Browse data

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))