rdhs
API Client and Dataset Management for the Demographic and Health Survey (DHS) Data
Provides a client for (1) querying the DHS API for survey indicators and metadata (< https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.
Motivation
The Demographic and Health Surveys (DHS) Program has collected population survey data from over 90 countries for over 30 years. In many countries, DHS provide the key data that mark progress towards targets such as the Sustainable Development Goals (SDGs) and inform health policy. Though standard health indicators are routinely published in survey final reports, much of the value of DHS is derived from the ability to download and analyse standardized microdata datasets for subgroup analysis, pooled multi-country analysis, and extended research studies. The suite of tools within rdhs improves the accessibility of these datasets for statistical analysis with R, with aim to support reproducible global health research and simplify common analytical pipelines.
rdhs is a package for management and analysis of Demographic and Health Survey (DHS) data. This includes functionality to:
- Access standard indicator data (i.e. DHS STATcompiler) in R via the DHS API.
- Identify surveys and datasets relevant to a particular analysis.
- Download survey datasets from the DHS website.
- Load datasets and associated metadata into R.
- Extract variables and combining datasets for pooled multi-survey analyses.
Installation
You can install the latest version from CRAN using:
install.packages("rdhs")You can also install the development version of rdhs with the latest patches from github with:
#install.packages("devtools")devtools::install_github("ropensci/rdhs")# Load the packagelibrary(rdhs)Getting started
To be able to download survey datasets from the DHS website, you will need to set up an account with the DHS website, which will enable you to request access to the datasets. Instructions on how to do this can be found here. The email, password, and project name that were used to create the account will then need to be provided to rdhs when attempting to download datasets.
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Request dataset access from the DHS website here.
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Full functionality is described in the tutorial here.
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An example workflow using
rdhsto calculate trends in anemia prevalence is available here.
Basic Functionality
Query the DHS API.
Obtain survey estimates for Malaria prevalence among children from the Democratic Republic of Congo and Tanzania in the last 5 years (since 2013) that included rapid diagnostic tests (RDTs).
dhs_indicators(indicatorIds = "ML_PMAL_C_RDT", returnFields=c("IndicatorId", "ShortName"))#> ShortName IndicatorId#> 1 Malaria prevalence according to RDT ML_PMAL_C_RDT dhs_data(countryIds = c("CD","TZ"), indicatorIds = "ML_PMAL_C_RDT", surveyYearStart = 2013, returnFields=c("Indicator", "SurveyId", "Value", "SurveyYearLabel", "CountryName"))#> Indicator SurveyId SurveyYearLabel Value#> 1 Malaria prevalence according to RDT CD2013DHS 2013-14 30.8#> 2 Malaria prevalence according to RDT TZ2015DHS 2015-16 14.4#> 3 Malaria prevalence according to RDT TZ2017MIS 2017 7.3#> CountryName#> 1 Congo Democratic Republic#> 2 Tanzania#> 3 TanzaniaIdentify survey datasets
Now, obtain survey microdatasets to analyze these same indicators. Query the surveyCharacteristics endpoint to identify the survey characteristic ID for malaria RDT testing.
## call with no arguments to return all charactersticssc <- dhs_survey_characteristics()sc[grepl("Malaria", sc$SurveyCharacteristicName), ]#> SurveyCharacteristicID SurveyCharacteristicName#> 57 96 Malaria - DBS#> 58 90 Malaria - Microscopy#> 59 89 Malaria - RDT#> 60 57 Malaria module #> 61 8 Malaria/bednet questionsUse dhs_surveys() identify surveys for the countries and years of interest.
## what are the countryIds - we can find that using this API requestids <- dhs_countries(returnFields=c("CountryName", "DHS_CountryCode")) ## find all the surveys that match the search criteriasurvs <- dhs_surveys(surveyCharacteristicIds = 89, countryIds = c("CD","TZ"), surveyYearStart = 2013)Lastly, identify the datasets required for download. By default, the recommended option is to download either the spss (.sav), fileFormat = "SV", or the flat file (.dat), fileFormat = "FL" datasets. The flat is quicker, but there are still one or two very old datasets that don't read correctly, whereas the .sav files are slower to read in but so far no datasets have been found that don't read in correctly. The household member recode (PR) reports the RDT status for children under five.
