA> 2016_38
## 7 2016_34 <NA> 2016_38 2016_38 <NA> <NA>
## 8 2016_37 2016_37 2016_38 2016_38 <NA> <NA>
## 9 2016_33 2016_33 2016_38 2016_38 2016_39 <NA>
## 10 2016_40 <NA> 2016_38 2016_38 2016_39 <NA>
## epiwdeath caseclass latitude longitude
## 1 <NA> Suspect NA NA
## 2 <NA> Suspect NA NA
## 3 2016_37 Not a case NA NA
## 4 2016_37 Confirmed 11.01991 20.28088
## 5 <NA> Not a case 11.05434 20.27419
## 6 <NA> Confirmed NA NA
## 7 <NA> Not a case NA NA
## 8 <NA> Confirmed NA NA
## 9 <NA> Confirmed 11.04281 20.27891
## 10 <NA> Not a case 11.04555 20.28320## view your whole dataset interactivley (in an excel style format)
## Remember that `View` needs to be written with a capital *V*
View(linelist_cleaned)## overview of variable types and contents
str(linelist_cleaned)## 'data.frame': 1447 obs. of 122 variables:
## $ number : num 1 2 3 4 5 6 7 8 9 10 ...
## $ case_number : num 1001 1002 1003 1004 1005 ...
## $ sex : chr "F" "F" "F" "F" ...
## $ age_years : chr "35" "21" "18" "25" ...
## $ agegroup : chr "3" "3" "3" "3" ...
## $ dateentry : chr "2016-09-01" "2016-09-06" "2016-09-09" "2016-09-12" ...
## $ epiquestdate : chr NA NA NA "2016-09-12" ...
## $ team : chr NA NA NA NA ...
## $ chw : chr NA NA NA NA ...
## $ patient_origin_free_text : chr NA NA NA NA ...
## $ hh : chr NA NA NA NA ...
## $ detected_by : chr NA NA NA NA ...
## $ patient_origin : chr "Rassalfil" "Anfandock" "Al-Hougna" "Dinguess" ...
## $ interviewee : chr NA NA NA "Parent" ...
## $ hhpers : chr NA NA NA NA ...
## $ hhmale : chr NA NA NA NA ...
## $ hhfemale : chr NA NA NA NA ...
## $ hhu5 : chr NA NA NA NA ...
## $ hpreferral : chr NA NA NA NA ...
## $ hprefpos : chr NA NA NA NA ...
## $ patientpresent : chr NA NA NA NA ...
## $ ptjaundice : chr NA NA NA NA ...
## $ ptvomit : chr NA NA NA NA ...
## $ mtmental : chr NA NA NA NA ...
## $ ptpregnant : chr NA NA NA NA ...
## $ ptu1 : chr NA NA NA NA ...
## $ referring : chr NA NA NA NA ...
## $ otherajs : chr NA NA NA NA ...
## $ otherajsnum : chr NA NA NA NA ...
## $ borehole : chr NA NA NA NA ...
## $ comtap : chr NA NA NA "Oui" ...
## $ river : chr NA NA NA NA ...
## $ citywater : chr NA NA NA NA ...
## $ otherwater : chr NA NA NA NA ...
## $ otherwatersp : chr NA NA NA NA ...
## $ watersourcefreq : chr NA NA NA NA ...
## $ ceramicjar : chr NA NA NA "Oui" ...
## $ jerrycan : chr NA NA NA "Oui" ...
## $ oildrum : chr NA NA NA NA ...
## $ reserother : chr NA NA NA NA ...
## $ reserothersp : chr NA NA NA NA ...
## $ resertype : chr NA NA NA NA ...
## $ chlorination : chr NA NA NA NA ...
## $ volumreser : chr NA NA NA NA ...
## $ handreser : chr NA NA NA NA ...
## $ hweating : chr NA NA NA NA ...
## $ hwwater : chr NA NA NA NA ...
## $ hwsoap : chr NA NA NA NA ...
## $ treatwater : chr NA NA NA "Non" ...
## $ tptreatwater : chr NA NA NA NA ...
## $ tptreatwaterother : chr NA NA NA NA ...
## $ nottreatwhy : chr NA NA NA NA ...
## $ defecriver : chr NA NA NA NA ...
## $ defecair : chr NA NA NA NA ...
## $ defeclatrine : chr NA NA NA "Oui" ...
## $ numlatrine : chr NA NA NA NA ...
## $ date_of_consultation_admission : chr "2016-09-01" "2016-09-06" "2016-09-09" "2016-09-12" ...
## $ treatment_facility_site : chr "633" "643" "649" "656" ...
## $ outreachscreened : chr NA NA NA "N" ...
## $ evaljaundice : chr NA NA NA NA ...
## $ jaundiceid : chr NA NA NA NA ...
## $ referredbychw : chr NA NA NA NA ...
## $ jaundiceid2 : chr NA NA NA NA ...
## $ medjaundice : chr NA NA NA NA ...
## $ date_of_onset : chr NA NA NA NA ...
## $ fever : chr "Oui" "Oui" "Non" "Non" ...
## $ nausea_anorexia : chr "Non" "Oui" "Oui" "Oui" ...
## $ vomiting : chr "Non" "Oui" "Oui" "Non" ...
## $ epigastric_pain_heartburn : chr "Non" "Oui" "Oui" "Oui" ...
## $ generalized_itch : chr "Non" "Non" "Non" "Non" ...
## $ headache : chr "Oui" "Oui" "Oui" "Oui" ...
## $ joint_pains : chr "Non" "Oui" "Non" "Non" ...
## $ diarrhoea : chr "Oui" "Oui" "Non" "Non" ...
## $ bleeding : chr "Non" "Non" "Oui" "Non" ...
## $ medfev38 : chr "Non" "Oui" "Oui" "Non" ...
## $ mental_state : chr "Normal" "Normal" "Confus/somnolent" "Confus/somnolent" ...
## $ other_symptoms : chr NA NA NA NA ...
## $ other_cases_in_hh : chr "Non" "Unknown" "Non" "Non" ...
## $ medothhhajsnum : chr NA NA NA NA ...
## $ othercaseid : chr NA NA NA NA ...
## $ pregnant : chr "Non" "Oui" "Oui" "Oui" ...
## $ trimester : chr NA "1" "3" "2" ...
## $ medpp : chr "Oui" "Non" "Non" "Non" ...
## $ medppdays : chr "5" NA NA NA ...
## $ pregnancy_outcome_at_exit : chr "Naissance, enfant toujours vivant" "Sortie, enceinte" "Naissance, enfant toujours vivant" "Avortement/mort.né" ...
## $ matdeathdt : logi NA NA NA NA NA NA ...
## $ medppga : chr NA NA NA "30" ...
## $ medblood : chr "Non" "Non" "Non" "Oui" ...
## $ date_lab_sample_taken : chr "No" "No" "Yes but not sent" "2016-09-14" ...
## $ malaria_rdt_at_admission : chr "Neg" "Pos" "Neg" "Neg" ...
## $ hep_b_rdt : chr NA NA "Neg" "Neg" ...
## $ hep_c_rdt : chr NA NA "Neg" "Neg" ...
## $ hep_e_rdt : chr NA NA "Neg" "Pos" ...
## $ test_hepatitis_e_virus : chr NA NA NA "IgG+/IgM+" ...
## $ test_hepatitis_e_igm : chr NA NA NA "1" ...
## $ hevpcr : chr NA NA NA "Pos" ...
## $ hevgenotest : chr NA NA NA NA ...
## $ test_hepatitis_e_genotype : chr NA NA NA NA ...
## $ test_hepatitis_a : chr NA NA NA "Neg" ...
## [list output truncated]## gives mean, median and max values of variables
## gives counts for categorical variables
## also gives number of NAs
summary(linelist_cleaned)## number case_number sex age_years
