garki_sero: dataset: Garki Project (Nigeria) serology data
In ben-arnold/tmleAb: Targeted maximum likelihood estimation for antibody measurements
Description
Usage
Format
Source
References
Description
The garki_sero dataset includes a semi-processed version of publicly available serology data from the Garki Project, Nigeria. This file includes merged data from the village, people, and serology tables in the original Garki files. The original files are documented through the Garki Project's website (http://garkiproject.nd.edu/). These data were downloaded originally from the Swiss Tropical Institute (http://www.swisstph.ch/fr/ressources/epidemiological-databases.html). The dictionary file from STI included important additional information about data labels. The Stata script that merged the original tables is located here: https://osf.io/7frw2/.
Usage
1
Format
A data frame with 20,441 observations and 52 variables. Variable labels below have been copied from http://garkiproject.nd.edu. The original table's source is added as a prefix, else it was derived.
idpeople: individual ID
villagevillage: village ID
compountpeople: compound ID
serosvyserology: Serological survey number
surveyvillage: Garki project survey number
areavillage: Garki project study area
gridvillage: Garki project grid number
fupvillage: The follow-up cluster village is in
vnamevillage: Village name
vuvillage: Code representing one village unit for a group
grouped1village: number of compounds in compact part? CD
grouped2village: unknown
scattered1village: number of compounds in scattered part? CD
scattered2village: unknown
populationvillage: Population of village (when?) CD
movepeople: unknown
perspeople: unknown
sfregpeople: The number of the survey the person first registered with.
sexpeople: Identifies the sex of the person. Coding unknown.
dobpeople: unknown
datebpeople: The date of birth of the person.
batch_iggserology: Batch number IgG.
batch_igmserology: Batch number IgM.
plate_iggserology: Plate number IgG.
plate_igmserology: Plate number IgM.
diam_iggserology: Specimen diameter IgG.
diam_igmserology: Specimen diameter IgM.
eval_iggserology: Specimen evaluation IgG.
eval_igmserology: Specimen evaluation IgM.
perc_iggserology: Percentage IgG.
perc_igmserology: Percentage IgM.
precipitinserology: Result of the precipitin reaction. Coded as follows: 0=Test not done, 1-7=Number of bands, 8=No bands
blank1serology: unknown
ifat_pfaserology: IFA test for Plasmodium falciparum, 0=no result, 1= Titre 20, 2=60, 3=180, 4=540, 5=1620,6=4860, 7=14580,8=titres >14580, 9= titre < 20 (for computations take 0); In general Titre=20*3**(code-1)
blank2serology: unknown
ifat_pmserology: IFA test for Plasmodium malariae, 0=no result, 1= Titre 20, 2=60, 3=180, 4=540, 5=1620,6=4860, 7=14580,8=titres >14580, 9= titre < 20 (for computations take 0); In general Titre=20*3**(code-1)
haem_codeserology: 1 = AA; 2 = AS, 3 = SS, 4 =AC, 5 = CC, 6 = SC, 9 = not done
haem_phbsserology: unknown
recd_ihaserology: Record identifier for IHA (code 116)
specnoserology: specimen number
titrcodeserology: IHA titre code, 4 to 16 = titre 2**4 to 2**16 (in general titre=2**code)
dateserology: unknown
tr(derived): factor: control or intervention village
phase(derived): factor: baseline, intervention, post-intervention phase
wetseason(derived): factor: dry or wet season
bdate(derived): individuals date of birth (standard date format)
mdate(derived): measurement date
agedays(derived): age in days at time of measurement
ageyrs(derived): age in years at time of measurement
ifatpftitre(derived): IFA test for P. falciparum antibody titres
ifatpmtitre(derived): IFA test for P. malariae antibody titres
ihatitre(derived): IHA test antibody titres
Source
http://www.swisstph.ch/fr/ressources/epidemiological-databases.html
References
Molineaux L, Gramiccia G, 1980. The Garki Project. Geneva: World Health Organisation.
http://whqlibdoc.who.int/publications/9241560614.pdf
http://garkiproject.nd.edu/
ben-arnold/tmleAb documentation built on May 12, 2019, 10:55 a.m.
