Code used to analyze malaria prevalence data from 2013-2017 field studies. For descriptions of the field studies, see:
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Golden CD, Anjaranirina EJG, Fernald LCH, Hartl DL, Kremen C, Milner DA Jr, et al. Cohort Profile: The Madagascar Health and Environmental Research (MAHERY) study in north-eastern Madagascar. Int J Epidemiol. 2017;46:1747–8d.
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Golden CD, Borgerson C, Rice BL, Allen LH, Anjaranirina EJG, Barrett CB, et al. Cohort Description of the Madagascar Health and Environmental Research-Antongil (MAHERY-Antongil) Study in Madagascar. Front Nutr. 2019;6:109.
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Golden CD, Rice BL, Randriamady HJ, Vonona AM, Randrianasolo JF, Tafangy AN, et al. Study Protocol: A Cross-Sectional Examination of Socio-Demographic and Ecological Determinants of Nutrition and Disease Across Madagascar. Front Public Health. 2020;8:500.
In addition to the code used in data cleaning and analysis, this repository will contain a the csv file with the malaria infection outcome line data used in analysis
Benjamin L. Rice 2021
Additional File 1 Additional File 1.csv contains the malaria rapid diagnostic test outcome data as a line list
Description of column names:
unique_ind_id : Unique numeric identifier for each sampled individual
region_id : Numeric identifier for each study region
region_name : Identifier for each study region (includes region code, e.g., NE for Northeast Region) and name of nearest urban center for which the region is named
site_code : Identifier for each study site (includes region code, e.g., NE for Northeast Region)
site_id : Numeric identifier for each study site
hh_id : Numeric identifier for each sampled household
ageyears : Age in years for the individual
sex : Male or female
time_point_code : Numeric code for the seasonal time point of sampling
time_point_date : The time period over which sampling for that time point occurred
sample_date : Day of sampling (day RDT was performed) for the individual
rdt_result : Negative (0) or positive (1) result for malaria RDT (see methods)
Supplementary Table 1 Supplementary Table 1.csv contains sampling dates and malaria prevalence data by site and household
Description of column names:
site_id : Numeric identifier for each study site
site_code : Identifier for each study site (includes region code, e.g., NE for Northeast Region)
time_point_code : Numeric code for the seasonal time point of sampling
site_tp : A combination of the site_id and time_point_code
time_point_date : The time period over which sampling for that time point occurred
sample_date_start : First day of sampling for that site for that time point
sample_date_end : Last day of sampling for that site for that time point
region_id : Numeric identifier for each study region
region_name : Includes the name of the urban center nearest the rural study communities
region_peak_mo : The estimated month of peak malaria incidence for that region per Arambepola et al 2020
n_site : Number of individuals sampled
n_rdt_pos_site : Number of RDT positive individuals observed
prev_site : Proportion of sampled individuals that were RDT positive
prev.2_10 : Proportion of sampled children aged 2-10 years that were RDT positive
n_hh_site : Number of households sampled
prev_hh : Proportion of sampled households with 1+ RDT positive individuals
adj_cons_area: Nearest conservation priority or officially protected area(s) for each study site
dist_to_cons_area : Approximate distance in km of study site to forest edge or edge of conservation area
district : Districts are second-level administrative divisions in Madagascar
commune : Communes are third-level administrative divisions in Madagascar