## Min. : 1.0 Min. :1001 Length:1447 Length:1447
## 1st Qu.: 361.5 1st Qu.:5532 Class :character Class :character
## Median : 722.0 Median :8102 Mode :character Mode :character
## Mean : 722.0 Mean :6729
## 3rd Qu.:1082.5 3rd Qu.:8554
## Max. :1443.0 Max. :9146
##
## agegroup dateentry epiquestdate
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## team chw patient_origin_free_text
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## hh detected_by patient_origin
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## interviewee hhpers hhmale
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## hhfemale hhu5 hpreferral
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## hprefpos patientpresent ptjaundice
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## ptvomit mtmental ptpregnant
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## ptu1 referring otherajs
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## otherajsnum borehole comtap
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## river citywater otherwater
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## otherwatersp watersourcefreq ceramicjar
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## jerrycan oildrum reserother
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## reserothersp resertype chlorination
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## volumreser handreser hweating
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## hwwater hwsoap treatwater
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## tptreatwater tptreatwaterother nottreatwhy
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## defecriver defecair defeclatrine
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## numlatrine date_of_consultation_admission treatment_facility_site
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## outreachscreened evaljaundice jaundiceid
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## referredbychw jaundiceid2 medjaundice
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## date_of_onset fever nausea_anorexia
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## vomiting epigastric_pain_heartburn generalized_itch
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## headache joint_pains diarrhoea
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## bleeding medfev38 mental_state
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## other_symptoms other_cases_in_hh medothhhajsnum
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## othercaseid pregnant trimester
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## medpp medppdays pregnancy_outcome_at_exit
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## matdeathdt medppga medblood
## Mode:logical Length:1447 Length:1447
## NA's:1447 Class :character Class :character
## Mode :character Mode :character
##
##
##
##
## date_lab_sample_taken malaria_rdt_at_admission hep_b_rdt
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## hep_c_rdt hep_e_rdt test_hepatitis_e_virus
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## test_hepatitis_e_igm hevpcr hevgenotest
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## test_hepatitis_e_genotype test_hepatitis_a test_hepatitis_b
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## test_hepatitis_c other_arthropod_transmitted_virus yellow_fever
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## zika dengue wnv
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## rvf chikungunya_onyongnyong patient_facility_type
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## dthospitalisation exit_status dtdeath
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## epiwajs epiwhevelisa epiwoutreach
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## epiwmed epiwepiquest epiwhp
## Length:1447 Length:1447 Length:1447
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## epiwdeath caseclass latitude longitude
## Length:1447 Length:1447 Min. :10.43 Min. :16.55
## Class :character Class :character 1st Qu.:11.04 1st Qu.:20.27
## Mode :character Mode :character Median :11.05 Median :20.28
## Mean :11.06 Mean :20.27
## 3rd Qu.:11.06 3rd Qu.:20.29
## Max. :12.59 Max. :20.89
## NA's :283 NA's :283## view unique values contained in variables
unique(linelist_cleaned$sex)## [1] "F" "M"## another alternative is with the "summarytools package"
## use the dfSummary function in combination with view
## note that view is not capitalised with this package
# install.packages("summarytools")
# summarytools::view(summarytools::dfSummary(linelist_cleaned))