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Description Usage Format Source References
Description
The garki_sero dataset includes a semi-processed version of publicly available serology data from the Garki Project, Nigeria. This file includes merged data from the village, people, and serology tables in the original Garki files. The original files are documented through the Garki Project's website (http://garkiproject.nd.edu/). These data were downloaded originally from the Swiss Tropical Institute (http://www.swisstph.ch/fr/ressources/epidemiological-databases.html). The dictionary file from STI included important additional information about data labels. The Stata script that merged the original tables is located here: https://osf.io/7frw2/.
Usage
1 |
Format
A data frame with 20,441 observations and 52 variables. Variable labels below have been copied from http://garkiproject.nd.edu. The original table's source is added as a prefix, else it was derived.
idpeople: individual ID
villagevillage: village ID
compountpeople: compound ID
serosvyserology: Serological survey number
surveyvillage: Garki project survey number
areavillage: Garki project study area
gridvillage: Garki project grid number
fupvillage: The follow-up cluster village is in
vnamevillage: Village name
vuvillage: Code representing one village unit for a group
grouped1village: number of compounds in compact part? CD
grouped2village: unknown
scattered1village: number of compounds in scattered part? CD
scattered2village: unknown
populationvillage: Population of village (when?) CD
movepeople: unknown
perspeople: unknown
sfregpeople: The number of the survey the person first registered with.
sexpeople: Identifies the sex of the person. Coding unknown.
dobpeople: unknown
datebpeople: The date of birth of the person.
batch_iggserology: Batch number IgG.
batch_igmserology: Batch number IgM.
plate_iggserology: Plate number IgG.
plate_igmserology: Plate number IgM.
diam_iggserology: Specimen diameter IgG.
diam_igmserology: Specimen diameter IgM.
eval_iggserology: Specimen evaluation IgG.
eval_igmserology: Specimen evaluation IgM.
perc_iggserology: Percentage IgG.
perc_igmserology: Percentage IgM.
precipitinserology: Result of the precipitin reaction. Coded as follows: 0=Test not done, 1-7=Number of bands, 8=No bands
blank1serology: unknown
ifat_pfaserology: IFA test for Plasmodium falciparum, 0=no result, 1= Titre 20, 2=60, 3=180, 4=540, 5=1620,6=4860, 7=14580,8=titres >14580, 9= titre < 20 (for computations take 0); In general Titre=20*3**(code-1)
blank2serology: unknown
ifat_pmserology: IFA test for Plasmodium malariae, 0=no result, 1= Titre 20, 2=60, 3=180, 4=540, 5=1620,6=4860, 7=14580,8=titres >14580, 9= titre < 20 (for computations take 0); In general Titre=20*3**(code-1)
haem_codeserology: 1 = AA; 2 = AS, 3 = SS, 4 =AC, 5 = CC, 6 = SC, 9 = not done
haem_phbsserology: unknown
recd_ihaserology: Record identifier for IHA (code 116)
specnoserology: specimen number
titrcodeserology: IHA titre code, 4 to 16 = titre 2**4 to 2**16 (in general titre=2**code)
dateserology: unknown
tr(derived): factor: control or intervention village
phase(derived): factor: baseline, intervention, post-intervention phase
wetseason(derived): factor: dry or wet season
bdate(derived): individuals date of birth (standard date format)
mdate(derived): measurement date
agedays(derived): age in days at time of measurement
ageyrs(derived): age in years at time of measurement
ifatpftitre(derived): IFA test for P. falciparum antibody titres
ifatpmtitre(derived): IFA test for P. malariae antibody titres
ihatitre(derived): IHA test antibody titres
Source
http://www.swisstph.ch/fr/ressources/epidemiological-databases.html
References
Molineaux L, Gramiccia G, 1980. The Garki Project. Geneva: World Health Organisation. http://whqlibdoc.who.int/publications/9241560614.pdf
http://garkiproject.nd.edu/
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