datasets <- dhs_datasets(surveyIds = survs$SurveyId, fileFormat = "FL", fileType = "PR")str(datasets)#> 'data.frame': 3 obs. of 13 variables:#> $ FileFormat : chr "Flat ASCII data (.dat)" "Flat ASCII data (.dat)" "Flat ASCII data (.dat)"#> $ FileSize : int 6595349 6622102 2172102#> $ DatasetType : chr "Survey Datasets" "Survey Datasets" "Survey Datasets"#> $ SurveyNum : int 421 485 529#> $ SurveyId : chr "CD2013DHS" "TZ2015DHS" "TZ2017MIS"#> $ FileType : chr "Household Member Recode" "Household Member Recode" "Household Member Recode"#> $ FileDateLastModified: chr "September, 19 2016 09:58:23" "August, 07 2018 17:36:25" "August, 23 2018 16:16:36"#> $ SurveyYearLabel : chr "2013-14" "2015-16" "2017"#> $ SurveyType : chr "DHS" "DHS" "MIS"#> $ SurveyYear : int 2013 2015 2017#> $ DHS_CountryCode : chr "CD" "TZ" "TZ"#> $ FileName : chr "CDPR61FL.ZIP" "TZPR7AFL.ZIP" "TZPR7QFL.ZIP"#> $ CountryName : chr "Congo Democratic Republic" "Tanzania" "Tanzania"Download datasets
We can now go ahead and download our datasets. To be able to download survey datasets from the DHS website, you will need to set up an account with them to enable you to request access to the datasets. Instructions on how to do this can be found here. The email, password, and project name that were used to create the account will then need to be provided to rdhs when attempting to download datasets.
Once we have created an account, we need to set up our credentials using the function set_rdhs_config(). This will require providing as arguments your email and project for which you want to download datasets from. You will then be prompted for your password.
You can also specify a directory for datasets and API calls to be cached to using cache_path. In order to comply with CRAN, this function will also ask you for your permission to write to files outside your temporary directory, and you must type out the filename for the config_path - "rdhs.json". (See introduction vignette for specific format for config, or ?set_rdhs_config).
## loginset_rdhs_config(email = "[email protected]", project = "Testing Malaria Investigations", config_path = "rdhs.json", global=FALSE)#> Writing your configuration to:#> -> rdhs.jsonThe path to your config is saved between sessions so you only have to set this once. With your credentials set, all API requests will be cached within the cache_path directory provided so that these can be returned when working remotely or with a poor internet connection.
# the first time this will take a few seconds microbenchmark::microbenchmark(dhs_datasets(surveyYearStart = 1986),times = 1)#> Unit: seconds#> expr min lq mean median#> dhs_datasets(surveyYearStart = 1986) 1.810807 1.810807 1.810807 1.810807#> uq max neval#> 1.810807 1.810807 1 # after caching, results will be available instantlymicrobenchmark::microbenchmark(dhs_datasets(surveyYearStart = 1986),times = 1)#> Unit: milliseconds#> expr min lq mean median#> dhs_datasets(surveyYearStart = 1986) 1.582677 1.582677 1.582677 1.582677#> uq max neval#> 1.582677 1.582677 1Now download datasets by providing a list of desired dataset filenames.
# download datasetsdownloads <- get_datasets(datasets$FileName) str(downloads)#> List of 3#> $ CDPR61FL: chr "/home/oj/.cache/rdhs/datasets/CDPR61FL.rds"#> $ TZPR7AFL: chr "/home/oj/.cache/rdhs/datasets/TZPR7AFL.rds"#> $ TZPR7QFL: chr "/home/oj/.cache/rdhs/datasets/TZPR7QFL.rds"#> - attr(*, "reformat")= logi FALSELoad datasets into R
The get_datasets() function returns a vector with a file path to the saved location of the downloaded datasets. These are read using readRDS():
# read in first datasetcdpr <- readRDS(downloads$CDPR61FL)Value labels are stored as attributes to each of the columns of the data frame using the labelled class (see haven::labelled or our introduction vignette for more details). Variable labels are stored in the label attribute.
Extract variables and pool datasets
The client also caches all variable labels to quickly query variables in each survey without loading the datasets.
# rapid diagnostic test searchvars <- search_variable_labels(datasets$FileName, search_terms = "malaria rapid test")Then extract these variables from the datasets. Optionally, geographic data may be added.
