diff --git a/R/utils_survey_dhs.R b/R/utils_survey_dhs.R index c3375b3..ccab94a 100644 --- a/R/utils_survey_dhs.R +++ b/R/utils_survey_dhs.R @@ -529,7 +529,7 @@ extract_individual_hiv_dhs <- function(SurveyId, ird_path, mrd_path, ard_path){ dob_cmc = v011, indweight = NA, artself) - + ## Male recode if (!is.null(mrd_path)) { @@ -554,17 +554,17 @@ extract_individual_hiv_dhs <- function(SurveyId, ird_path, mrd_path, ard_path){ indweight = NA, artself) ) - + } - + if (!is.null(ard_path)) { - + ar <- readRDS(ard_path) - + if (SurveyId == "CI2005AIS") { ar$hivnumb <- 100L*ar$hivstruct + ar$hivnumb } - + if (SurveyId == "ZM2013DHS") { ar$hiv03 <- ar$shiv51 } @@ -635,7 +635,9 @@ create_survey_meta_dhs <- function(surveys) { ## Unsure if filtering on PublicationTitle == "Final Report" is most robust ## way to do this. final_rep <- dplyr::filter(publications, PublicationTitle == "Final Report") - final_rep <- dplyr::select(final_rep, SurveyId, report_url = PublicationURL) + final_rep <- dplyr::select(final_rep, SurveyId, report_url = PublicationURL) %>% + dplyr::group_by(SurveyId) %>% + dplyr::filter(row_number() == 1) stopifnot( !duplicated(final_rep$SurveyId) ) @@ -778,13 +780,13 @@ plot_survey_coordinate_check <- function(survey_clusters, survey_region_areas <- dplyr::semi_join(survey_region_areas, survey_region_boundaries, by = c("survey_id", "survey_region_id")) - + clust_spl <- split(survey_clusters, survey_clusters$survey_id) region_spl <- split(survey_region_boundaries, survey_region_boundaries$survey_id) area_spl <- split(survey_region_areas, survey_region_areas$survey_id) - + plot_one <- function(clust, regions, areas) { - + subtitle <- sprintf("Total survey clusters: %d\nClusters missing coordinates: %d\nClusters outside region boundaries: %d", nrow(clust), sum(is.na(clust$geoloc_area_id)), @@ -792,7 +794,7 @@ plot_survey_coordinate_check <- function(survey_clusters, regions <- dplyr::arrange(regions, survey_id, survey_region_id) regions$survey_region_name <- forcats::as_factor(regions$survey_region_name) - + clust <- dplyr::left_join( clust, sf::st_drop_geometry(regions),