# and now extract the dataextract <- extract_dhs(vars, add_geo = FALSE)#> Starting Survey 1 out of 3 surveys:CDPR61FL#> Starting Survey 2 out of 3 surveys:TZPR7AFL#> Starting Survey 3 out of 3 surveys:TZPR7QFLThe returned object is a list of extracted datasets.
Dataset extracts can alternate be specified by providing a vector of surveys and vector of variable names:
# and grab the questions from this now utilising the survey variablesvars <- search_variables(datasets$FileName, variables = c("hv024","hml35")) # and now extract the dataextract <- extract_dhs(vars, add_geo = FALSE)#> Starting Survey 1 out of 3 surveys:CDPR61FL#> Starting Survey 2 out of 3 surveys:TZPR7AFL#> Starting Survey 3 out of 3 surveys:TZPR7QFLFinally, the two datasets are pooled using the function rbind_labelled(). This function works specifically with our lists of labelled data.frames. Labels are specified for each variable: for hv024 all labels are retained (concatenate) but for hml35 labels across both datasets to be "Neg" and "Pos".
# now let's try our second extractionextract <- rbind_labelled(extract, labels = list("hv024" = "concatenate", "hml35" = c("Neg"=0, "Pos"=1)))There is also an option to process downloaded datasets with labelled variables coded as strings, rather than labelled variables. This is specified by the argument reformat=TRUE.
# identify questions but specifying the reformat argumentquestions <- search_variables(datasets$FileName, variables = c("hv024", "hml35"), reformat=TRUE) # and now extract the dataextract <- extract_dhs(questions, add_geo = FALSE)#> Starting Survey 1 out of 3 surveys:CDPR61FL#> Starting Survey 2 out of 3 surveys:TZPR7AFL#> Starting Survey 3 out of 3 surveys:TZPR7QFL # group our resultsextract <- rbind_labelled(extract) # our hv024 variable is now just character strings, so you can decide when/how to factor/label it laterstr(extract)#> Classes 'dhs_dataset' and 'data.frame': 208595 obs. of 4 variables:#> $ hv024 : chr "equateur" "equateur" "equateur" "equateur" ...#> ..- attr(*, "label")= chr "Province"#> $ hml35 : chr NA NA NA NA ...#> ..- attr(*, "label")= chr "Result of malaria rapid test"#> $ SurveyId: chr "CD2013DHS" "CD2013DHS" "CD2013DHS" "CD2013DHS" ...#> $ DATASET : chr "CDPR61FL" "CDPR61FL" "CDPR61FL" "CDPR61FL" ...
News
rdhs 0.6.2
- Duplicate labels when parsing flat data files corrected (#79)
rdhs 0.6.1
extraction(add_geo=TRUE)correction for Kenya 2014 surveys (#67)- Geospatial covariate data sets now supported correctly (#64)
rdhs 0.6.0
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New
as_factor.labelledfor backward compatibility withhaven <2.0.0labelledclasses. -
model_datasetsnow internal and exported dataset (#60).
rdhs 0.5.2
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New vignettes:
country_codes -
Documentation typos corrected (#55)
rdhs 0.5.0
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New
set_rdhs_configfor providing login credentials. This deprecatesset_dhs_credentials. -
New
get_rdhs_configshows the credentials currently used byrdhs
rdhs 0.4.0
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Permissionn from user now required for file saving.
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API requests can now ignore any cached responses (
force = TRUE) argument (#23):
dat <- dhs_countries(force = TRUE)-
get_datasets(clear_cache = TRUE)will clear the cached available datasets, enabling newly requested datasets to be downloaded (@kaisero, #29). -
geojson objects can now be requested from the API so that you can return geojson objects for mapping purposes (#28) e.g. :
d <- dhs_data(countryIds = "SN", surveyYearStart = 2014, breakdown = "subnational", returnGeometry = TRUE, f = "geojson") # convert to spatial objectsp <- geojsonio::as.json(d) %>% geojsonio::geojson_sp rdhs 0.3.0
- New
dhs_data(),dhs_countries()and other API functions (dhs_x()).
rdhs 0.2.1
authenticate_dhs()now works with short project names.
rdhs 0.2.0
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New vignettes:
anemia -
New
read_dhs_flat()for reading flat datasets.
rdhs 0.1.0
- Initial share on Feb, 24th 2018 to colleagues at UNC.